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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Effective size of density-dependent two-sex populations: the effect of mating systems.

PubMed

Myhre, A M; Engen, S; SAEther, B-E

2017-08-01

Density dependence in vital rates is a key feature affecting temporal fluctuations of natural populations. This has important implications for the rate of random genetic drift. Mating systems also greatly affect effective population sizes, but knowledge of how mating system and density regulation interact to affect random genetic drift is poor. Using theoretical models and simulations, we compare N e in short-lived, density-dependent animal populations with different mating systems. We study the impact of a fluctuating, density-dependent sex ratio and consider both a stable and a fluctuating environment. We find a negative relationship between annual N e /N and adult population size N due to density dependence, suggesting that loss of genetic variation is reduced at small densities. The magnitude of this decrease was affected by mating system and life history. A male-biased, density-dependent sex ratio reduces the rate of genetic drift compared to an equal, density-independent sex ratio, but a stochastic change towards male bias reduces the N e /N ratio. Environmental stochasticity amplifies temporal fluctuations in population size and is thus vital to consider in estimation of effective population sizes over longer time periods. Our results on the reduced loss of genetic variation at small densities, particularly in polygamous populations, indicate that density regulation may facilitate adaptive evolution at small population sizes. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Indirect interactions among tropical tree species through shared rodent seed predators: a novel mechanism of tree species coexistence.

PubMed

Garzon-Lopez, Carol X; Ballesteros-Mejia, Liliana; Ordoñez, Alejandro; Bohlman, Stephanie A; Olff, Han; Jansen, Patrick A

2015-08-01

The coexistence of numerous tree species in tropical forests is commonly explained by negative dependence of recruitment on the conspecific seed and tree density due to specialist natural enemies that attack seeds and seedlings ('Janzen-Connell' effects). Less known is whether guilds of shared seed predators can induce a negative dependence of recruitment on the density of different species of the same plant functional group. We studied 54 plots in tropical forest on Barro Colorado Island, Panama, with contrasting mature tree densities of three coexisting large seeded tree species with shared seed predators. Levels of seed predation were far better explained by incorporating seed densities of all three focal species than by conspecific seed density alone. Both positive and negative density dependencies were observed for different species combinations. Thus, indirect interactions via shared seed predators can either promote or reduce the coexistence of different plant functional groups in tropical forest. © 2015 John Wiley & Sons Ltd/CNRS.

Influence of Coulomb interaction of tunable shapes on the collective transport of ultradilute two-dimensional holes.

PubMed

Huang, Jian; Pfeiffer, L N; West, K W

2014-01-24

In high quality updoped GaAs field-effect transistors, the two-dimensional charge carrier concentrations can be tuned to very low values similar to the density of electrons on helium surfaces. An important interaction effect, screening of the Coulomb interaction by the gate, rises as a result of the large charge spacing comparable to the distance between the channel and the gate. Based on the results of the temperature (T) dependence of the resistivity from measuring four different samples, a power-law characteristic is found for charge densities ≤2×10(9)  cm(-2). Moreover, the exponent exhibits a universal dependence on a single dimensionless parameter, the ratio between the mean carrier separation and the distance to the metallic gate that screens the Coulomb interaction. Thus, the electronic properties are tuned through varying the shape of the interaction potential.

Effective homogeneity of the exchange-correlation and non-interacting kinetic energy functionals under density scaling.

PubMed

Borgoo, Alex; Teale, Andrew M; Tozer, David J

2012-01-21

Correlated electron densities, experimental ionisation potentials, and experimental electron affinities are used to investigate the homogeneity of the exchange-correlation and non-interacting kinetic energy functionals of Kohn-Sham density functional theory under density scaling. Results are presented for atoms and small molecules, paying attention to the influence of the integer discontinuity and the choice of the electron affinity. For the exchange-correlation functional, effective homogeneities are highly system-dependent on either side of the integer discontinuity. By contrast, the average homogeneity-associated with the potential that averages over the discontinuity-is generally close to 4/3 when the discontinuity is computed using positive affinities for systems that do bind an excess electron and negative affinities for those that do not. The proximity to 4/3 becomes increasingly pronounced with increasing atomic number. Evaluating the discontinuity using a zero affinity in systems that do not bind an excess electron instead leads to effective homogeneities on the electron abundant side that are close to 4/3. For the non-interacting kinetic energy functional, the effective homogeneities are less system-dependent and the effect of the integer discontinuity is less pronounced. Average values are uniformly below 5/3. The study provides information that may aid the development of improved exchange-correlation and non-interacting kinetic energy functionals. © 2012 American Institute of Physics

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

PubMed

Schrader, Matthew; Jarrett, Benjamin J M; Kilner, Rebecca M

2015-04-01

Studies of siblings have focused mainly on their competitive interactions and to a lesser extent on their cooperation. However, competition and cooperation are at opposite ends on a continuum of possible interactions and the nature of these interactions may be flexible with ecological factors tipping the balance toward competition in some environments and cooperation in others. Here we show that the presence of parental care and the density of larvae on the breeding carcass change the outcome of sibling interactions in burying beetle broods. With full parental care there was a strong negative relationship between larval density and larval mass, consistent with sibling competition for resources. In the absence of care, initial increases in larval density had beneficial effects on larval mass but further increases in larval density reduced larval mass. This likely reflects a density-dependent shift between cooperation and competition. In a second experiment, we manipulated larval density and removed parental care. We found that the ability of larvae to penetrate the breeding carcass increased with larval density and that feeding within the carcass resulted in heavier larvae than feeding outside the carcass. However, larval density did not influence carcass decay. © 2015 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Effect of electron-phonon coupling on energy and density of states renormalizations of dynamically screened graphene

NASA Astrophysics Data System (ADS)

Leblanc, J. P. F.; Carbotte, J. P.; Nicol, E. J.

2012-02-01

Motivated by recent tunneling and angle-resolved photoemission (ARPES) work [1,2], we explore the combined effect of electron-electron and electron-phonon couplings on the renormalized energy dispersion, the spectral function, and the density of states of doped graphene. We find that the plasmarons seen in ARPES are also observable in the density of states and appear as structures with quadratic dependence on energy about the minima. Further, we illustrate how knowledge of the slopes of both the density of states and the renormalized dispersion near the Fermi level can allow for the separation of momentum and frequency dependent renormalizations to the Fermi velocity. This analysis should allow for the isolation of the renormalization due to the electron-phonon interaction from that of the electron-electron interaction. [4pt] [1] Brar et al. Phys. Rev. Lett. 104, 036805 (2010) [2] Bostwick et al. Science 328, p.999 (2010)

High population density enhances recruitment and survival of a harvested coral reef fish.

PubMed

Wormald, Clare L; Steele, Mark A; Forrester, Graham E

2013-03-01

A negative relationship between population growth and population density (direct density dependence) is necessary for population regulation and is assumed in most models of harvested populations. Experimental tests for density dependence are lacking for large-bodied, harvested fish because of the difficulty of manipulating population density over large areas. We studied a harvested coral reef fish, Lutjanus apodus (schoolmaster snapper), using eight large, isolated natural reefs (0.4-1.6 ha) in the Bahamas as replicates. An initial observational test for density dependence was followed by a manipulation of population density. The manipulation weakened an association between density and shelter-providing habitat features and revealed a positive effect of population density on recruitment and survival (inverse density dependence), but no effect of density on somatic growth. The snappers on an individual reef were organized into a few shoals, and we hypothesize that large shoals on high-density reefs were less vulnerable to large piscivores (groupers and barracudas) than the small shoals on low-density reefs. Reductions in predation risk for individuals in large social groups are well documented, but because snapper shoals occupied reefs the size of small marine reserves, these ecological interactions may influence the outcome of management actions.

Causes and consequences of complex population dynamics in an annual plant, Cardamine pensylvanica

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

Crone, E.E.

1995-11-08

The relative importance of density-dependent and density-independent factors in determining the population dynamics of plants has been widely debated with little resolution. In this thesis, the author explores the effects of density-dependent population regulation on population dynamics in Cardamine pensylvanica, an annual plant. In the first chapter, she shows that experimental populations of C. pensylvanica cycled from high to low density in controlled constant-environment conditions. These cycles could not be explained by external environmental changes or simple models of direct density dependence (N{sub t+1} = f[N{sub t}]), but they could be explained by delayed density dependence (N{sub t+1} = f[N{submore » t}, N{sub t+1}]). In the second chapter, she shows that the difference in the stability properties of population growth models with and without delayed density dependence is due to the presence of Hopf as well as slip bifurcations from stable to chaotic population dynamics. She also measures delayed density dependence due to effects of parental density on offspring quality in C. pensylvanica and shows that this is large enough to be the cause of the population dynamics observed in C. pensylvanica. In the third chapter, the author extends her analyses of density-dependent population growth models to include interactions between competing species. In the final chapter, she compares the effects of fixed spatial environmental variation and variation in population size on the evolutionary response of C. pensylvanica populations.« less

Analysis of compaction shock interactions during DDT of low density HMX

NASA Astrophysics Data System (ADS)

Rao, Pratap T.; Gonthier, Keith A.

2017-01-01

Deflagration-to-Detonation Transition (DDT) in confined, low density granular HMX occurs by a complex mechanism that involves compaction shock interactions within the material. Piston driven DDT experiments indicate that detonation is abruptly triggered by the interaction of a strong combustion-supported secondary shock and a piston-supported primary (input) shock, where the nature of the interaction depends on initial packing density and primary shock strength. These interactions influence transition by affecting dissipative heating within the microstructure during pore collapse. Inert meso-scale simulations of successive shock loading of low density HMX are performed to examine how dissipation and hot-spot formation are affected by the initial density, and the primary and secondary shock strengths. This information is used to formulate an ignition and burn model for low density HMX that accounts for the effect of shock densensitization on burn. Preliminary DDT predictions are presented that illustrate how primary shock strength affects the transition mechanism.

Size effects under homogeneous deformation of single crystals: A discrete dislocation analysis

NASA Astrophysics Data System (ADS)

Guruprasad, P. J.; Benzerga, A. A.

Mechanism-based discrete dislocation plasticity is used to investigate the effect of size on micron scale crystal plasticity under conditions of macroscopically homogeneous deformation. Long-range interactions among dislocations are naturally incorporated through elasticity. Constitutive rules are used which account for key short-range dislocation interactions. These include junction formation and dynamic source and obstacle creation. Two-dimensional calculations are carried out which can handle high dislocation densities and large strains up to 0.1. The focus is laid on the effect of dimensional constraints on plastic flow and hardening processes. Specimen dimensions ranging from hundreds of nanometers to tens of microns are considered. Our findings show a strong size-dependence of flow strength and work-hardening rate at the micron scale. Taylor-like hardening is shown to be insufficient as a rationale for the flow stress scaling with specimen dimensions. The predicted size effect is associated with the emergence, at sufficient resolution, of a signed dislocation density. Heuristic correlations between macroscopic flow stress and macroscopic measures of dislocation density are sought. Most accurate among those is a correlation based on two state variables: the total dislocation density and an effective, scale-dependent measure of signed density.

The importance of multi-level Rydberg interaction in electric field tuned Förster resonances

NASA Astrophysics Data System (ADS)

Kondo, Jorge; Booth, Donald; Gonçalves, Luis; Shaffer, James; Marcassa, Luis

2016-05-01

Many-body physics has been investigated in ultracold Rydberg atom systems, mainly because important parameters, such as density and interaction strength, can be controlled. Several puzzling experimental observations on Förster resonances have been associated to many-body effects, usually by comparison to complex theoretical models. In this work, we investigate the dc electric field dependence of 2 Förster resonant processes in ultracold 85 Rb, 37D5 / 2 + 37D5 / 2 --> 35 L(L = O , Q) + 39P3 / 2 , as a function of the atomic density in an optical dipole trap. At low densities, the 39 P yield as a function of electric field exhibits resonances. With increasing density, the linewidths increase until the peaks merge. Even under these extreme conditions, where many-body effects were expected to play a role, the 39 P population depends quadratically on the total Rydberg atom population. In order to explain our results, we implement a theoretical model which takes into account the multi-level character of the interactions and Rydberg atom blockade process using only atom pair interactions. The comparison between the experimental data and the model is very good, suggesting that the Förster resonant processes are dominated by 2-body interactions. This work is supported by FAPESP, AFOSR, NSF, INCT-IQ and CNPq.

Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

NASA Astrophysics Data System (ADS)

Sanyal, Tanmoy; Shell, M. Scott

2016-07-01

Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one at which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.

Impact of Many-Body Effects on Landau Levels in Graphene

NASA Astrophysics Data System (ADS)

Sonntag, J.; Reichardt, S.; Wirtz, L.; Beschoten, B.; Katsnelson, M. I.; Libisch, F.; Stampfer, C.

2018-05-01

We present magneto-Raman spectroscopy measurements on suspended graphene to investigate the charge carrier density-dependent electron-electron interaction in the presence of Landau levels. Utilizing gate-tunable magnetophonon resonances, we extract the charge carrier density dependence of the Landau level transition energies and the associated effective Fermi velocity vF. In contrast to the logarithmic divergence of vF at zero magnetic field, we find a piecewise linear scaling of vF as a function of the charge carrier density, due to a magnetic-field-induced suppression of the long-range Coulomb interaction. We quantitatively confirm our experimental findings by performing tight-binding calculations on the level of the Hartree-Fock approximation, which also allow us to estimate an excitonic binding energy of ≈6 meV contained in the experimentally extracted Landau level transitions energies.

Density functional theory and experimental study of the electronic structure and transport properties of La, V, Nb, and Ta doped SrTiO3

NASA Astrophysics Data System (ADS)

Baniecki, J. D.; Ishii, M.; Aso, H.; Kurihara, K.; Ricinschi, Dan

2013-01-01

The electronic structure and transport properties of donor doped SrTiO3 are studied using density functional theory with spin-orbit coupling and conductivity, Hall, and Seebeck effect measurements over a wide temperature range (100 K to 600 K). Split-off energies ΔSO are tunable through the dopant SO interaction strength and concentration varying from 28.1 meV for pure STO to 70.93 meV for SrTi0.5Nb0.5O3. At lower carrier concentrations and temperatures, SO coupling has a marked effect on both the filling dependence of the density-of-states mass as well as the temperature dependence of the Seebeck coefficient, with quantitative theoretical predictions based on DFT calculations that include the SO interaction in closer agreement to the experimental data. Moreover, the results suggest that the predictive power of the current theory is not unlimited, with less accuracy for the calculated S predicting the magnitude of the experimental S data at lower dopant concentrations than for degenerately doped systems. A concentration dependent mass enhancement of ˜2-5, relative to the density-of-states mass in the local density approximation, possibly due to the influence of electronic screening of the electron-phonon interaction, would bring the theoretical S in accord with the experimental S data. This additional carrier-dependent enhancement mechanism for S may give an additional degree of freedom in terms of designing new higher efficiency thermoelectric energy materials.

Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction.

PubMed

Yang, Yang; Yu, Haibo; York, Darrin; Cui, Qiang; Elstner, Marcus

2007-10-25

The standard self-consistent-charge density-functional-tight-binding (SCC-DFTB) method (Phys. Rev. B 1998, 58, 7260) is derived by a second-order expansion of the density functional theory total energy expression, followed by an approximation of the charge density fluctuations by charge monopoles and an effective damped Coulomb interaction between the atomic net charges. The central assumptions behind this effective charge-charge interaction are the inverse relation of atomic size and chemical hardness and the use of a fixed chemical hardness parameter independent of the atomic charge state. While these approximations seem to be unproblematic for many covalently bound systems, they are quantitatively insufficient for hydrogen-bonding interactions and (anionic) molecules with localized net charges. Here, we present an extension of the SCC-DFTB method to incorporate third-order terms in the charge density fluctuations, leading to chemical hardness parameters that are dependent on the atomic charge state and a modification of the Coulomb scaling to improve the electrostatic treatment within the second-order terms. These modifications lead to a significant improvement in the description of hydrogen-bonding interactions and proton affinities of biologically relevant molecules.

Contact angle of sessile drops in Lennard-Jones systems.

PubMed

Becker, Stefan; Urbassek, Herbert M; Horsch, Martin; Hasse, Hans

2014-11-18

Molecular dynamics simulations are used for studying the contact angle of nanoscale sessile drops on a planar solid wall in a system interacting via the truncated and shifted Lennard-Jones potential. The entire range between total wetting and dewetting is investigated by varying the solid-fluid dispersive interaction energy. The temperature is varied between the triple point and the critical temperature. A correlation is obtained for the contact angle in dependence of the temperature and the dispersive interaction energy. Size effects are studied by varying the number of fluid particles at otherwise constant conditions, using up to 150,000 particles. For particle numbers below 10,000, a decrease of the contact angle is found. This is attributed to a dependence of the solid-liquid surface tension on the droplet size. A convergence to a constant contact angle is observed for larger system sizes. The influence of the wall model is studied by varying the density of the wall. The effective solid-fluid dispersive interaction energy at a contact angle of θ = 90° is found to be independent of temperature and to decrease linearly with the solid density. A correlation is developed that describes the contact angle as a function of the dispersive interaction, the temperature, and the solid density. The density profile of the sessile drop and the surrounding vapor phase is described by a correlation combining a sigmoidal function and an oscillation term.

Effective mass in bilayer graphene at low carrier densities: The role of potential disorder and electron-electron interaction

NASA Astrophysics Data System (ADS)

Li, J.; Tan, L. Z.; Zou, K.; Stabile, A. A.; Seiwell, D. J.; Watanabe, K.; Taniguchi, T.; Louie, Steven G.; Zhu, J.

2016-10-01

In a two-dimensional electron gas, the electron-electron interaction generally becomes stronger at lower carrier densities and renormalizes the Fermi-liquid parameters, such as the effective mass of carriers. We combine experiment and theory to study the effective masses of electrons and holes me* and mh* in bilayer graphene in the low carrier density regime on the order of 1 ×1011c m-2 . Measurements use temperature-dependent low-field Shubnikov-de Haas oscillations observed in high-mobility hexagonal boron nitride supported samples. We find that while me* follows a tight-binding description in the whole density range, mh* starts to drop rapidly below the tight-binding description at a carrier density of n =6 ×1011c m-2 and exhibits a strong suppression of 30% when n reaches 2 ×1011c m-2 . Contributions from the electron-electron interaction alone, evaluated using several different approximations, cannot explain the experimental trend. Instead, the effect of the potential fluctuation and the resulting electron-hole puddles play a crucial role. Calculations including both the electron-electron interaction and disorder effects explain the experimental data qualitatively and quantitatively. This Rapid Communication reveals an unusual disorder effect unique to two-dimensional semimetallic systems.

Cascading effects of predator-detritivore interactions depend on environmental context in a Tibetan alpine meadow.

PubMed

Wu, Xinwei; Griffin, John N; Sun, Shucun

2014-05-01

Studies of grazing food webs show that species traits can interact with environmental factors to determine the strength of trophic cascades, but analogous context dependencies in detrital food webs remain poorly understood. In predator-detritivore-plant interaction chains, predators are expected to indirectly suppress plant biomass by reducing the density of plant-facilitating detritivores. However, this outcome can be reversed where above-ground predators drive burrowing detritivores to lower soil levels, strengthening their plant-facilitating effects. Here, we show that these trait-mediated indirect interactions further depend on environmental context in a Tibetan alpine meadow. In our study system, undulating topography generates higher (dry soil) patches interspersed with lower (wet soil) patches. Because the ability of detritivores to form deep burrows is likely to be limited by oxygen availability in low patches (wet soil), we hypothesized that (i) burrowing detritivores would undergo a vertical habitat shift, allowing them to more effectively avoid predation, in high - but not low - patches, and (ii) this shift would transmit positive effects of predators to plants in high patches by improving conditions in the lower soil layer. We tested these hypotheses using complementary field and glasshouse experiments examining whether the cascading effects of above-ground predatory beetles (presence/absence) on the density and behaviour of tunnel-forming detritivorous beetles, soil properties, and plant growth varied with patch type (low/high). Results revealed that predatory beetles did not reduce the density of detritivores in either patch type but had context-dependent trait-mediated effects, increasing the tunnelling depth of detritivores, improving soil conditions and ultimately increasing plant biomass in the high but not low patches. This study adds to an emerging predictive framework linking predators to plants in detritus food webs, demonstrating that these indirect interactions depend not just on the relative habitat domains of predators and prey, but also on environmental conditions that can predictably constrain the behavioural response of detritivores to predation risk. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

On the influence of substrate morphology and surface area on phytofauna

USGS Publications Warehouse

Becerra-Munoz, S.; Schramm, H.L.

2007-01-01

The independent effects and interactions between substrate morphology and substrate surface area on invertebrate density or biomass colonizing artificial plant beds were assessed in a clear-water and a turbid playa lake in Castro County, Texas, USA. Total invertebrate density and biomass were consistently greater on filiform substrates than on laminar substrates with equivalent substrate surface areas. The relationship among treatments (substrates with different morphologies and surface areas) and response (invertebrate density or biomass) was assessed with equally spaced surface areas. Few statistically significant interactions between substrate morphology and surface area were detected, indicating that these factors were mostly independent from each other in their effect on colonizing invertebrates. Although infrequently, when substrate morphology and surface area were not independent, the effects of equally spaced changes in substrate surface area on the rate of change of phytofauna density or biomass per unit of substrate surface area were dependent upon substrate morphology. The absence of three-way interactions indicated that effects of substrate morphology and substrate area on phytofauna density or biomass were independent of environmental conditions outside and inside exclosures. ?? 2006 Springer Science+Business Media B.V.

Ecological and evolutionary consequences of tri-trophic interactions: Spatial variation and effects of plant density.

PubMed

Abdala-Roberts, Luis; Parra-Tabla, Víctor; Moreira, Xoaquín; Ramos-Zapata, José

2017-02-01

The factors driving variation in species interactions are often unknown, and few studies have made a link between changes in interactions and the strength of selection. We report on spatial variation in functional responses by a seed predator (SP) and its parasitic wasps associated with the herb Ruellia nudiflora . We assessed the influence of plant density on consumer responses and determined whether density effects and spatial variation in functional responses altered natural selection by these consumers on the plant. We established common gardens at two sites in Yucatan, Mexico, and planted R. nudiflora at two densities in each garden. We recorded fruit output and SP and parasitoid attack; calculated relative fitness (seed number) under scenarios of three trophic levels (accounting for SP and parasitoid effects), two trophic levels (accounting for SP but not parasitoid effects), and one trophic level (no consumer effects); and compared selection strength on fruit number under these scenarios across sites and densities. There was spatial variation in SP recruitment, whereby the SP functional response was negatively density-dependent at one site but density-independent at the other; parasitoid responses were density-independent and invariant across sites. Site variation in SP attack led, in turn, to differences in SP selection on fruit output, and parasitoids did not alter SP selection. There were no significant effects of density at either site. Our results provide a link between consumer functional responses and consumer selection on plants, which deepens our understanding of geographic variation in the evolutionary outcomes of multitrophic interactions. © 2017 Botanical Society of America.

Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

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

Sanyal, Tanmoy; Shell, M. Scott, E-mail: shell@engineering.ucsb.edu

Bottom-up multiscale techniques are frequently used to develop coarse-grained (CG) models for simulations at extended length and time scales but are often limited by a compromise between computational efficiency and accuracy. The conventional approach to CG nonbonded interactions uses pair potentials which, while computationally efficient, can neglect the inherently multibody contributions of the local environment of a site to its energy, due to degrees of freedom that were coarse-grained out. This effect often causes the CG potential to depend strongly on the overall system density, composition, or other properties, which limits its transferability to states other than the one atmore » which it was parameterized. Here, we propose to incorporate multibody effects into CG potentials through additional nonbonded terms, beyond pair interactions, that depend in a mean-field manner on local densities of different atomic species. This approach is analogous to embedded atom and bond-order models that seek to capture multibody electronic effects in metallic systems. We show that the relative entropy coarse-graining framework offers a systematic route to parameterizing such local density potentials. We then characterize this approach in the development of implicit solvation strategies for interactions between model hydrophobes in an aqueous environment.« less

Equation of State for Isospin Asymmetric Nuclear Matter Using Lane Potential

NASA Astrophysics Data System (ADS)

Basu, D. N.; Chowdhury, P. Roy; Samanta, C.

2006-10-01

A mean field calculation for obtaining the equation of state (EOS) for symmetric nuclear matter from a density dependent M3Y interaction supplemented by a zero-range potential is described. The energy per nucleon is minimized to obtain the ground state of symmetric nuclear matter. The saturation energy per nucleon used for nuclear matter calculations is determined from the co-efficient of the volume term of Bethe--Weizsäcker mass formula which is evaluated by fitting the recent experimental and estimated atomic mass excesses from Audi--Wapstra--Thibault atomic mass table by minimizing the mean square deviation. The constants of density dependence of the effective interaction are obtained by reproducing the saturation energy per nucleon and the saturation density of spin and isospin symmetric cold infinite nuclear matter. The EOS of symmetric nuclear matter, thus obtained, provide reasonably good estimate of nuclear incompressibility. Once the constants of density dependence are determined, EOS for asymmetric nuclear matter is calculated by adding to the isoscalar part, the isovector component of the M3Y interaction that do not contribute to the EOS of symmetric nuclear matter. These EOS are then used to calculate the pressure, the energy density and the velocity of sound in symmetric as well as isospin asymmetric nuclear matter.

Predator Cue and Prey Density Interactively Influence Indirect Effects on Basal Resources in Intertidal Oyster Reefs

PubMed Central

Hughes, A. Randall; Rooker, Kelly; Murdock, Meagan; Kimbro, David L.

2012-01-01

Predators can influence prey abundance and traits by direct consumption, as well as by non-consumptive effects of visual, olfactory, or tactile cues. The strength of these non-consumptive effects (NCEs) can be influenced by a variety of factors, including predator foraging mode, temporal variation in predator cues, and the density of competing prey. Testing the relative importance of these factors for determining NCEs is critical to our understanding of predator-prey interactions in a variety of settings. We addressed this knowledge gap by conducting two mesocosm experiments in a tri-trophic intertidal oyster reef food web. More specifically, we tested how a predatory fish (hardhead catfish, Ariopsis felis) directly influenced their prey (mud crabs, Panopeus spp.) and indirectly affected basal resources (juvenile oysters, Crassostrea virginica), as well as whether these direct and indirect effects changed across a density gradient of competing prey. Per capita crab foraging rates were inversely influenced by crab density, but they were not affected by water-borne predator cues. As a result, direct consumptive effects on prey foraging rates were stronger than non-consumptive effects. In contrast, predator cue and crab density interactively influenced indirect predator effects on oyster mortality in two experiments, with trait-mediated and density-mediated effects of similar magnitude operating to enhance oyster abundance. Consistent differences between a variable predator cue environment and other predator cue treatments (no cue and constant cue) suggests that an understanding of the natural risk environment experienced by prey is critical to testing and interpreting trait-mediated indirect interactions. Further, the prey response to the risk environment may be highly dependent on prey density, particularly in prey populations with strong intra-specific interactions. PMID:22970316

Systematic analysis of inelastic α scattering off self-conjugate A =4 n nuclei

NASA Astrophysics Data System (ADS)

Adachi, S.; Kawabata, T.; Minomo, K.; Kadoya, T.; Yokota, N.; Akimune, H.; Baba, T.; Fujimura, H.; Fujiwara, M.; Funaki, Y.; Furuno, T.; Hashimoto, T.; Hatanaka, K.; Inaba, K.; Ishii, Y.; Itoh, M.; Iwamoto, C.; Kawase, K.; Maeda, Y.; Matsubara, H.; Matsuda, Y.; Matsuno, H.; Morimoto, T.; Morita, H.; Murata, M.; Nanamura, T.; Ou, I.; Sakaguchi, S.; Sasamoto, Y.; Sawada, R.; Shimizu, Y.; Suda, K.; Tamii, A.; Tameshige, Y.; Tsumura, M.; Uchida, M.; Uesaka, T.; Yoshida, H. P.; Yoshida, S.

2018-01-01

We systematically measured the differential cross sections of inelastic α scattering off self-conjugate A =4 n nuclei at two incident energies Eα=130 MeV and 386 MeV at Research Center for Nuclear Physics, Osaka University. The measured cross sections were analyzed by the distorted-wave Born-approximation (DWBA) calculation using the single-folding potentials, which are obtained by folding macroscopic transition densities with the phenomenological α N interaction. The DWBA calculation with the density-dependent α N interaction systematically overestimates the cross sections for the Δ L =0 transitions. However, the DWBA calculation using the density-independent α N interaction reasonably well describes all the transitions with Δ L =0 -4. We examined uncertainties in the present DWBA calculation stemming from the macroscopic transition densities, distorting potentials, phenomenological α N interaction, and coupled channel effects in 12C. It was found that the DWBA calculation is not sensitive to details of the transition densities nor the distorting potentials, and the phenomenological density-independent α N interaction gives reasonable results. The coupled-channel effects are negligibly small for the 21+ and 31- states in 12C, but not for the 02+ state. However, the DWBA calculation using the density-independent interaction at Eα=386 MeV is still reasonable even for the 02+ state. We concluded that the macroscopic DWBA calculations using the density-independent interaction are reliably applicable to the analysis of inelastic α scattering at Eα˜100 MeV /u .

Facilitation drives 65 years of vegetation change in the Sonoran Desert

USGS Publications Warehouse

Butterfield, Bradley J.; Betancourt, Julio L.; Turner, Raymond M.; Briggs, John M.

2010-01-01

Ecological processes of low-productivity ecosystems have long been considered to be driven by abiotic controls with biotic interactions playing an insignificant role. However, existing studies present conflicting evidence concerning the roles of these factors, in part due to the short temporal extent of most data sets and inability to test indirect effects of environmental variables modulated by biotic interactions. Using structural equation modeling to analyze 65 years of perennial vegetation change in the Sonoran Desert, we found that precipitation had a stronger positive effect on recruitment beneath existing canopies than in open microsites due to reduced evaporation rates. Variation in perennial canopy cover had additional facilitative effects on juvenile recruitment, which was indirectly driven by effects of density and precipitation on cover. Mortality was strongly influenced by competition as indicated by negative density-dependence, whereas precipitation had no effect. The combined direct, indirect, and interactive facilitative effects of precipitation and cover on recruitment were substantial, as was the effect of competition on mortality, providing strong evidence for dual control of community dynamics by climate and biotic interactions. Through an empirically derived simulation model, we also found that the positive feedback of density on cover produces unique temporal abundance patterns, buffering changes in abundance from high frequency variation in precipitation, amplifying effects of low frequency variation, and decoupling community abundance from precipitation patterns at high abundance. Such dynamics should be generally applicable to low-productivity systems in which facilitation is important and can only be understood within the context of long-term variation in climatic patterns. This predictive model can be applied to better manage low-productivity ecosystems, in which variation in biogeochemical processes and trophic dynamics may be driven by positive density-dependent feedbacks that influence temporal abundance and productivity patterns.

Field manipulations of resources mediate the transition from intraspecific competition to facilitation.

PubMed

Svanfeldt, Karin; Monro, Keyne; Marshall, Dustin J

2017-05-01

Population density affects individual performance, though its effects are often mixed. For sessile species, increases in population density typically reduce performance. Still, cases of positive density-dependence do occur in sessile systems and demand explanation. The stress gradient hypothesis (SGH) predicts that under stressful conditions, positive effects of facilitation may outweigh the negative effects of competition. While some elements of the SGH are well studied, its potential to explain intraspecific facilitation has received little attention. Further, there have been questions regarding whether the SGH holds if the stressor is a resource. Most studies of interactions between the environment and intraspecific facilitation have relied on natural environmental gradients; manipulative studies are much rarer. To test the effects of intraspecific density and resources, we manipulated resource availability over natural population densities for the marine bryozoan Watersipora subtorquata. We found negative effects of density on colony performance in low resource environments, but mainly positive density-dependence in high resource environments. By adding resources, competition effects were reduced and the positive effects of facilitation were revealed. Our results suggest that resource availability mediates the relative strength of competition and facilitation in our system. We also suggest that intraspecific facilitation is more common than may be appreciated and that environmental variation may mediate the balance between negative and positive density-dependence. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Interaction between colloidal particles on an oil-water interface in dilute and dense phases.

PubMed

Parolini, Lucia; Law, Adam D; Maestro, Armando; Buzza, D Martin A; Cicuta, Pietro

2015-05-20

The interaction between micron-sized charged colloidal particles at polar/non-polar liquid interfaces remains surprisingly poorly understood for a relatively simple physical chemistry system. By measuring the pair correlation function g(r) for different densities of polystyrene particles at the decane-water interface, and using a powerful predictor-corrector inversion scheme, effective pair-interaction potentials can be obtained up to fairly high densities, and these reproduce the experimental g(r) in forward simulations, so are self consistent. While at low densities these potentials agree with published dipole-dipole repulsion, measured by various methods, an apparent density dependence and long range attraction are obtained when the density is higher. This condition is thus explored in an alternative fashion, measuring the local mobility of colloids when confined by their neighbors. This method of extracting interaction potentials gives results that are consistent with dipolar repulsion throughout the concentration range, with the same magnitude as in the dilute limit. We are unable to rule out the density dependence based on the experimental accuracy of our data, but we show that incomplete equilibration of the experimental system, which would be possible despite long waiting times due to the very strong repulsions, is a possible cause of artefacts in the inverted potentials. We conclude that to within the precision of these measurements, the dilute pair potential remains valid at high density in this system.

UHF Radar observations at HAARP with HF pump frequencies near electron gyro-harmonics and associated ionospheric effects

NASA Astrophysics Data System (ADS)

Watkins, Brenton; Fallen, Christopher; Secan, James

Results for HF modification experiments at the HAARP facility in Alaska are presented for experiments with the HF pump frequency near third and fourth electron gyro-harmonics. A UHF diagnostic radar with range resolution of 600 m was used to determine time-dependent altitudes of scattering from plasma turbulence during heating experiments. Experiments were conducted with multiple HF frequencies stepped by 20 kHz above and below the gyro-harmonic values. During times of HF heating the HAARP facility has sufficient power to enhance large-scale ionospheric densities in the lower ionosphere (about 150-200 km altitude) and also in the topside ionosphere (above about 350 km). In the lower ionosphere, time-dependent decreases of the altitude of radar scatter result from electron density enhancements. The effects are substantially different even for relatively small frequency steps of 20 kHz. In all cases the time-varying altitude decrease of radar scatter stops about 5-10 km below the gyro-harmonic altitude that is frequency dependent; we infer that electron density enhancements stop at this altitude where the radar signals stop decreasing with altitude. Experiments with corresponding total electron content (TEC) data show that for HF interaction altitudes above about 170 km there is substantial topside electron density increases due to upward electron thermal conduction. For lower altitudes of HF interaction the majority of the thermal energy is transferred to the neutral gas and no significant topside density increases are observed. By selecting an appropriate HF frequency a little greater than the gyro-harmonic value we have demonstrated that the ionospheric response to HF heating is a self-oscillating mode where the HF interaction altitude moves up and down with a period of several minutes. If the interaction region is above about 170 km this also produces a continuously enhanced topside electron density and upward plasma flux. Experiments using an FM scan with the HF frequency increasing near the gyro-harmonic value were conducted. The FM scan rate was sufficiently slow that the electron density was approximately in an equilibrium state. For these experiments the altitude of the HF interaction follows a near straight line downward parallel to the altitude-dependent gyro-harmonic level.

Surface-peaked medium effects in the interaction of nucleons with finite nuclei

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

Aguayo, F. J.; Arellano, H. F.

We investigate the asymptotic separation of the optical model potential for nucleon-nucleus scattering in momentum space, where the potential is split into a medium-independent term and another depending exclusively on the gradient of the density-dependent g matrix. This decomposition confines the medium sensitivity of the nucleon-nucleus coupling to the surface of the nucleus. We examine this feature in the context of proton-nucleus scattering at beam energies between 30 and 100 MeV and find that the pn coupling accounts for most of this sensitivity. Additionally, based on this general structure of the optical potential we are able to treat both, themore » medium dependence of the effective interaction and the full mixed density as described by single-particle shell models. The calculated scattering observables agree within 10% with those obtained by Arellano, Brieva, and Love in their momentum-space g-folding approach.« less

Population density of North American elk: effects on plant diversity.

PubMed

Stewart, Kelley M; Bowyer, R Terry; Kie, John G; Dick, Brian L; Ruess, Roger W

2009-08-01

Large, herbivorous mammals have profound effects on ecosystem structure and function and often act as keystone species in ecosystems they inhabit. Density-dependent processes associated with population structure of large mammals may interact with ecosystem functioning to increase or decrease biodiversity, depending on the relationship of herbivore populations relative to the carrying capacity (K) of the ecosystem. We tested for indirect effects of population density of large herbivores on plant species richness and diversity in a montane ecosystem, where increased net aboveground primary productivity (NAPP) in response to low levels of herbivory has been reported. We documented a positive, linear relationship between plant-species diversity and richness with NAPP. Structural equation modeling revealed significant indirect relationships between population density of herbivores, NAPP, and species diversity. We observed an indirect effect of density-dependent processes in large, herbivorous mammals and species diversity of plants through changes in NAPP in this montane ecosystem. Changes in species diversity of plants in response to herbivory may be more indirect in ecosystems with long histories of herbivory. Those subtle or indirect effects of herbivory may have strong effects on ecosystem functioning, but may be overlooked in plant communities that are relatively resilient to herbivory.

Persistence of Neighborhood Demographic Influences over Long Phylogenetic Distances May Help Drive Post-Speciation Adaptation in Tropical Forests

PubMed Central

Wills, Christopher; Harms, Kyle E.; Wiegand, Thorsten; Punchi-Manage, Ruwan; Gilbert, Gregory S.; Erickson, David; Kress, W. John; Hubbell, Stephen P.; Gunatilleke, C. V. Savitri; Gunatilleke, I. A. U. Nimal

2016-01-01

Studies of forest dynamics plots (FDPs) have revealed a variety of negative density-dependent (NDD) demographic interactions, especially among conspecific trees. These interactions can affect growth rate, recruitment and mortality, and they play a central role in the maintenance of species diversity in these complex ecosystems. Here we use an equal area annulus (EAA) point-pattern method to comprehensively analyze data from two tropical FDPs, Barro Colorado Island in Panama and Sinharaja in Sri Lanka. We show that these NDD interactions also influence the continued evolutionary diversification of even distantly related tree species in these FDPs. We examine the details of a wide range of these interactions between individual trees and the trees that surround them. All these interactions, and their cumulative effects, are strongest among conspecific focal and surrounding tree species in both FDPs. They diminish in magnitude with increasing phylogenetic distance between heterospecific focal and surrounding trees, but do not disappear or change the pattern of their dependence on size, density, frequency or physical distance even among the most distantly related trees. The phylogenetic persistence of all these effects provides evidence that interactions between tree species that share an ecosystem may continue to promote adaptive divergence even after the species’ gene pools have become separated. Adaptive divergence among taxa would operate in stark contrast to an alternative possibility that has previously been suggested, that distantly related species with dispersal-limited distributions and confronted with unpredictable neighbors will tend to converge on common strategies of resource use. In addition, we have also uncovered a positive density-dependent effect: growth rates of large trees are boosted in the presence of a smaller basal area of surrounding trees. We also show that many of the NDD interactions switch sign rapidly as focal trees grow in size, and that their cumulative effect can strongly influence the distributions and species composition of the trees that surround the focal trees during the focal trees’ lifetimes. PMID:27305092

Persistence of Neighborhood Demographic Influences over Long Phylogenetic Distances May Help Drive Post-Speciation Adaptation in Tropical Forests.

PubMed

Wills, Christopher; Harms, Kyle E; Wiegand, Thorsten; Punchi-Manage, Ruwan; Gilbert, Gregory S; Erickson, David; Kress, W John; Hubbell, Stephen P; Gunatilleke, C V Savitri; Gunatilleke, I A U Nimal

2016-01-01

Studies of forest dynamics plots (FDPs) have revealed a variety of negative density-dependent (NDD) demographic interactions, especially among conspecific trees. These interactions can affect growth rate, recruitment and mortality, and they play a central role in the maintenance of species diversity in these complex ecosystems. Here we use an equal area annulus (EAA) point-pattern method to comprehensively analyze data from two tropical FDPs, Barro Colorado Island in Panama and Sinharaja in Sri Lanka. We show that these NDD interactions also influence the continued evolutionary diversification of even distantly related tree species in these FDPs. We examine the details of a wide range of these interactions between individual trees and the trees that surround them. All these interactions, and their cumulative effects, are strongest among conspecific focal and surrounding tree species in both FDPs. They diminish in magnitude with increasing phylogenetic distance between heterospecific focal and surrounding trees, but do not disappear or change the pattern of their dependence on size, density, frequency or physical distance even among the most distantly related trees. The phylogenetic persistence of all these effects provides evidence that interactions between tree species that share an ecosystem may continue to promote adaptive divergence even after the species' gene pools have become separated. Adaptive divergence among taxa would operate in stark contrast to an alternative possibility that has previously been suggested, that distantly related species with dispersal-limited distributions and confronted with unpredictable neighbors will tend to converge on common strategies of resource use. In addition, we have also uncovered a positive density-dependent effect: growth rates of large trees are boosted in the presence of a smaller basal area of surrounding trees. We also show that many of the NDD interactions switch sign rapidly as focal trees grow in size, and that their cumulative effect can strongly influence the distributions and species composition of the trees that surround the focal trees during the focal trees' lifetimes.

Non-integrable dynamics of matter-wave solitons in a density-dependent gauge theory

NASA Astrophysics Data System (ADS)

Dingwall, R. J.; Edmonds, M. J.; Helm, J. L.; Malomed, B. A.; Öhberg, P.

2018-04-01

We study interactions between bright matter-wave solitons which acquire chiral transport dynamics due to an optically-induced density-dependent gauge potential. Through numerical simulations, we find that the collision dynamics feature several non-integrable phenomena, from inelastic collisions including population transfer and radiation losses to the formation of short-lived bound states and soliton fission. An effective quasi-particle model for the interaction between the solitons is derived by means of a variational approximation, which demonstrates that the inelastic nature of the collision arises from a coupling of the gauge field to velocities of the solitons. In addition, we derive a set of interaction potentials which show that the influence of the gauge field appears as a short-range potential, that can give rise to both attractive and repulsive interactions.

Modelling density-dependent resistance in insect-pathogen interactions.

PubMed

White, K A; Wilson, K

1999-10-01

We consider a mathematical model for a host-pathogen interaction where the host population is split into two categories: those susceptible to disease and those resistant to disease. Since the model was motivated by studies on insect populations, we consider a discrete-time model to reflect the discrete generations which are common among insect species. Whether an individual is born susceptible or resistant to disease depends on the local population levels at the start of each generation. In particular, we are interested in the case where the fraction of resistant individuals in the population increases as the total population increases. This may be seen as a positive feedback mechanism since disease is the only population control imposed upon the system. Moreover, it reflects recent experimental observations from noctuid moth-baculovirus interactions that pathogen resistance may increase with larval density. We find that the inclusion of a resistant class can stabilise unstable host-pathogen interactions but there is greatest regulation when the fraction born resistant is density independent. Nonetheless, inclusion of density dependence can still allow intrinsically unstable host-pathogen dynamics to be stabilised provided that this effect is sufficiently small. Moreover, inclusion of density-dependent resistance to disease allows the system to give rise to bistable dynamics in which the final outcome is dictated by the initial conditions for the model system. This has implications for the management of agricultural pests using biocontrol agents-in particular, it is suggested that the propensity for density-dependent resistance be determined prior to such a biocontrol attempt in order to be sure that this will result in the prevention of pest outbreaks, rather than their facilitation. Finally we consider how the cost of resistance to disease affects model outcomes and discover that when there is no cost to resistance, the model predicts stable periodic outbreaks of the insect population. The results are interpreted ecologically and future avenues for research to address the shortfalls in the present model system are discussed. Copyright 1999 Academic Press.

Multielectron effects in the photoelectron momentum distribution of noble-gas atoms driven by visible-to-infrared-frequency laser pulses: A time-dependent density-functional-theory approach

NASA Astrophysics Data System (ADS)

Murakami, Mitsuko; Zhang, G. P.; Chu, Shih-I.

2017-05-01

We present the photoelectron momentum distributions (PMDs) of helium, neon, and argon atoms driven by a linearly polarized, visible (527-nm) or near-infrared (800-nm) laser pulse (20 optical cycles in duration) based on the time-dependent density-functional theory (TDDFT) under the local-density approximation with a self-interaction correction. A set of time-dependent Kohn-Sham equations for all electrons in an atom is numerically solved using the generalized pseudospectral method. An effect of the electron-electron interaction driven by a visible laser field is not recognizable in the helium and neon PMDs except for a reduction of the overall photoelectron yield, but there is a clear difference between the PMDs of an argon atom calculated with the frozen-core approximation and TDDFT, indicating an interference of its M -shell wave functions during the ionization. Furthermore, we find that the PMDs of degenerate p states are well separated in intensity when driven by a near-infrared laser field, so that the single-active-electron approximation can be adopted safely.

Effects of medium on nuclear properties in multifragmentation

NASA Astrophysics Data System (ADS)

De, J. N.; Samaddar, S. K.; Viñas, X.; Centelles, M.; Mishustin, I. N.; Greiner, W.

2012-08-01

In multifragmentation of hot nuclear matter, properties of fragments embedded in a soup of nucleonic gas and other fragments should be modified as compared with isolated nuclei. Such modifications are studied within a simple model where only nucleons and one kind of heavy nuclei are considered. The interaction between different species is described with a momentum-dependent two-body potential whose parameters are fitted to reproduce properties of cold isolated nuclei. The internal energy of heavy fragments is parametrized according to a liquid-drop model with density- and temperature-dependent parameters. Calculations are carried out for several subnuclear densities and moderate temperatures, for isospin-symmetric and asymmetric systems. We find that the fragments get stretched due to interactions with the medium and their binding energies decrease with increasing temperature and density of nuclear matter.

Crossover to the anomalous quantum regime in the extrinsic spin Hall effect of graphene

NASA Astrophysics Data System (ADS)

Ferreira, Aires; Milletari, Mirco

Recent reports of spin-orbit coupling enhancement in chemically modified graphene have opened doors to studies of the spin Hall effect with massless chiral fermions. Here, we theoretically investigate the interaction and impurity density dependence of the extrinsic spin Hall effect in spin-orbit coupled graphene. We present a nonperturbative quantum diagrammatic calculation of the spin Hall response function in the strong-coupling regime that incorporates skew scattering and anomalous impurity density-independent contributions on equal footing. The spin Hall conductivity dependence on Fermi energy and electron-impurity interaction strength reveals the existence of experimentally accessible regions where anomalous quantum processes dominate. Our findings suggest that spin-orbit-coupled graphene is an ideal model system for probing the competition between semiclassical and bona fide quantum scattering mechanisms underlying the spin Hall effect. A.F. gratefully acknowledges the financial support of the Royal Society (U.K.).

Numerical studies on alpha production from high energy proton beam interaction with Boron

NASA Astrophysics Data System (ADS)

Moustaizis, S. D.; Lalousis, P.; Hora, H.; Korn, G.

2017-05-01

Numerical investigations on high energy proton beam interaction with high density Boron plasma allows to simulate conditions concerning the alpha production from recent experimental measurements . The experiments measure the alpha production due to p11B nuclear fusion reactions when a laser-driven high energy proton beam interacts with Boron plasma produced by laser beam interaction with solid Boron. The alpha production and consequently the efficiency of the process depends on the initial proton beam energy, proton beam density, the Boron plasma density and temperature, and their temporal evolution. The main advantage for the p11B nuclear fusion reaction is the production of three alphas with total energy of 8.9 MeV, which could enhance the alpha heating effect and improve the alpha production. This particular effect is termed in the international literature as the alpha avalanche effect. Numerical results using a multi-fluid, global particle and energy balance, code shows the alpha production efficiency as a function of the initial energy of the proton beam, the Boron plasma density, the initial Boron plasma temperature and the temporal evolution of the plasma parameters. The simulations enable us to determine the interaction conditions (proton beam - B plasma) for which the alpha heating effect becomes important.

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

PubMed

Holland, J Nathaniel; DeAngelis, Donald L

2010-05-01

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.

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

USGS Publications Warehouse

Holland, J. Nathaniel; DeAngelis, Donald L.

2010-01-01

Like predation and competition, mutualism is now recognized as a consumer resource (C-R) interaction, including, in particular, bi-directional (e.g., coral, plant- mycorrhizae) and uni-directional (e.g., ant-plant defense, plant-pollinator) C-R mutualisms. Here, we develop general theory for the density-dependent population dynamics of mutualism based on the C-R mechanism of interspecific interaction. To test the influence of C-R interactions on the dynamics and stability of bi- and uni-directional C-R mutualisms, we developed simple models that link consumer functional response of one mutualistic species with the resources supplied by another. Phase-plane analyses show that the ecological dynamics of C-R mutualisms are stable in general. Most transient behavior leads to an equilibrium of mutualistic coexistence, at which both species densities are greater than in the absence of interactions. However, due to the basic nature of C-R interactions, certain density-dependent conditions can lead to C-R dynamics characteristic of predator-prey interactions, in which one species overexploits and causes the other to go extinct. Consistent with empirical phenomena, these results suggest that the C-R interaction can provide a broad mechanism for understanding density-dependent population dynamics of mutualism. By unifying predation, competition, and mutualism under the common ecological framework of consumer-resource theory, we may also gain a better understanding of the universal features of interspecific interactions in general.

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

PubMed

McPeek, Mark A

2012-12-01

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

Effects of an electric field on interaction of aromatic systems.

PubMed

Youn, Il Seung; Cho, Woo Jong; Kim, Kwang S

2016-04-30

The effect of uniform external electric field on the interactions between small aromatic compounds and an argon atom is investigated using post-HF (MP2, SCS-MP2, and CCSD(T)) and density functional (PBE0-D3, PBE0-TS, and vdW-DF2) methods. The electric field effect is quantified by the difference of interaction energy calculated in the presence and absence of the electric field. All the post-HF methods describe electric field effects accurately although the interaction energy itself is overestimated by MP2. The electric field effect is explained by classical electrostatic models, where the permanent dipole moment from mutual polarization mainly determines its sign. The size of π-conjugated system does not have significant effect on the electric field dependence. We found out that PBE0-based methods give reasonable interaction energies and electric field response in every case, while vdW-DF2 sometimes shows spurious artifact owing to its sensitivity toward the real space electron density. © 2015 Wiley Periodicals, Inc.

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

PubMed

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

2018-01-01

Sexually reproducing organisms require males and females to find each other. Increased difficulty of females finding mates as male density declines is the most frequently reported mechanism of Allee effects in animals. Evolving more effective mate search may alleviate Allee effects, but may depend on density regimes a population experiences. In particular, high-density populations may evolve mechanisms that induce Allee effects which become detrimental when populations are reduced and maintained at a low density. We develop an individual-based, eco-genetic model to study how mating systems and fitness trade-offs interact with changes in population density to drive evolution of the rate at which males or females search for mates. Finite mate search rate triggers Allee effects in our model and we explore how these Allee effects respond to such evolution. We allow a population to adapt to several population density regimes and examine whether high-density populations are likely to reverse adaptations attained at low densities. We find density-dependent selection in most of scenarios, leading to search rates that result in lower Allee thresholds in populations kept at lower densities. This mainly occurs when fecundity costs are imposed on mate search, and provides an explanation for why Allee effects are often observed in anthropogenically rare species. Optimizing selection, where the attained trait value minimizes the Allee threshold independent of population density, depended on the trade-off between search and survival, combined with monogamy when females were searching. Other scenarios led to runaway selection on the mate search rate, including evolutionary suicide. Trade-offs involved in mate search may thus be crucial to determining how density influences the evolution of Allee effects. Previous studies did not examine evolution of a trait related to the strength of Allee effects under density variation. We emphasize the crucial role that mating systems, fitness trade-offs and the evolving sex have in determining the density threshold for population persistence, in particular since evolution need not always take the Allee threshold to its minimum value. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Density dependence, spatial scale and patterning in sessile biota.

PubMed

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

2005-09-01

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

Aerothermodynamics of the Mars Global Surveyor Spacecraft

NASA Technical Reports Server (NTRS)

Shane, Russell W.; Tolson, Robert H.

1998-01-01

The aerothermodynamics characteristics of the Mars Global Surveyor spacecraft are investigated and reported. These results have been used by the Mars Global Surveyor mission planners to design the aerobraking phase of the mission. Analytical and Direct Simulation Monte Carlo computer codes were used with a detailed, three dimensional model of the spacecraft to evaluate spacecraft aerobraking characteristics for flight in free molecular and transitional flow regimes. The spacecraft is found to be aerodynamically stable in aerobraking and planned contingency configurations. Aerodynamic forces, moments, and heating are found to be highly dependent on atmospheric density. Accommodation coefficient. is seen to strongly influence drag coefficient. Transitional flow effects are found to reduce overall solar panel heating. Attitude control thruster plumes are shown to interact with the freestream, diminishing the effectiveness of the attitude control system and even leading to thrust reversal. These plume-freestream interaction effects are found to be highly dependent on freestream density.

Effects of gas interparticle interaction on dissipative wake-mediated forces.

PubMed

Kliushnychenko, O V; Lukyanets, S P

2017-01-01

We examine how the short-range repulsive interaction in a gas of Brownian particles affects behavior of the nonequilibrium depletion forces between obstacles embedded into the gas flow. It is shown that for an ensemble of small and widely separated obstacles the dissipative wake-mediated interaction belongs to the type of induced dipole-dipole interaction governed by an anisotropic screened Coulomb-like potential. For closely located obstacles, formation of a common density perturbation "coat" around them leads to enhancement of dissipative interaction, manifested by characteristic peaks in its dependence on both the bath fraction and the external driving field. Moreover, additional screening of the gas flow due to nonlinear blockade effect gives rise to generation of a pronounced step-like profile of gas density distribution around the obstacles. This can lead to additional enhancement of dissipative interaction between obstacles. The possibility of the dissipative pairing effect and dissipative interaction switching provoked by wake inversion is briefly discussed. All the results are obtained within the classical lattice-gas model.

Interactions between demography and environmental effects are important determinants of population dynamics

PubMed Central

Gamelon, Marlène; Grøtan, Vidar; Nilsson, Anna L. K.; Engen, Steinar; Hurrell, James W.; Jerstad, Kurt; Phillips, Adam S.; Røstad, Ole W.; Slagsvold, Tore; Walseng, Bjørn; Stenseth, Nils C.; Sæther, Bernt-Erik

2017-01-01

Climate change will affect the population dynamics of many species, yet the consequences for the long-term persistence of populations are poorly understood. A major reason for this is that density-dependent feedback effects caused by fluctuations in population size are considered independent of stochastic variation in the environment. We show that an interplay between winter temperature and population density can influence the persistence of a small passerine population under global warming. Although warmer winters favor an increased mean population size, density-dependent feedback can cause the local population to be less buffered against occasional poor environmental conditions (cold winters). This shows that it is essential to go beyond the population size and explore climate effects on the full dynamics to elaborate targeted management actions. PMID:28164157

Effects of NN potentials on p Nuclides in the A ˜100-120 region

NASA Astrophysics Data System (ADS)

Lahiri, C.; Biswal, S. K.; Patra, S. K.

2016-02-01

Microscopic optical potentials for low-energy proton reactions have been obtained by folding density dependent M3Y (DDM3Y) interaction derived from nuclear matter calculation with densities from mean field approach to study astrophysically important proton rich nuclei in mass 100-120 region. We compare S factors for low-energy (p,γ) reactions with available experimental data and further calculate astrophysical reaction rates for (p,γ) and (p,n) reactions. Again, we choose some nonlinear R3Y (NR3Y) interactions from relativistic mean field (RMF) calculation and folded them with corresponding RMF densities to reproduce experimental S-factor values in this mass region. Finally, the effect of nonlinearity on our result is discussed.

Observation of number-density-dependent growth of plasmonic nanobubbles

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

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

PubMed

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

2016-06-29

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

Arbuscular mycorrhizal mediation of biomass-density relationship of Medicago sativa L. under two water conditions in a field experiment.

PubMed

Zhang, Qian; Xu, Liming; Tang, Jianjun; Bai, Minge; Chen, Xin

2011-05-01

The biomass-density relationship (whereby the biomass of individual plants decreases as plant density increases) has generally been explained by competition for resources. Arbuscular mycorrhizal fungi (AMF) are able to affect plant interactions by mediating resource utilization, but whether this AMF-mediated interaction will change the biomass-density relationship is unclear. We conducted an experiment to test the hypothesis that AMF will shift the biomass-density relationship by affecting intraspecific competition. Four population densities (10, 100, 1,000, or 10,000 seedlings per square meter) of Medicago sativa L. were planted in field plots. Water application (1,435 or 327.7 mm/year) simulated precipitation in wet areas (sufficient water) and arid areas (insufficient water). The fungicide benomyl was applied to suppress AMF in some plots ("low-AMF" treatment) and not in others ("high-AMF" treatment). The effect of the AMF treatment on the biomass-density relationship depended on water conditions. High AMF enhanced the decrease of individual biomass with increasing density (the biomass-density line had a steeper slope) when water was sufficient but not when water was insufficient. AMF treatment did not affect plant survival rate or population size but did affect absolute competition intensity (ACI). When water was sufficient, ACI was significantly higher in the high-AMF treatment than in the low-AMF treatment, but ACI was unaffected by AMF treatment when water was insufficient. Our results suggest that AMF status did not impact survival rate and population size but did shift the biomass-density relationship via effects on intraspecific competition. This effect of AMF on the biomass-density relationship depended on the availability of water.

Interplay between Rashba interaction and electromagnetic field in the edge states of a two-dimensional topological insulator

NASA Astrophysics Data System (ADS)

Dolcini, Fabrizio

2017-02-01

The effects of Rashba interaction and electromagnetic field on the edge states of a two-dimensional topological insulator are investigated in a nonperturbative way. We show that the electron dynamics is equivalent to a problem of massless Dirac fermions propagating with an inhomogeneous velocity, enhanced by the Rashba profile with respect to the bare Fermi value vF. Despite the inelastic and time-reversal breaking processes induced by the electromagnetic field, no backscattering occurs without interaction. The photoexcited electron densities are explicitly obtained in terms of the electric field and the Rashba interaction, and are shown to fulfill generalized chiral anomaly equations. The case of a Gaussian electromagnetic pulse is analyzed in detail. When the photoexcitation occurs far from the Rashba region, the latter effectively acts as a "superluminal gate" boosting the photoexcited wave packet outside the light-cone determined by vF. In contrast, for an electric pulse overlapping the Rashba region, the emerging wave packets are squeezed in a manner that depends on the overlap area. The electron-electron interaction effects are also discussed, for both intraspin and interspin density-density coupling. The results suggest that Rashba interaction, often considered as an unwanted disorder effect, may be exploited to tailor the shape and the propagation time of photoexcited spin-polarized wave packets.

Generalized thermodynamics of phase equilibria in scalar active matter

NASA Astrophysics Data System (ADS)

Solon, Alexandre P.; Stenhammar, Joakim; Cates, Michael E.; Kafri, Yariv; Tailleur, Julien

2018-02-01

Motility-induced phase separation (MIPS) arises generically in fluids of self-propelled particles when interactions lead to a kinetic slowdown at high densities. Starting from a continuum description of scalar active matter akin to a generalized Cahn-Hilliard equation, we give a general prescription for the mean densities of coexisting phases in flux-free steady states that amounts, at a hydrodynamics scale, to extremizing an effective free energy. We illustrate our approach on two well-known models: self-propelled particles interacting either through a density-dependent propulsion speed or via direct pairwise forces. Our theory accounts quantitatively for their phase diagrams, providing a unified description of MIPS.

Vicinage effect in the energy loss of H2 dimers: Experiment and calculations based on time-dependent density-functional theory

NASA Astrophysics Data System (ADS)

Koval, N. E.; Borisov, A. G.; Rosa, L. F. S.; Stori, E. M.; Dias, J. F.; Grande, P. L.; Sánchez-Portal, D.; Muiño, R. Díez

2017-06-01

We present a combined theoretical and experimental study of the energy loss of H2+ molecular ions interacting with thin oxide and carbon films. As a result of quantum mechanical interference of the target electrons, the energy loss of a molecular projectile differs from the sum of the energy losses of individual atomic projectiles. This difference is known as the vicinage effect. Calculations based on the time-dependent density functional theory allow the first-principles description of the dynamics of target excitations produced by the correlated motion of the nucleons forming the molecule. We investigate in detail the dependence of the vicinage effect on the speed and charge state of the projectile and find an excellent agreement between calculated and measured data.

Predation and fragmentation portrayed in the statistical structure of prey time series

PubMed Central

Hendrichsen, Ditte K; Topping, Chris J; Forchhammer, Mads C

2009-01-01

Background Statistical autoregressive analyses of direct and delayed density dependence are widespread in ecological research. The models suggest that changes in ecological factors affecting density dependence, like predation and landscape heterogeneity are directly portrayed in the first and second order autoregressive parameters, and the models are therefore used to decipher complex biological patterns. However, independent tests of model predictions are complicated by the inherent variability of natural populations, where differences in landscape structure, climate or species composition prevent controlled repeated analyses. To circumvent this problem, we applied second-order autoregressive time series analyses to data generated by a realistic agent-based computer model. The model simulated life history decisions of individual field voles under controlled variations in predator pressure and landscape fragmentation. Analyses were made on three levels: comparisons between predated and non-predated populations, between populations exposed to different types of predators and between populations experiencing different degrees of habitat fragmentation. Results The results are unambiguous: Changes in landscape fragmentation and the numerical response of predators are clearly portrayed in the statistical time series structure as predicted by the autoregressive model. Populations without predators displayed significantly stronger negative direct density dependence than did those exposed to predators, where direct density dependence was only moderately negative. The effects of predation versus no predation had an even stronger effect on the delayed density dependence of the simulated prey populations. In non-predated prey populations, the coefficients of delayed density dependence were distinctly positive, whereas they were negative in predated populations. Similarly, increasing the degree of fragmentation of optimal habitat available to the prey was accompanied with a shift in the delayed density dependence, from strongly negative to gradually becoming less negative. Conclusion We conclude that statistical second-order autoregressive time series analyses are capable of deciphering interactions within and across trophic levels and their effect on direct and delayed density dependence. PMID:19419539

Density dependence governs when population responses to multiple stressors are magnified or mitigated.

PubMed

Hodgson, Emma E; Essington, Timothy E; Halpern, Benjamin S

2017-10-01

Population endangerment typically arises from multiple, potentially interacting anthropogenic stressors. Extensive research has investigated the consequences of multiple stressors on organisms, frequently focusing on individual life stages. Less is known about population-level consequences of exposure to multiple stressors, especially when exposure varies through life. We provide the first theoretical basis for identifying species at risk of magnified effects from multiple stressors across life history. By applying a population modeling framework, we reveal conditions under which population responses from stressors applied to distinct life stages are either magnified (synergistic) or mitigated. We find that magnification or mitigation critically depends on the shape of density dependence, but not the life stage in which it occurs. Stressors are always magnified when density dependence is linear or concave, and magnified or mitigated when it is convex. Using Bayesian numerical methods, we estimated the shape of density dependence for eight species across diverse taxa, finding support for all three shapes. © 2017 by the Ecological Society of America.

Neighbourhood density and genetic relatedness interact to determine fruit set and abortion rates in a continuous tropical tree population

PubMed Central

Jones, F.A; Comita, L.S

2008-01-01

Tropical trees may show positive density dependence in fruit set and maturation due to pollen limitation in low-density populations. However, pollen from closely related individuals in the local neighbourhood might reduce fruit set or increase fruit abortion in self-incompatible tree species. We investigated the role of neighbourhood density and genetic relatedness on individual fruit set and abortion in the neotropical tree Jacaranda copaia in a large forest plot in central Panama. Using nested neighbourhood models, we found a strong positive effect of increased conspecific density on fruit set and maturation. However, high neighbourhood genetic relatedness interacted with density to reduce total fruit set and increase the proportion of aborted fruit. Our results imply a fitness advantage for individuals growing in high densities as measured by fruit set, but realized fruit set is lowered by increased neighbourhood relatedness. We hypothesize that the mechanism involved is increased visitation by density-dependent invertebrate pollinators in high-density populations, which increases pollen quantity and carry-over and increases fruit set and maturation, coupled with self-incompatibility at early and late stages due to biparental inbreeding that lowers fruit set and increases fruit abortion. Implications for the reproductive ecology and conservation of tropical tree communities in continuous and fragmented habitats are discussed. PMID:18713714

Experimental evidence that density dependence strongly influences plant invasions through fragmented landscapes.

PubMed

Williams, Jennifer L; Levine, Jonathan M

2018-04-01

Populations of range expanding species encounter patches of both favorable and unfavorable habitat as they spread across landscapes. Theory shows that increasing patchiness slows the spread of populations modeled with continuously varying population density when dispersal is not influence by the environment or individual behavior. However, as is found in uniformly favorable landscapes, spread remains driven by fecundity and dispersal from low density individuals at the invasion front. In contrast, when modeled populations are composed of discrete individuals, patchiness causes populations to build up to high density before dispersing past unsuitable habitat, introducing an important influence of density dependence on spread velocity. To test the hypothesized interaction between habitat patchiness and density dependence, we simultaneously manipulated these factors in a greenhouse system of annual plants spreading through replicated experimental landscapes. We found that increasing the size of gaps and amplifying the strength of density dependence both slowed spread velocity, but contrary to predictions, the effect of amplified density dependence was similar across all landscape types. Our results demonstrate that the discrete nature of individuals in spreading populations has a strong influence on how both landscape patchiness and density dependence influence spread through demographic and dispersal stochasticity. Both finiteness and landscape structure should be critical components to theoretical predictions of future spread for range expanding native species or invasive species colonizing new habitat. © 2018 by the Ecological Society of America.

A global analysis of bidirectional interactions in alpine plant communities shows facilitators experiencing strong reciprocal fitness costs.

PubMed

Schöb, Christian; Michalet, Richard; Cavieres, Lohengrin A; Pugnaire, Francisco I; Brooker, Rob W; Butterfield, Bradley J; Cook, Bradley J; Kikvidze, Zaal; Lortie, Christopher J; Xiao, Sa; Al Hayek, Patrick; Anthelme, Fabien; Cranston, Brittany H; García, Mary-Carolina; Le Bagousse-Pinguet, Yoann; Reid, Anya M; le Roux, Peter C; Lingua, Emanuele; Nyakatya, Mawethu J; Touzard, Blaise; Zhao, Liang; Callaway, Ragan M

2014-04-01

Facilitative interactions are defined as positive effects of one species on another, but bidirectional feedbacks may be positive, neutral, or negative. Understanding the bidirectional nature of these interactions is a fundamental prerequisite for the assessment of the potential evolutionary consequences of facilitation. In a global study combining observational and experimental approaches, we quantified the impact of the cover and richness of species associated with alpine cushion plants on reproductive traits of the benefactor cushions. We found a decline in cushion seed production with increasing cover of cushion-associated species, indicating that being a benefactor came at an overall cost. The effect of cushion-associated species was negative for flower density and seed set of cushions, but not for fruit set and seed quality. Richness of cushion-associated species had positive effects on seed density and modulated the effects of their abundance on flower density and fruit set, indicating that the costs and benefits of harboring associated species depend on the composition of the plant assemblage. Our study demonstrates 'parasitic' interactions among plants over a wide range of species and environments in alpine systems, and we consider their implications for the possible selective effects of interactions between benefactor and beneficiary species. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Alternative stable states and alternative endstates of community assembly through intra- and interspecific positive and negative interactions.

PubMed

Gerla, Daan J; Mooij, Wolf M

2014-09-01

Positive and negative interactions within and between species may occur simultaneously, with the net effect depending on population densities. For instance, at low densities plants may ameliorate stress, while competition for resources dominates at higher densities. Here, we propose a simple two-species model in which con- and heterospecifics have a positive effect on per capita growth rate at low densities, while negative interactions dominate at high densities. The model thus includes both Allee effects (intraspecific positive effects) and mutualism (interspecific positive effects), as well as intra- and interspecific competition. Using graphical methods we derive conditions for alternative stable states and species coexistence. We show that mutual non-invasibility (i.e. the inability of each species to invade a population of the other) is more likely when species have a strong positive effect on the own species or a strong negative effect on the other species. Mutual non-invasibility implies alternative stable states, however, there may also be alternative stable states at which species coexist. In the case of species symmetry (i.e. when species are indistinguishable), such alternative coexistence states require that if the positive effect exerted at low densities at the own species is stronger than on the other species, the negative effect at higher densities is also stronger on the own species than on the other species, or, vice versa, if the interspecific positive effects at low densities are stronger than the intraspecific effects, the negative effects at higher densities are also stronger between species than within species. However, the reachability of alternative stable states is restricted by the frequency and density at which species are introduced during community assembly, so that alternative stable states do not always represent alternative endstates of community assembly. Copyright © 2014 Elsevier Inc. All rights reserved.

Discreteness effects in a reacting system of particles with finite interaction radius.

PubMed

Berti, S; López, C; Vergni, D; Vulpiani, A

2007-09-01

An autocatalytic reacting system with particles interacting at a finite distance is studied. We investigate the effects of the discrete-particle character of the model on properties like reaction rate, quenching phenomenon, and front propagation, focusing on differences with respect to the continuous case. We introduce a renormalized reaction rate depending both on the interaction radius and the particle density, and we relate it to macroscopic observables (e.g., front speed and front thickness) of the system.

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

PubMed Central

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

2016-01-01

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

Effect of mass and density of ambient gas on the interaction of laser-blow-off plasma plumes propagating in close proximity

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

Kumar, Bhupesh; Singh, R. K.; Kumar, Ajai, E-mail: ajai@ipr.res.in

2016-04-15

The effects of mass and pressure of ambient gas on the propagation dynamics of two laser-blow-off plasma plumes created in close proximity are investigated. A time gated fast imaging technique is used for recording the images of the laterally colliding plumes under different experimental conditions. Pressure is varied from 0.1 to 3 mbar in three ambient, i.e., helium, neon, and argon. Emphasis is given on the nature of shock-shock interaction under different ambient conditions. It has been observed that the shock-velocity, shape, strength, and their interactions are strongly dependent on the mass and density of the ambient gases. The rolemore » of the interacting shocks and their subsequent reflections on the formation and geometrical shape of the interaction region in different ambient conditions is briefly described.« less

Entanglement entropy in a one-dimensional disordered interacting system: the role of localization.

PubMed

Berkovits, Richard

2012-04-27

The properties of the entanglement entropy (EE) in one-dimensional disordered interacting systems are studied. Anderson localization leaves a clear signature on the average EE, as it saturates on the length scale exceeding the localization length. This is verified by numerically calculating the EE for an ensemble of disordered realizations using the density matrix renormalization group method. A heuristic expression describing the dependence of the EE on the localization length, which takes into account finite-size effects, is proposed. This is used to extract the localization length as a function of the interaction strength. The localization length dependence on the interaction fits nicely with the expectations.

Dynamic multipopulation and density dependent evolutionary games related to replicator dynamics. A metasimplex concept.

PubMed

Argasinski, Krzysztof

2006-07-01

This paper contains the basic extensions of classical evolutionary games (multipopulation and density dependent models). It is shown that classical bimatrix approach is inconsistent with other approaches because it does not depend on proportion between populations. The main conclusion is that interspecific proportion parameter is important and must be considered in multipopulation models. The paper provides a synthesis of both extensions (a metasimplex concept) which solves the problem intrinsic in the bimatrix model. It allows us to model interactions among any number of subpopulations including density dependence effects. We prove that all modern approaches to evolutionary games are closely related. All evolutionary models (except classical bimatrix approaches) can be reduced to a single population general model by a simple change of variables. Differences between classic bimatrix evolutionary games and a new model which is dependent on interspecific proportion are shown by examples.

Community-level consequences of cannibalism.

PubMed

Ohlberger, Jan; Langangen, Oystein; Stenseth, Nils C; Vøllestad, L Asbjørn

2012-12-01

Ecological interactions determine the structure and dynamics of communities and their responses to the environment. Understanding the community-level effects of ecological interactions, such as intra- and interspecifc competition, predation, and cannibalism, is therefore central to ecological theory and ecosystem management. Here, we investigate the community-level consequences of cannibalism in populations with density-dependent maturation and reproduction. We model a stage-structured consumer population with an ontogenetic diet shift to analyze how cannibalism alters the conditions for the invasion and persistence of stage-specific predators and competitors. Our results demonstrate that cannibalistic interactions can facilitate coexistence with other species at both trophic levels. This effect of cannibalism critically depends on the food dependence of the demographic processes. The underlying mechanism is a cannibalism-induced shift in the biomass distribution between the consumer life stages. These findings suggest that cannibalism may alter the structure of ecological communities through its effects on species coexistence.

Modeling ecological traps for the control of feral pigs

PubMed Central

Dexter, Nick; McLeod, Steven R

2015-01-01

Ecological traps are habitat sinks that are preferred by dispersing animals but have higher mortality or reduced fecundity compared to source habitats. Theory suggests that if mortality rates are sufficiently high, then ecological traps can result in extinction. An ecological trap may be created when pest animals are controlled in one area, but not in another area of equal habitat quality, and when there is density-dependent immigration from the high-density uncontrolled area to the low-density controlled area. We used a logistic population model to explore how varying the proportion of habitat controlled, control mortality rate, and strength of density-dependent immigration for feral pigs could affect the long-term population abundance and time to extinction. Increasing control mortality, the proportion of habitat controlled and the strength of density-dependent immigration decreased abundance both within and outside the area controlled. At higher levels of these parameters, extinction was achieved for feral pigs. We extended the analysis with a more complex stochastic, interactive model of feral pig dynamics in the Australian rangelands to examine how the same variables as the logistic model affected long-term abundance in the controlled and uncontrolled area and time to extinction. Compared to the logistic model of feral pig dynamics, the stochastic interactive model predicted lower abundances and extinction at lower control mortalities and proportions of habitat controlled. To improve the realism of the stochastic interactive model, we substituted fixed mortality rates with a density-dependent control mortality function, empirically derived from helicopter shooting exercises in Australia. Compared to the stochastic interactive model with fixed mortality rates, the model with the density-dependent control mortality function did not predict as substantial decline in abundance in controlled or uncontrolled areas or extinction for any combination of variables. These models demonstrate that pest eradication is theoretically possible without the pest being controlled throughout its range because of density-dependent immigration into the area controlled. The stronger the density-dependent immigration, the better the overall control in controlled and uncontrolled habitat combined. However, the stronger the density-dependent immigration, the poorer the control in the area controlled. For feral pigs, incorporating environmental stochasticity improves the prospects for eradication, but adding a realistic density-dependent control function eliminates these prospects. PMID:26045954

Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect

NASA Astrophysics Data System (ADS)

Nakagawa, Satoshi; Kurniawan, Isman; Kodama, Koichi; Arwansyah, Muhammad Saleh; Kawaguchi, Kazutomo; Nagao, Hidemi

2018-03-01

We present a simple coarse-grained model with the molecular crowding effect in solvent to investigate the structure and dynamics of protein complexes including association and/or dissociation processes and investigate some physical properties such as the structure and the reaction rate from the viewpoint of the hydrophobic intermolecular interactions of protein complex. In the present coarse-grained model, a function depending upon the density of hydrophobic amino acid residues in a binding area of the complex is introduced, and the function involves the molecular crowding effect for the intermolecular interactions of hydrophobic amino acid residues between proteins. We propose a hydrophobic intermolecular potential energy between proteins by using the density-dependent function. The present coarse-grained model is applied to the complex of cytochrome f and plastocyanin by using the Langevin dynamics simulation to investigate some physical properties such as the complex structure, the electron transfer reaction rate constant from plastocyanin to cytochrome f and so on. We find that for proceeding the electron transfer reaction, the distance between metals in their active sites is necessary within about 18 Å. We discuss some typical complex structures formed in the present simulation in relation to the molecular crowding effect on hydrophobic interactions.

Multiphoton ionization of many-electron atoms and highly-charged ions in intense laser fields: a relativistic time-dependent density functional theory approach

NASA Astrophysics Data System (ADS)

Tumakov, Dmitry A.; Telnov, Dmitry A.; Maltsev, Ilia A.; Plunien, Günter; Shabaev, Vladimir M.

2017-10-01

We develop an efficient numerical implementation of the relativistic time-dependent density functional theory (RTDDFT) to study multielectron highly-charged ions subject to intense linearly-polarized laser fields. The interaction with the electromagnetic field is described within the electric dipole approximation. The resulting time-dependent relativistic Kohn-Sham (RKS) equations possess an axial symmetry and are solved accurately and efficiently with the help of the time-dependent generalized pseudospectral method. As a case study, we calculate multiphoton ionization probabilities of the neutral argon atom and argon-like xenon ion. Relativistic effects are assessed by comparison of our present results with existing non-relativistic data.

Equilibrium finite-frequency noise of an interacting mesoscopic capacitor studied in time-dependent density functional theory

NASA Astrophysics Data System (ADS)

Dittmann, Niklas; Splettstoesser, Janine; Helbig, Nicole

2018-03-01

We calculate the frequency-dependent equilibrium noise of a mesoscopic capacitor in time-dependent density functional theory (TDDFT). The capacitor is modeled as a single-level quantum dot with on-site Coulomb interaction and tunnel coupling to a nearby reservoir. The noise spectra are derived from linear-response conductances via the fluctuation-dissipation theorem. Thereby, we analyze the performance of a recently derived exchange-correlation potential with time-nonlocal density dependence in the finite-frequency linear-response regime. We compare our TDDFT noise spectra with real-time perturbation theory and find excellent agreement for noise frequencies below the reservoir temperature.

Disentangling endogenous versus exogenous pattern formation in spatial ecology: a case study of the ant Azteca sericeasur in southern Mexico.

PubMed

Li, Kevin; Vandermeer, John H; Perfecto, Ivette

2016-05-01

Spatial patterns in ecology can be described as reflective of environmental heterogeneity (exogenous), or emergent from dynamic relationships between interacting species (endogenous), but few empirical studies focus on the combination. The spatial distribution of the nests of Azteca sericeasur, a keystone tropical arboreal ant, is thought to form endogenous spatial patterns among the shade trees of a coffee plantation through self-regulating interactions with controlling agents (i.e. natural enemies). Using inhomogeneous point process models, we found evidence for both types of processes in the spatial distribution of A. sericeasur. Each year's nest distribution was determined mainly by a density-dependent relationship with the previous year's lagged nest density; but using a novel application of a Thomas cluster process to account for the effects of nest clustering, we found that nest distribution also correlated significantly with tree density in the later years of the study. This coincided with the initiation of agricultural intensification and tree felling on the coffee farm. The emergence of this significant exogenous effect, along with the changing character of the density-dependent effect of lagged nest density, provides clues to the mechanism behind a unique phenomenon observed in the plot, that of an increase in nest population despite resource limitation in nest sites. Our results have implications in coffee agroecological management, as this system provides important biocontrol ecosystem services. Further research is needed, however, to understand the effective scales at which these relationships occur.

Study on Solution Properties of Binary Mixtures of Some Industrially Important Solvents with Cyclohexylamine and Cyclohexanone at 298.15 K

NASA Astrophysics Data System (ADS)

Roy, Mahendra Nath; Das, Rajesh Kumar; Chanda, Riju

2010-03-01

Densities and viscosities were measured for the binary mixtures of cyclohexylamine and cyclohexanone with butyl acetate, butanone, butylamine, tert-butylamine, and 2-butoxyethanol at 298.15 K over the entire composition range. From density data, the values of the excess molar volume ( V E) have been calculated. The experimental viscosity data were correlated by means of the equation of Grunberg-Nissan. The density and viscosity data have been analyzed in terms of some semiempirical viscosity models. The results are discussed in terms of molecular interactions and structural effects. The excess molar volume is found to be either negative or positive depending on the molecular interactions and the nature of the liquid mixtures and is discussed in terms of molecular interactions and structural changes.

Folding model analyses of 12C-12C and 16O-16O elastic scattering using the density-dependent LOCV-averaged effective interaction

NASA Astrophysics Data System (ADS)

Rahmat, M.; Modarres, M.

2018-03-01

The averaged effective two-body interaction (AEI), which can be generated through the lowest order constrained variational (LOCV) method for symmetric nuclear matter (SNM) with the input [Reid68, Ann. Phys. 50, 411 (1968), 10.1016/0003-4916(68)90126-7] nucleon-nucleon potential, is used as the effective nucleon-nucleon potential in the folding model to describe the heavy-ion (HI) elastic scattering cross sections. The elastic scattering cross sections of 12C-12C and 16O-16O systems are calculated in the above framework. The results are compared with the corresponding calculations coming from the fitting procedures with the input finite range D D M 3 Y 1 -Reid potential and the available experimental data at different incident energies. It is shown that a reasonable description of the elastic 12C-12C and 16O-16O scattering data at the low and medium energies can be obtained by using the above LOCV AEI, without any need to define a parametrized density-dependent function in the effective nucleon-nucleon potential, which is formally considered in the typical D D M 3 Y 1 -Reid interactions.

Universal functions of nuclear proximity potential for Skyrme nucleus-nucleus interaction in a semiclassical approach

NASA Astrophysics Data System (ADS)

Gupta, Raj K.; Singh, Dalip; Kumar, Raj; Greiner, Walter

2009-07-01

The universal function of the nuclear proximity potential is obtained for the Skyrme nucleus-nucleus interaction in the semiclassical extended Thomas-Fermi (ETF) approach. This is obtained as a sum of the spin-orbit-density-independent and spin-orbit-density-dependent parts of the Hamiltonian density, since the two terms behave differently, the spin-orbit-density-independent part mainly attractive and the spin-orbit-density-dependent part mainly repulsive. The semiclassical expansions of kinetic energy density and spin-orbit density are allowed up to second order, and the two-parameter Fermi density, with its parameters fitted to experiments, is used for the nuclear density. The universal functions or the resulting nuclear proximity potential reproduce the 'exact' Skyrme nucleus-nucleus interaction potential in the semiclassical approach, within less than ~1 MeV of difference, both at the maximum attraction and in the surface region. An application of the resulting interaction potential to fusion excitation functions shows clearly that the parameterized universal functions of nuclear proximity potential substitute completely the 'exact' potential in the Skyrme energy density formalism based on the semiclassical ETF method, including also the modifications of interaction barriers at sub-barrier energies in terms of modifying the constants of the universal functions.

Density dependent interactions between VA mycorrhizal fungi and even-aged seedlings of two perennial Fabaceae species.

PubMed

Allsopp, N; Stock, W D

1992-08-01

The interaction of density and mycorrhizal effects on the growth, mineral nutrition and size distribution of seedlings of two perennial members of the Fabaceae was investigated in pot culture. Seedlings of Otholobium hirtum and Aspalathus linearis were grown at densities of 1, 4, 8 and 16 plants per 13-cm pot with or without vesicular-arbuscular (VA) mycorrhizal inoculum for 120 days. Plant mass, relative growth rates, height and leaf number all decreased with increasing plant density. This was ascribed to the decreasing availability of phosphorus per plant as density increased. O. hirtum was highly dependent on mycorrhizas for P uptake but both mycorrhizal and non-mycorrhizal A. linearis seedlings were able to extract soil P with equal ease. Plant size distribution as measured by the coefficient of variation (CV) of shoot mass was greater at higher densities. CVs of mycorrhizal O. hirtum plants were higher than those of non-mycorrhizal plants. CVs of the facultatively mycorrhizal A. linearis were similar for both mycorrhizal and non-mycorrhizal plants. Higher CVs are attributed to resource preemption by larger individuals. Individuals in populations with high CVs will probably survive stress which would result in the extinction of populations with low CVs. Mass of mycorrhizal plants of both species decreased more rapidly with increasing density than did non-mycorrhizal plant mass. It is concluded that the cost of being mycorrhizal increases as plant density increases, while the benefit decreases. The results suggest that mycorrhizas will influence density-dependent population processes of faculative and obligate mycorrhizal species.

You can't run but you can hide: refuge use in frog tadpoles elicits density-dependent predation by dragonfly larvae.

PubMed

Hossie, Thomas John; Murray, Dennis L

2010-06-01

The potential role of prey refuges in stabilizing predator-prey interactions is of longstanding interest to ecologists, but mechanisms underlying a sigmoidal predator functional response remain to be fully elucidated. Authors have disagreed on whether the stabilizing effect of prey refuges is driven by prey- versus predator-centric mechanisms, but to date few studies have married predator and prey behavioural observations to distinguish between these possibilities. We used a dragonfly nymph-tadpole system to study the effect of a structural refuge (leaf litter) on the predator's functional response, and paired this with behavioural observations of both predator and prey. Our study confirmed that hyperbolic (type II) functional responses were characteristic of foraging predators when structural cover was low or absent, whereas the functional response was sigmoidal (type III) when prey were provided with sufficient refuge. Prey activity and refuge use were density independent across cover treatments, thereby eliminating a prey-centric mechanism as being the genesis for density-dependent predation. In contrast, the predator's pursuit length, capture success, and handling time were altered by the amount of structure implying that observed shifts in density-dependent predation likely were related to predator hunting efficiency. Our study advances current theory by revealing that despite fixed-proportion refuge use by prey, presence of a prey refuge can induce density-dependent predation through its effect on predator hunting strategy. Ultimately, responses of predator foraging decisions in response to changes in prey availability and search efficiency may be more important in producing density-dependent predation than the form of prey refuge use.

Density Dependent Functional Forms Drive Compensation in Populations Exposed to Stressors

EPA Science Inventory

The interaction between density dependence (DD) and environmental stressors can result in a compensatory or synergistic response in population growth, and population models that use density-independent demographic rates or generic DD functions may be introducing bias into managem...

Temperature dependence of the symmetry energy and neutron skins in Ni, Sn, and Pb isotopic chains

NASA Astrophysics Data System (ADS)

Antonov, A. N.; Kadrev, D. N.; Gaidarov, M. K.; Sarriguren, P.; de Guerra, E. Moya

2017-02-01

The temperature dependence of the symmetry energy for isotopic chains of even-even Ni, Sn, and Pb nuclei is investigated in the framework of the local density approximation (LDA). The Skyrme energy density functional with two Skyrme-class effective interactions, SkM* and SLy4, is used in the calculations. The temperature-dependent proton and neutron densities are calculated through the hfbtho code that solves the nuclear Skyrme-Hartree-Fock-Bogoliubov problem by using the cylindrical transformed deformed harmonic-oscillator basis. In addition, two other density distributions of 208Pb, namely the Fermi-type density determined within the extended Thomas-Fermi (TF) method and symmetrized-Fermi local density obtained within the rigorous density functional approach, are used. The kinetic energy densities are calculated either by the hfbtho code or, for a comparison, by the extended TF method up to second order in temperature (with T2 term). Alternative ways to calculate the symmetry energy coefficient within the LDA are proposed. The results for the thermal evolution of the symmetry energy coefficient in the interval T =0 -4 MeV show that its values decrease with temperature. The temperature dependence of the neutron and proton root-mean-square radii and corresponding neutron skin thickness is also investigated, showing that the effect of temperature leads mainly to a substantial increase of the neutron radii and skins, especially in the more neutron-rich nuclei, a feature that may have consequences on astrophysical processes and neutron stars.

Influences of pea morphology and interacting factors on pea aphid (Homoptera: Aphididae) reproduction.

PubMed

Buchman, N; Cuddington, K

2009-08-01

It has been claimed that plant architecture can alter aphid reproductive rates, but the mechanism driving this effect has not been identified. We studied interactions between plant architecture, aphid density, environmental conditions, and nutrient availability on the reproduction of pea aphids [Acyrthosiphon pisum (Harris)] using four near-isogenic peas (Pisum sativum L.) that differ in morphology. Manipulations of aphid density (1, 5, and 10 adults per plant) allowed us to examine any effects of plant morphology on crowding and consequently reproduction. Pea morphology per se did not alter pea aphid crowding, as measured by mean nearest neighbor distance, and there was no effect on reproduction. In addition, reproduction increased with increasing adult density, indicating positive density dependence. In a separate experiment, peas were fertilized to determine whether differences between nutrient availability of the four different morphologies might drive any observed differences in aphid reproduction. Although plant nitrogen content was altered by fertilization treatments, this did not have an impact on aphid reproduction. Greenhouse experiments, however, suggested that pea morphology can interact with environmental conditions to reduce aphid reproduction under some conditions. We conclude that plant morphology only influences aphid reproduction when environmental conditions are less than optimal.

Orbital order and effective mass enhancement in t2 g two-dimensional electron gases

NASA Astrophysics Data System (ADS)

Tolsma, John; Principi, Alessandro; Polini, Marco; MacDonald, Allan

2015-03-01

It is now possible to prepare d-electron two-dimensional electron gas systems that are confined near oxide heterojunctions and contain t2 g electrons with a density much smaller than one electron per metal atom. I will discuss a generic model that captures all qualitative features of electron-electron interaction physics in t2 g two-dimensional electron gas systems, and the use of a GW approximation to explore t2 g quasiparticle properties in this new context. t2 g electron gases contain a high density isotropic light mass xy component and low-density xz and yz anisotropic components with light and heavy masses in orthogonal directions. The high density light mass band screens interactions within the heavy bands. As a result the wave vector dependence of the self-energy is reduced and the effective mass is increased. When the density in the heavy bands is low, the difference in anisotropy between the two heavy bands favors orbital order. When orbital order does not occur, interactions still reshape the heavy-band Fermi surfaces. I will discuss these results in the context of recently reported magnetotransport experiments.

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

PubMed

Flick, Johannes; Ruggenthaler, Michael; Appel, Heiko; Rubio, Angel

2015-12-15

The density-functional approach to quantum electrodynamics extends traditional density-functional theory and opens the possibility to describe electron-photon interactions in terms of effective Kohn-Sham potentials. In this work, we numerically construct the exact electron-photon Kohn-Sham potentials for a prototype system that consists of a trapped electron coupled to a quantized electromagnetic mode in an optical high-Q cavity. Although the effective current that acts on the photons is known explicitly, the exact effective potential that describes the forces exerted by the photons on the electrons is obtained from a fixed-point inversion scheme. This procedure allows us to uncover important beyond-mean-field features of the effective potential that mark the breakdown of classical light-matter interactions. We observe peak and step structures in the effective potentials, which can be attributed solely to the quantum nature of light; i.e., they are real-space signatures of the photons. Our findings show how the ubiquitous dipole interaction with a classical electromagnetic field has to be modified in real space to take the quantum nature of the electromagnetic field fully into account.

The symmetry energy, neutron skin thickness and isovector dipole response of neutron-rich nuclei

NASA Astrophysics Data System (ADS)

Horvat, A.; Paar, N.

2015-04-01

The isotopic evolution of the relationship between the symmetry energy at saturation density of nuclear matter (J), neutron skin thickness (ΔR) and relevant observables related to isovector dipole excitations in neutron rich 116-136Sn isotopes has been investigated in the framework of relativistic nuclear energy density functional theory. The description employs a family of effective interactions with density dependent meson-nucleon couplings (DDME) spanning the range of values J = 30 - 38 MeV.

Effective atomic numbers and electron densities of bioactive glasses for photon interaction

NASA Astrophysics Data System (ADS)

Shantappa, Anil; Hanagodimath, S. M.

2015-08-01

This work was carried out to study the nature of mass attenuation coefficient of bioactive glasses for gamma rays. Bioactive glasses are a group of synthetic silica-based bioactive materials with unique bone bonding properties. In the present study, we have calculated the effective atomic number, electron density for photon interaction of some selected bioactive glasses viz., SiO2-Na2O, SiO2-Na2O-CaO and SiO2-Na2O-P2O5 in the energy range 1 keV to 100 MeV. We have also computed the single valued effective atomic number by using XMuDat program. It is observed that variation in effective atomic number (ZPI, eff) depends also upon the weight fractions of selected bioactive glasses and range of atomic numbers of the elements. The results shown here on effective atomic number, electron density will be more useful in the medical dosimetry for the calculation of absorbed dose and dose rate.

Interactive effects of childhood maltreatment and recent stressful life events on alcohol consumption in adulthood.

PubMed

Young-Wolff, Kelly C; Kendler, Kenneth S; Prescott, Carol A

2012-07-01

Childhood maltreatment is associated with early alcohol use initiation, alcohol-related problem behaviors, and alcohol use disorders in adulthood. Heavy drinking risk among individuals exposed to childhood maltreatment could be partly attributable to stress sensitization, whereby early adversity leads to psychobiological changes that heighten sensitivity to subsequent stressors and increase risk for stress-related drinking. We addressed this issue by examining whether the association between past-year stressful life events and past-year drinking density, a weighted quantity-frequency measure of alcohol consumption, was stronger among adults exposed to childhood maltreatment. Drinking density, stressful life events, and child maltreatment were assessed using structured clinical interviews in a sample of 4,038 male and female participants ages 20-58 years from the Virginia Adult Twin Study of Psychiatric and Substance Use Disorders. Stress sensitization was examined using hierarchical multiple regression analyses to test whether stressful events moderated the association between maltreatment and drinking density. Analyses were stratified by sex and whether the impact was different for independent stressful events or dependent stressful events as related to a participant's actions. Independent stressful events were associated with heavier drinking density among women exposed to maltreatment. In contrast, drinking density was roughly the same across independent stressful life events exposure among women not exposed to maltreatment. There was little evidence for Maltreatment × Independent Stressor interactions in men or Maltreatment × Dependent Stressor interactions in either gender. Early maltreatment may have direct effects on vulnerability to stress-related drinking among women, particularly in association with stressors that are out of one's control.

A BASIC Program for Use in Teaching Population Dynamics.

ERIC Educational Resources Information Center

Kidd, N. A. C.

1984-01-01

Describes an interactive simulation model which can be used to demonstrate population growth with discrete or overlapping populations and the effects of random, constant, or density-dependent mortality. The program listing (for Commodore PET 4032 microcomputer) is included. (Author/DH)

Generation of mechanical vibrations in metal samples by the use of the pinch effect

NASA Astrophysics Data System (ADS)

Troitskiy, O. A.; Skvortsov, O. B.; Stashenko, V. I.

2017-07-01

The article presents the recent research in electrodynamic processes for metal samples exposed to current pulses. The pinch effect and the skin effect cause the vibration of the metal rods. The results of these studies show how current and magnetic field interact with material samples of gold, silver and copper. The analysis allowed establishing the dependences of peak acceleration on current density and conductor diameter. The dependencies can be used in metal workings and for nondestructive testing.

Consequences of stage-structured predators: cannibalism, behavioral effects, and trophic cascades.

PubMed

Rudolf, Volker H W

2007-12-01

Cannibalistic and asymmetrical behavioral interactions between stages are common within stage-structured predator populations. Such direct interactions between predator stages can result in density- and trait-mediated indirect interactions between a predator and its prey. A set of structured predator-prey models is used to explore how such indirect interactions affect the dynamics and structure of communities. Analyses of the separate and combined effects of stage-structured cannibalism and behavior-mediated avoidance of cannibals under different ecological scenarios show that both cannibalism and behavioral avoidance of cannibalism can result in short- and long-term positive indirect connections between predator stages and the prey, including "apparent mutualism." These positive interactions alter the strength of trophic cascades such that the system's dynamics are determined by the interaction between bottom-up and top-down effects. Contrary to the expectation of simpler models, enrichment increases both predator and prey abundance in systems with cannibalism or behavioral avoidance of cannibalism. The effect of behavioral avoidance of cannibalism, however, depends on how strongly it affects the maturation rate of the predator. Behavioral interactions between predator stages reduce the short-term positive effect of cannibalism on the prey density, but can enhance its positive long-term effects. Both interaction types reduce the destabilizing effect of enrichment. These results suggest that inconsistencies between data and simple models can be resolved by accounting for stage-structured interactions within and among species.

Neutron-proton effective mass splitting in neutron-rich matter and its impacts on nuclear reactions

NASA Astrophysics Data System (ADS)

Li, Bao-An; Chen, Lie-Wen

2015-04-01

The neutron-proton effective mass splitting in neutron-rich nucleonic matter reflects the spacetime nonlocality of the isovector nuclear interaction. It affects the neutron/proton ratio during the earlier evolution of the Universe, cooling of proto-neutron stars, structure of rare isotopes and dynamics of heavy-ion collisions. While there is still no consensus on whether the neutron-proton effective mass splitting is negative, zero or positive and how it depends on the density as well as the isospin-asymmetry of the medium, significant progress has been made in recent years in addressing these issues. There are different kinds of nucleon effective masses. In this mini-review, we focus on the total effective masses often used in the non-relativistic description of nuclear dynamics. We first recall the connections among the neutron-proton effective mass splitting, the momentum dependence of the isovector potential and the density dependence of the symmetry energy. We then make a few observations about the progress in calculating the neutron-proton effective mass splitting using various nuclear many-body theories and its effects on the isospin-dependence of in-medium nucleon-nucleon cross-sections. Perhaps, our most reliable knowledge so far about the neutron-proton effective mass splitting at saturation density of nuclear matter comes from optical model analyses of huge sets of nucleon-nucleus scattering data accumulated over the last five decades. The momentum dependence of the symmetry potential from these analyses provide a useful boundary condition at saturation density for calibrating nuclear many-body calculations. Several observables in heavy-ion collisions have been identified as sensitive probes of the neutron-proton effective mass splitting in dense neutron-rich matter based on transport model simulations. We review these observables and comment on the latest experimental findings.

Repetition rate dependency of low-density plasma effects during femtosecond-laser-based surgery of biological tissue

NASA Astrophysics Data System (ADS)

Kuetemeyer, K.; Baumgart, J.; Lubatschowski, H.; Heisterkamp, A.

2009-11-01

Femtosecond laser based nanosurgery of biological tissue is usually done in two different regimes. Depending on the application, low kHz repetition rates above the optical breakdown threshold or high MHz repetition rates in the low-density plasma regime are used. In contrast to the well understood optical breakdown, mechanisms leading to dissection below this threshold are not well known due to the complexity of chemical effects with high numbers of interacting molecules. Furthermore, the laser repetition rate may influence their efficiency. In this paper, we present our study on low-density plasma effects in biological tissue depending on repetition rate by static exposure of porcine corneal stroma to femtosecond pulses. We observed a continuous increase of the laser-induced damage with decreasing repetition rate over two orders of magnitude at constant numbers of applied laser pulses or constant laser pulse energies. Therefore, low repetition rates in the kHz regime are advantageous to minimize the total delivered energy to biological tissue during femtosecond laser irradiation. However, due to frequent excessive damage in this regime directly above the threshold, MHz repetition rates are preferable to create nanometer-sized cuts in the low-density plasma regime.

The role of nurse functional types in seedling recruitment dynamics of alternative states in rangelands

NASA Astrophysics Data System (ADS)

López, Dardo R.; Cavallero, Laura

2017-02-01

In arid ecosystems, recruitment dynamics are limited by harsh environmental conditions and greatly depend on the net outcome of the balance between facilitation and competition. This outcome can change as a consequence of degradation caused by livestock overgrazing. Also, distinct plant species may show a differential response to a common neighbour under the same environmental conditions. Therefore, ecosystem degradation could affect the net balance of plant-plant interactions, which can also depend on the functional traits of potential nurse species. The aim of this study is to assess the influence of alternative degradation states on (i) the density of seedlings of perennial species emerging in four microsite types, and on (ii) the relative interaction intensity (RII) between seedlings and potential nurses belonging to three functional types (deep- and shallow-rooted shrubs, and tussock grasses). During three years, we recorded seedling density of perennial species in four alternative degradation states in grass-shrubby steppes from northwestern Patagonia. The density of emerged seedlings of perennial species decreased sharply as degradation increased, showing non-linear responses in most microsites. Seedling density underneath deep-rooted shrubs was higher than underneath shallow-rooted shrubs and tussock grasses. Also, deep-rooted shrubs were the only functional type that recorded seedling emergence in highly degraded states. Deep-rooted shrubs had facilitative effects on the seedlings emerging and surviving underneath them, independently of ecosystem degradation. In contrast, RII between shallow-rooted shrubs and recently emerged seedlings, switched from positive effects in the less degraded states, to negative effects in the most degraded state. Tussock grasses recorded the weakest intensity of facilitative interactions with recently emerged seedlings, switching to competitive interactions as degradation increased. Our results suggest that species with key functional traits should be considered in management and restoration plans for rangelands with different degradation levels, since they have a strong influence in the net outcome of plant-plant interactions and in the recruitment dynamics of arid ecosystems.

Interspecific and intraspecific competition as causes of direct and delayed density dependence in a fluctuating vole population

PubMed Central

Hansen, Thomas F.; Stenseth, Nils C.; Henttonen, Heikki; Tast, Johan

1999-01-01

A 3- to 5-year cycle of vole abundances is a characteristic phenomenon in the ecology of northern regions, and their explanation stands as a central theoretical challenge in population ecology. Although many species of voles usually coexist and are in severe competition for food and breeding space, the role of interspecific competition in vole cycles has never been evaluated statistically. After studying community effects on the population dynamics of the gray-sided vole (Clethrionomys rufocanus) in the subarctic birch forest at Kilpisjärvi, Finland, we report statistical results showing that both interspecific and intraspecific effects are important in the direct year-to-year density dependence. However, interspecific effects are not detectable in the 2-year delayed density dependence that is crucial for generating the characteristic cycles. Furthermore, we show that most of the competition takes place during the winter. The results are evaluated against two models of community dynamics. One assumes that the delayed effects are caused by an interaction with a specialist predator, and the other assumes that they are caused by overgrazing food plants. These statistical results show that vole cycles may be generated by a species-specific trophic interaction. The results also suggest that the gray-sided vole may be the focal species in the birch-forest community, as field voles may be in the taiga and as lemmings may be on the tundra. PMID:9927680

A generalized population dynamics model for reproductive interference with absolute density dependence.

PubMed

Kyogoku, Daisuke; Sota, Teiji

2017-05-17

Interspecific mating interactions, or reproductive interference, can affect population dynamics, species distribution and abundance. Previous population dynamics models have assumed that the impact of frequency-dependent reproductive interference depends on the relative abundances of species. However, this assumption could be an oversimplification inappropriate for making quantitative predictions. Therefore, a more general model to forecast population dynamics in the presence of reproductive interference is required. Here we developed a population dynamics model to describe the absolute density dependence of reproductive interference, which appears likely when encounter rate between individuals is important. Our model (i) can produce diverse shapes of isoclines depending on parameter values and (ii) predicts weaker reproductive interference when absolute density is low. These novel characteristics can create conditions where coexistence is stable and independent from the initial conditions. We assessed the utility of our model in an empirical study using an experimental pair of seed beetle species, Callosobruchus maculatus and Callosobruchus chinensis. Reproductive interference became stronger with increasing total beetle density even when the frequencies of the two species were kept constant. Our model described the effects of absolute density and showed a better fit to the empirical data than the existing model overall.

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

PubMed

Cubaynes, Sarah; MacNulty, Daniel R; Stahler, Daniel R; Quimby, Kira A; Smith, Douglas W; Coulson, Tim

2014-11-01

Understanding the population dynamics of top-predators is essential to assess their impact on ecosystems and to guide their management. Key to this understanding is identifying the mechanisms regulating vital rates. Determining the influence of density on survival is necessary to understand the extent to which human-caused mortality is compensatory or additive. In wolves (Canis lupus), empirical evidence for density-dependent survival is lacking. Dispersal is considered the principal way in which wolves adjust their numbers to prey supply or compensate for human exploitation. However, studies to date have primarily focused on exploited wolf populations, in which density-dependent mechanisms are likely weak due to artificially low wolf densities. Using 13 years of data on 280 collared wolves in Yellowstone National Park, we assessed the effect of wolf density, prey abundance and population structure, as well as winter severity, on age-specific survival in two areas (prey-rich vs. prey-poor) of the national park. We further analysed cause-specific mortality and explored the factors driving intraspecific aggression in the prey-rich northern area of the park. Overall, survival rates decreased during the study. In northern Yellowstone, density dependence regulated adult survival through an increase in intraspecific aggression, independent of prey availability. In the interior of the park, adult survival was less variable and density-independent, despite reduced prey availability. There was no effect of prey population structure in northern Yellowstone, or of winter severity in either area. Survival was similar among yearlings and adults, but lower for adults older than 6 years. Our results indicate that density-dependent intraspecific aggression is a major driver of adult wolf survival in northern Yellowstone, suggesting intrinsic density-dependent mechanisms have the potential to regulate wolf populations at high ungulate densities. When low prey availability or high 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. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

Relative importance of competition and plant-soil feedback, their synergy, context dependency and implications for coexistence.

PubMed

Lekberg, Ylva; Bever, James D; Bunn, Rebecca A; Callaway, Ragan M; Hart, Miranda M; Kivlin, Stephanie N; Klironomos, John; Larkin, Beau G; Maron, John L; Reinhart, Kurt O; Remke, Michael; van der Putten, Wim H

2018-06-12

Plants interact simultaneously with each other and with soil biota, yet the relative importance of competition vs. plant-soil feedback (PSF) on plant performance is poorly understood. Using a meta-analysis of 38 published studies and 150 plant species, we show that effects of interspecific competition (either growing plants with a competitor or singly, or comparing inter- vs. intraspecific competition) and PSF (comparing home vs. away soil, live vs. sterile soil, or control vs. fungicide-treated soil) depended on treatments but were predominantly negative, broadly comparable in magnitude, and additive or synergistic. Stronger competitors experienced more negative PSF than weaker competitors when controlling for density (inter- to intraspecific competition), suggesting that PSF could prevent competitive dominance and promote coexistence. When competition was measured against plants growing singly, the strength of competition overwhelmed PSF, indicating that the relative importance of PSF may depend not only on neighbour identity but also density. We evaluate how competition and PSFs might interact across resource gradients; PSF will likely strengthen competitive interactions in high resource environments and enhance facilitative interactions in low-resource environments. Finally, we provide a framework for filling key knowledge gaps and advancing our understanding of how these biotic interactions influence community structure. © 2018 John Wiley & Sons Ltd/CNRS.

Interdependence of different symmetry energy elements

NASA Astrophysics Data System (ADS)

Mondal, C.; Agrawal, B. K.; De, J. N.; Samaddar, S. K.; Centelles, M.; Viñas, X.

2017-08-01

Relations between the nuclear symmetry energy coefficient and its density derivatives are derived. The relations hold for a class of interactions with quadratic momentum dependence and a power-law density dependence. The structural connection between the different symmetry energy elements as obtained seems to be followed by almost all reasonable nuclear energy density functionals, both relativistic and nonrelativistic, suggesting a universality in the correlation structure. This, coupled with known values of some well-accepted constants related to nuclear matter, helps in constraining values of different density derivatives of the nuclear symmetry energy, shedding light on the isovector part of the nuclear interaction.

First-principles electron dynamics control simulation of diamond under femtosecond laser pulse train irradiation.

PubMed

Wang, Cong; Jiang, Lan; Wang, Feng; Li, Xin; Yuan, Yanping; Xiao, Hai; Tsai, Hai-Lung; Lu, Yongfeng

2012-07-11

A real-time and real-space time-dependent density functional is applied to simulate the nonlinear electron-photon interactions during shaped femtosecond laser pulse train ablation of diamond. Effects of the key pulse train parameters such as the pulse separation, spatial/temporal pulse energy distribution and pulse number per train on the electron excitation and energy absorption are discussed. The calculations show that photon-electron interactions and transient localized electron dynamics can be controlled including photon absorption, electron excitation, electron density, and free electron distribution by the ultrafast laser pulse train.

Ligand interaction with the purified serotonin transporter in solution and at the air/water interface

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

Faivre, V.; Manivet, P.; Callaway, J.C.

2000-06-01

The purified serotonin transporter (SERT) was spread at the air/water interface and the effects both of its surface density and of the temperature on its interfacial behavior were studied. The recorded isotherms evidenced the existence of a stable monolayer undergoing a lengthy rearrangement. SERT/ligand interactions appeared to be dependent on the nature of the studied molecules. Whereas an unrelated drug (chlorcyclizine) did not bind to the spread SERT, it interacted with its specific ligands. Compared to heterocyclic drugs, for which binding appeared to be concentration-dependent, a 'two-site' mechanism was evidenced for pinoline and imipramine.

Spin polarization effects and their time evolutions

NASA Astrophysics Data System (ADS)

Vernes, A.; Weinberger, P.

2015-04-01

The time evolution of the density corresponding to the polarization operator, originally constructed to commute with the Dirac Hamiltonian in the absence of an external electromagnetic field, is investigated in terms of the time-dependent Dirac equation taking the presence of an external electromagnetic field into account. It is found that this time evolution leads to 'tensorial' and 'vectorial' particle current densities and to the interaction of the spin density with the external electromagnetic field. As the time evolution of the spin density does not refer to a constant of motion (continuity condition) it only serves as auxiliary density. By taking the non-relativistic limit, it is shown that the polarization, spin and magnetization densities are independent of electric field effects and, in addition, no preferred directions can be defined.

Dissipative time-dependent quantum transport theory.

PubMed

Zhang, Yu; Yam, Chi Yung; Chen, GuanHua

2013-04-28

A dissipative time-dependent quantum transport theory is developed to treat the transient current through molecular or nanoscopic devices in presence of electron-phonon interaction. The dissipation via phonon is taken into account by introducing a self-energy for the electron-phonon coupling in addition to the self-energy caused by the electrodes. Based on this, a numerical method is proposed. For practical implementation, the lowest order expansion is employed for the weak electron-phonon coupling case and the wide-band limit approximation is adopted for device and electrodes coupling. The corresponding hierarchical equation of motion is derived, which leads to an efficient and accurate time-dependent treatment of inelastic effect on transport for the weak electron-phonon interaction. The resulting method is applied to a one-level model system and a gold wire described by tight-binding model to demonstrate its validity and the importance of electron-phonon interaction for the quantum transport. As it is based on the effective single-electron model, the method can be readily extended to time-dependent density functional theory.

Electronic structure calculations of PbS quantum rods and tubes

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

Pimachev, Artem; Dahnovsky, Yuri, E-mail: yurid@uwyo.edu

2014-01-28

We study absorption spectra, optical and HOMO-LUMO gaps, and the density of states for PbS quantum rods (QRs) and tubes (QTs). We find some similarities and also differences in QR and QT properties. For both QRs and QTs, the optical and HOMO-LUMO gaps reach the plateaus for small lengths. We find that tubes are as stable as rods. The optical spectra exhibit a peak that can be due to the electron-hole interaction or be a prototype of an S{sub e}–S{sub h} transition in the effective mass approximation. We also calculate the density of states by the density functional theory (DFT)more » and time-dependent density functional theory (TDDFT) methods. The TDDFT density of states function is shifted towards the red side by 0.5 eV indicating the strong e-h interaction.« less

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

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

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

2009-10-28

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

Consumer-resource theory predicts dynamic transitions between outcomes of interspecific interactions.

PubMed

Holland, J Nathaniel; DeAngelis, Donald L

2009-12-01

Interactions between two populations are often defined by their interaction outcomes; that is, the positive, neutral, or negative effects of species on one another. Yet, signs of outcomes are not absolute, but vary with the biotic and abiotic contexts of interactions. Here, we develop a general theory for transitions between outcomes based on consumer-resource (C-R) interactions in which one or both species exploit the other as a resource. Simple models of C-R interactions revealed multiple equilibria, including one for species coexistence and others for extinction of one or both species, indicating that species' densities alone could determine the fate of interactions. All possible outcomes [(+ +), (+ -), (--), (+ 0), (- 0), (0 0)] of species coexistence emerged merely through changes in parameter values of C-R interactions, indicating that variation in C-R interactions resulting from biotic and abiotic conditions could determine shifts in outcomes. These results suggest that C-R interactions can provide a broad mechanism for understanding context- and density-dependent transitions between interaction outcomes.

Consumer-resource theory predicts dynamic transitions between outcomes of interspecific interactions

USGS Publications Warehouse

Holland, J. Nathaniel; DeAngelis, Donald L.

2009-01-01

Interactions between two populations are often defined by their interaction outcomes; that is, the positive, neutral, or negative effects of species on one another. Yet, signs of outcomes are not absolute, but vary with the biotic and abiotic contexts of interactions. Here, we develop a general theory for transitions between outcomes based on consumer-resource (C-R) interactions in which one or both species exploit the other as a resource. Simple models of C-R interactions revealed multiple equilibria, including one for species coexistence and others for extinction of one or both species, indicating that species densities alone could determine the fate of interactions. All possible outcomes (+ +), (+ -), (- -), (+ 0), (- 0), (0 0) of species coexistence emerged merely through changes in parameter values of C-R interactions, indicating that variation in C-R interactions resulting from biotic and abiotic conditions could determine shifts in outcomes. These results suggest that C-R interactions can provide a broad mechanism for understanding context- and density-dependent transitions between interaction outcomes.

Ecology of dark matter haloes - II. Effects of interactions on the alignment of halo pairs

NASA Astrophysics Data System (ADS)

L'Huillier, Benjamin; Park, Changbom; Kim, Juhan

2017-04-01

We use the Horizon Run 4 cosmological N-body simulation to study the effects of distant and close interactions on the alignments of the shapes, spins and orbits of targets haloes with their neighbours, and their dependence on the local density environment and neighbour separation. Interacting targets have a significantly lower spin and higher sphericity and oblateness than all targets. Interacting pairs initially have antiparallel spins, but the spins develop parallel alignment as time goes on. Neighbours tend to evolve in the plane of rotation of the target, and in the direction of the major axis of prolate haloes. Moreover, interactions are preferentially radial, while pairs with non-radial orbits are preferentially prograde. The alignment signals are stronger at high mass and for close separations, and independent of the large-scale density. Positive alignment signals are found at redshifts up to 4, and increase with decreasing redshifts. Moreover, the orbits tend to become prograde at low redshift, while no alignment is found at high redshift (z = 4).

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

PubMed

Benkwitt, Cassandra E

2017-04-01

During major life-history transitions, animals often experience high mortality rates due to predation, making predator avoidance particularly advantageous during these times. There is mixed evidence from a limited number of studies, however, regarding how predator presence influences settlement of coral-reef fishes and it is unknown how other potentially mediating factors, including predator origin (native vs. nonnative) or interactions among conspecific recruits, mediate the non-consumptive effects of predators on reef fish settlement. During a field experiment in the Caribbean, approximately 52% fewer mahogany snapper (Lutjanus mahogoni) recruited to reefs with a native predator (graysby grouper, Cephalopholis cruentata) than to predator-free control reefs and reefs with an invasive predator (red lionfish, Pterois volitans) regardless of predator diet. These results suggest that snapper recruits do not recognize nonnative lionfish as a threat. However, these effects depended on the density of conspecific recruits, with evidence that competition may limit the response of snapper to even native predators at the highest recruit densities. In contrast, there was no effect of predator presence or conspecific density on the recruitment of bicolor damselfish (Stegastes partitus). These context-dependent responses of coral-reef fishes to predators during settlement may influence individual survival and shape subsequent population and community dynamics. © 2017 by the Ecological Society of America.

Coherent Excitation of Optical Phonons in GaAs by Broadband Terahertz Pulses

PubMed Central

Fu, Zhengping; Yamaguchi, Masashi

2016-01-01

Coherent excitation and control of lattice motion by electromagnetic radiation in optical frequency range has been reported through variety of indirect interaction mechanisms with phonon modes. However, coherent phonon excitation by direct interaction of electromagnetic radiation and nuclei has not been demonstrated experimentally in terahertz (THz) frequency range mainly due to the lack of THz emitters with broad bandwidth suitable for the purpose. We report the experimental observation of coherent phonon excitation and detection in GaAs using ultrafast THz-pump/optical-probe scheme. From the results of THz pump field dependence, pump/probe polarization dependence, and crystal orientation dependence, we attributed THz wave absorption and linear electro-optic effect to the excitation and detection mechanisms of coherent polar TO phonons. Furthermore, the carrier density dependence of the interaction of coherent phonons and free carriers is reported. PMID:27905563

NONLINEAR AND FIBER OPTICS: Thermal self-interaction of laser beams in water within the anomalous density range

NASA Astrophysics Data System (ADS)

Gribova, E. Z.; Sorokin, Yu M.

1990-04-01

A theoretical model is proposed in order to account for the temperature dependence of the refractive index of water in the range of parameters not far from the crystallization point. It is shown that the thermal self-interaction results in defocusing in supercooled water and in the temperature range of the anomalous density. Penetrating self-convection is predicted and confirmed experimentally for this case: this is manifested by a local change of the sign of the buoyancy forces in the region occupied by a laser beam. The possibility of suppression of such self-convection and enhancement of symmetric nonlinear refraction effects near an extremum of the density of water is also predicted and demonstrated experimentally.

Excitation energies from range-separated time-dependent density and density matrix functional theory.

PubMed

Pernal, Katarzyna

2012-05-14

Time-dependent density functional theory (TD-DFT) in the adiabatic formulation exhibits known failures when applied to predicting excitation energies. One of them is the lack of the doubly excited configurations. On the other hand, the time-dependent theory based on a one-electron reduced density matrix functional (time-dependent density matrix functional theory, TD-DMFT) has proven accurate in determining single and double excitations of H(2) molecule if the exact functional is employed in the adiabatic approximation. We propose a new approach for computing excited state energies that relies on functionals of electron density and one-electron reduced density matrix, where the latter is applied in the long-range region of electron-electron interactions. A similar approach has been recently successfully employed in predicting ground state potential energy curves of diatomic molecules even in the dissociation limit, where static correlation effects are dominating. In the paper, a time-dependent functional theory based on the range-separation of electronic interaction operator is rigorously formulated. To turn the approach into a practical scheme the adiabatic approximation is proposed for the short- and long-range components of the coupling matrix present in the linear response equations. In the end, the problem of finding excitation energies is turned into an eigenproblem for a symmetric matrix. Assignment of obtained excitations is discussed and it is shown how to identify double excitations from the analysis of approximate transition density matrix elements. The proposed method used with the short-range local density approximation (srLDA) and the long-range Buijse-Baerends density matrix functional (lrBB) is applied to H(2) molecule (at equilibrium geometry and in the dissociation limit) and to Be atom. The method accounts for double excitations in the investigated systems but, unfortunately, the accuracy of some of them is poor. The quality of the other excitations is in general much better than that offered by TD-DFT-LDA or TD-DMFT-BB approximations if the range-separation parameter is properly chosen. The latter remains an open problem.

Effects of Differing Energy Dependences in Three Level-Density Models on Calculated Cross Sections

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

Fu, C.Y.

2000-07-15

Three level-density formalisms commonly used for cross-section calculations are examined. Residual nuclides in neutron interaction with {sup 58}Ni are chosen to quantify the well-known differences in the energy dependences of the three formalisms. Level-density parameters for the Gilbert and Cameron model are determined from experimental information. Parameters for the back-shifted Fermi-gas and generalized superfluid models are obtained by fitting their level densities at two selected energies for each nuclide to those of the Gilbert and Cameron model, forcing the level densities of the three models to be as close as physically allowed. The remaining differences are in their energy dependencesmore » that, it is shown, can change the calculated cross sections and particle emission spectra significantly, in some cases or energy ranges by a factor of 2.« less

Lateral cascade of indirect effects in food webs with different types of adaptive behavior.

PubMed

Kamran-Disfani, Ahmad R; Golubski, Antonio J

2013-12-21

It is widely recognized that indirect effects due to adaptive behaviors can have important effects on food webs. One consequence may be to change how readily perturbations propagate through the web, because species' behaviors as well as densities may respond to perturbations. It is not well understood which types of behavior are more likely to facilitate versus inhibit propagation of disturbances through a food web, or how this might be affected by the shape of a food web or the patterns of interaction strengths within it. We model two simple, laterally expanded food webs (one with three trophic levels and one with four), and compare how various adaptive behaviors affect the potential for a newly introduced predator to change the equilibrium densities of distant species. Patterns of changes in response to the introduction were qualitatively similar across most models, as were the ways in which patterns of direct interaction strengths affected those responses. Depending on both the web structure and the specific adaptive behavior, the potential for density changes to propagate through the web could be either increased or diminished relative to the no-behavior model. Two behaviors allowed density changes to propagate through a four-level web that precluded such propagation in the no-behavior model, and each of these two behaviors led to qualitatively different patterns of density changes. In the one model (diet choice) in which density changes were able to propagate in both web structures, patterns of density changes differed qualitatively between webs. Some of our results flowed from the fact that behaviors did not interact directly in the systems we considered, so that indirect effects on distant species had to be at least partly density-mediated. Our models highlight this as an inherent limitation of considering in isolation behaviors that are strictly foraging-related or strictly defense-related, making a case for the value of simultaneously considering multiple interacting types of behavior in the same model. Copyright © 2013 Elsevier Ltd. All rights reserved.

Environmental conditions and biotic interactions influence ecosystem structure and function in a drying stream

USGS Publications Warehouse

Ludlam, J.P.; Magoulick, D.D.

2010-01-01

Benthic consumers influence stream ecosystem structure and function, but these interactions depend on environmental context. We experimentally quantified the effects of central stoneroller minnows (Campostoma anomalum (Rafinesque) and Meek's crayfish (Orconectes meeki meeki (Faxon)) on benthic communities using electric exclusion quadrats in Little Mulberry Creek before (June) and during (August) seasonal stream drying. Unglazed ceramic tiles were deployed in June and August to measure periphyton and invertebrate abundance, and leafpack decomposition and primary production were also measured in August. Relationships between stoneroller and crayfish density and the size of consumer effects were evaluated with multiple linear regression models. Average chlorophyll a abundance was greater on exposed than exclusion tiles in August, but not in June. Sediment dry mass, periphyton ash-free dry mass (AFDM), and chironomid densities on tiles did not differ among treatments in either period. Leaf packs decayed faster in exposed than exclusion treatments (kexposed = 0.038 ?? 0.013, kexclusion = 0.007 ?? 0.002), but consumer effects were stronger in some pools than others. Leafpack invertebrate biomass and abundance and tile primary productivity did not differ among treatments. Consumer effects on chlorophyll a were related to crayfish and stoneroller density, and effects on chironomid density were related to stoneroller density. These results contrast with a previous exclusion experiment in Little Mulberry Creek that demonstrated strong consumer effects. The influence of stream drying on consumer effects appears to have been reduced by strong spates, underscoring the importance of conducting multi-year studies to determine the magnitude of variability in ecological interactions. ?? US Government: USGS 2010.

Three-dimensional modeling of the neutral gas depletion effect in a helicon discharge plasma

NASA Astrophysics Data System (ADS)

Kollasch, Jeffrey; Schmitz, Oliver; Norval, Ryan; Reiter, Detlev; Sovinec, Carl

2016-10-01

Helicon discharges provide an attractive radio-frequency driven regime for plasma, but neutral-particle dynamics present a challenge to extending performance. A neutral gas depletion effect occurs when neutrals in the plasma core are not replenished at a sufficient rate to sustain a higher plasma density. The Monte Carlo neutral particle tracking code EIRENE was setup for the MARIA helicon experiment at UW Madison to study its neutral particle dynamics. Prescribed plasma temperature and density profiles similar to those in the MARIA device are used in EIRENE to investigate the main causes of the neutral gas depletion effect. The most dominant plasma-neutral interactions are included so far, namely electron impact ionization of neutrals, charge exchange interactions of neutrals with plasma ions, and recycling at the wall. Parameter scans show how the neutral depletion effect depends on parameters such as Knudsen number, plasma density and temperature, and gas-surface interaction accommodation coefficients. Results are compared to similar analytic studies in the low Knudsen number limit. Plans to incorporate a similar Monte Carlo neutral model into a larger helicon modeling framework are discussed. This work is funded by the NSF CAREER Award PHY-1455210.

Interaction-induced effects on Bose-Hubbard parameters

NASA Astrophysics Data System (ADS)

Kremer, Mark; Sachdeva, Rashi; Benseny, Albert; Busch, Thomas

2017-12-01

We study the effects of repulsive on-site interactions on the broadening of the localized Wannier functions used for calculating the parameters to describe ultracold atoms in optical lattices. For this, we replace the common single-particle Wannier functions, which do not contain any information about the interactions, by two-particle Wannier functions obtained from an exact solution which takes the interactions into account. We then use these interaction-dependent basis functions to calculate the Bose-Hubbard model parameters, showing that they are substantially different both at low and high lattice depths from the ones calculated using single-particle Wannier functions. Our results suggest that density effects are not negligible for many parameter ranges and need to be taken into account in metrology experiments.

Large effective mass and interaction-enhanced Zeeman splitting of K -valley electrons in MoSe2

NASA Astrophysics Data System (ADS)

Larentis, Stefano; Movva, Hema C. P.; Fallahazad, Babak; Kim, Kyounghwan; Behroozi, Armand; Taniguchi, Takashi; Watanabe, Kenji; Banerjee, Sanjay K.; Tutuc, Emanuel

2018-05-01

We study the magnetotransport of high-mobility electrons in monolayer and bilayer MoSe2, which show Shubnikov-de Haas (SdH) oscillations and quantum Hall states in high magnetic fields. An electron effective mass of 0.8 me is extracted from the SdH oscillations' temperature dependence; me is the bare electron mass. At a fixed electron density the longitudinal resistance shows minima at filling factors (FFs) that are either predominantly odd, or predominantly even, with a parity that changes as the density is tuned. The SdH oscillations are insensitive to an in-plane magnetic field, consistent with an out-of-plane spin orientation of electrons at the K point. We attribute the FF parity transitions to an interaction enhancement of the Zeeman energy as the density is reduced, resulting in an increased Zeeman-to-cyclotron energy ratio.

Pairing in exotic neutron-rich nuclei near the drip line and in the crust of neutron stars

NASA Astrophysics Data System (ADS)

Pastore, A.; Margueron, J.; Schuck, P.; Viñas, X.

2013-09-01

Exotic and drip-line nuclei as well as nuclei immersed in a low-density gas of neutrons in the inner crust of neutron stars are systematically investigated with respect to their neutron pairing properties. This is done using Skyrme density-functional and different pairing forces such as a density-dependent contact interaction and a separable form of a finite-range Gogny interaction. Hartree-Fock-Bogoliubov (HFB) and Bardeen-Cooper-Schrieffer (BCS) theories are compared. It is found that neutron pairing is reduced towards the drip line while overcast by strong shell effects. Furthermore, resonances in the continuum can have an important effect counterbalancing the tendency of reduction and leading to a persistence of pairing at the drip line. It is also shown that in these systems the difference between HFB and BCS approaches can be quantitatively large.

Space charge in nanostructure resonances

NASA Astrophysics Data System (ADS)

Price, Peter J.

1996-10-01

In quantum ballistic propagation of electrons through a variety of nanostructures, resonance in the energy-dependent transmission and reflection probabilities generically is associated with (1) a quasi-level with a decay lifetime, and (2) a bulge in electron density within the structure. It can be shown that, to a good approximation, a simple formula in all cases connects the density of states for the latter to the energy dependence of the phase angles of the eigen values of the S-matrix governing the propagation. For both the Lorentzian resonances (normal or inverted) and for the Fano-type resonances, as a consequence of this eigen value formula, the space charge due to filled states over the energy range of a resonance is just equal (for each spin state) to one electron charge. The Coulomb interaction within this space charge is known to 'distort' the electrical characteristics of resonant nanostructures. In these systems, however, the exchange effect should effectively cancel the interaction between states with parallel spins, leaving only the anti-parallel spin contribution.

Environmental variability and population dynamics: Do European and North American ducks play by the same rules?

USGS Publications Warehouse

Pöysä, Hannu; Rintala, Jukka; Johnson, Douglas H.; Kauppinen, Jukka; Lammi, Esa; Nudds, Thomas D.; Väänänen, Veli-Matti

2016-01-01

Density dependence, population regulation, and variability in population size are fundamental population processes, the manifestation and interrelationships of which are affected by environmental variability. However, there are surprisingly few empirical studies that distinguish the effect of environmental variability from the effects of population processes. We took advantage of a unique system, in which populations of the same duck species or close ecological counterparts live in highly variable (north American prairies) and in stable (north European lakes) environments, to distinguish the relative contributions of environmental variability (measured as between-year fluctuations in wetland numbers) and intraspecific interactions (density dependence) in driving population dynamics. We tested whether populations living in stable environments (in northern Europe) were more strongly governed by density dependence than populations living in variable environments (in North America). We also addressed whether relative population dynamical responses to environmental variability versus density corresponded to differences in life history strategies between dabbling (relatively “fast species” and governed by environmental variability) and diving (relatively “slow species” and governed by density) ducks. As expected, the variance component of population fluctuations caused by changes in breeding environments was greater in North America than in Europe. Contrary to expectations, however, populations in more stable environments were not less variable nor clearly more strongly density dependent than populations in highly variable environments. Also, contrary to expectations, populations of diving ducks were neither more stable nor stronger density dependent than populations of dabbling ducks, and the effect of environmental variability on population dynamics was greater in diving than in dabbling ducks. In general, irrespective of continent and species life history, environmental variability contributed more to variation in species abundances than did density. Our findings underscore the need for more studies on populations of the same species in different environments to verify the generality of current explanations about population dynamics and its association with species life history.

Environmental variability and population dynamics: do European and North American ducks play by the same rules?

PubMed

Pöysä, Hannu; Rintala, Jukka; Johnson, Douglas H; Kauppinen, Jukka; Lammi, Esa; Nudds, Thomas D; Väänänen, Veli-Matti

2016-10-01

Density dependence, population regulation, and variability in population size are fundamental population processes, the manifestation and interrelationships of which are affected by environmental variability. However, there are surprisingly few empirical studies that distinguish the effect of environmental variability from the effects of population processes. We took advantage of a unique system, in which populations of the same duck species or close ecological counterparts live in highly variable (north American prairies) and in stable (north European lakes) environments, to distinguish the relative contributions of environmental variability (measured as between-year fluctuations in wetland numbers) and intraspecific interactions (density dependence) in driving population dynamics. We tested whether populations living in stable environments (in northern Europe) were more strongly governed by density dependence than populations living in variable environments (in North America). We also addressed whether relative population dynamical responses to environmental variability versus density corresponded to differences in life history strategies between dabbling (relatively "fast species" and governed by environmental variability) and diving (relatively "slow species" and governed by density) ducks. As expected, the variance component of population fluctuations caused by changes in breeding environments was greater in North America than in Europe. Contrary to expectations, however, populations in more stable environments were not less variable nor clearly more strongly density dependent than populations in highly variable environments. Also, contrary to expectations, populations of diving ducks were neither more stable nor stronger density dependent than populations of dabbling ducks, and the effect of environmental variability on population dynamics was greater in diving than in dabbling ducks. In general, irrespective of continent and species life history, environmental variability contributed more to variation in species abundances than did density. Our findings underscore the need for more studies on populations of the same species in different environments to verify the generality of current explanations about population dynamics and its association with species life history.

Impacts of warming revealed by linking resource growth rates with consumer functional responses.

PubMed

West, Derek C; Post, David M

2016-05-01

Warming global temperatures are driving changes in species distributions, growth and timing, but much uncertainty remains regarding how climate change will alter species interactions. Consumer-Resource interactions in particular can be strongly impacted by changes to the relative performance of interacting species. While consumers generally gain an advantage over their resources with increasing temperatures, nonlinearities can change this relation near temperature extremes. We use an experimental approach to determine how temperature changes between 5 and 30 °C will alter the growth of the algae Scenedesmus obliquus and the functional responses of the small-bodied Daphnia ambigua and the larger Daphnia pulicaria. The impact of warming generally followed expectations, making both Daphnia species more effective grazers, with the increase in feeding rates outpacing the increases in algal growth rate. At the extremes of our temperature range, however, warming resulted in a decrease in Daphnia grazing effectiveness. Between 25 and 30 °C, both species of Daphnia experienced a precipitous drop in feeding rates, while algal growth rates remained high, increasing the likelihood of algal blooms in warming summer temperatures. Daphnia pulicaria performed significantly better at cold temperatures than D. ambigua, but by 20 °C, there was no significant difference between the two species, and at 25 °C, D. ambigua outperformed D. pulicaria. Warming summer temperatures will favour the smaller D. ambigua, but only over a narrow temperature range, and warming beyond 25 °C could open D. ambigua to invasion from tropical species. By fitting our results to temperature-dependent functions, we develop a temperature- and density-dependent model, which produces a metric of grazing effectiveness, quantifying the grazer density necessary to halt algal growth. This approach should prove useful for tracking the transient dynamics of other density-dependent consumer-resource interactions, such as agricultural pests and biological-control agents. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

How will species respond to climate change? Examining the effects of temperature and population density on an herbivorous insect.

PubMed

Laws, Angela Nardoni; Belovsky, Gary E

2010-04-01

An important challenge facing ecologists is to understand how climate change may affect species performance and species interactions. However, predicting how changes in abiotic variables associated with climate change may affect species performance also depends on the biotic context, which can mediate species responses to climatic change. We conducted a 3-yr field experiment to determine how the herbivorous grasshopper Camnula pellucida (Scudder) responds to manipulations of temperature and population density. Grasshopper survival and fecundity decreased with density, indicating the importance of intraspecific competition. Female fecundity tended to increase with temperature, whereas grasshopper survival exhibited a unimodal response to temperature, with highest survival at intermediate temperatures. Grasshopper performance responses to temperature also depended on density. Peak survival in the low-density treatment occurred in warmer conditions than for the high-density treatment, indicating that the intensity of intraspecific competition varies with temperature. Our data show that changes to the temperature regimen can alter grasshopper performance and determine the intensity of intraspecific competition. However, the effects of temperature on grasshopper performance varied with density. Our data indicate the importance of the biotic context in mediating species responses to climatic factors associated with global change.

A single-electron picture based on the multiconfiguration time-dependent Hartree-Fock method: application to the anisotropic ionization and subsequent high-harmonic generation of the CO molecule

NASA Astrophysics Data System (ADS)

Ohmura, S.; Kato, T.; Oyamada, T.; Koseki, S.; Ohmura, H.; Kono, H.

2018-02-01

The mechanisms of anisotropic near-IR tunnel ionization and high-order harmonic generation (HHG) in a CO molecule are theoretically investigated by using the multiconfiguration time-dependent Hartree-Fock (MCTDHF) method developed for the simulation of multielectron dynamics of molecules. The multielectron dynamics obtained by numerically solving the equations of motion (EOMs) in the MCTDHF method is converted to a single orbital picture in the natural orbital representation where the first-order reduced density matrix is diagonalized. The ionization through each natural orbital is examined and the process of HHG is classified into different optical paths designated by a combinations of initial, intermediate and final natural orbitals. The EOMs for natural spin-orbitals are also derived within the framework of the MCTDHF, which maintains the first-order reduced density matrix to be a diagonal one throughout the time propagation of a many-electron wave function. The orbital dependent, time-dependent effective potentials that govern the dynamics of respective time-dependent natural orbitals are deduced from the derived EOMs, of which the temporal variation can be used to interpret the motion of the electron density associated with each natural spin-orbital. The roles of the orbital shape, multiorbital ionization, linear Stark effect and multielectron interaction in the ionization and HHG of a CO molecule are revealed by the effective potentials obtained. When the laser electric field points to the nucleus O from C, tunnel ionization from the C atom side is enhanced; a hump structure originating from multielectron interaction is then formed on the top of the field-induced distorted barrier of the HOMO effective potential. This hump formation, responsible for the directional anisotropy of tunnel ionization, restrains the influence of the linear Stark effect on the energy shifts of bound states.

The Power Spectrum of Ionic Nanopore Currents: The Role of Ion Correlations.

PubMed

Zorkot, Mira; Golestanian, Ramin; Bonthuis, Douwe Jan

2016-04-13

We calculate the power spectrum of electric-field-driven ion transport through nanometer-scale membrane pores using both linearized mean-field theory and Langevin dynamics simulations. Remarkably, the linearized mean-field theory predicts a plateau in the power spectral density at low frequency ω, which is confirmed by the simulations at low ion concentration. At high ion concentration, however, the power spectral density follows a power law that is reminiscent of the 1/ω(α) dependence found experimentally at low frequency. On the basis of simulations with and without ion-ion interactions, we attribute the low-frequency power-law dependence to ion-ion correlations. We show that neither a static surface charge density, nor an increased pore length, nor an increased ion valency have a significant effect on the shape of the power spectral density at low frequency.

Coarse-grained forms for equations describing the microscopic motion of particles in a fluid.

PubMed

Das, Shankar P; Yoshimori, Akira

2013-10-01

Exact equations of motion for the microscopically defined collective density ρ(x,t) and the momentum density ĝ(x,t) of a fluid have been obtained in the past starting from the corresponding Langevin equations representing the dynamics of the fluid particles. In the present work we average these exact equations of microscopic dynamics over the local equilibrium distribution to obtain stochastic partial differential equations for the coarse-grained densities with smooth spatial and temporal dependence. In particular, we consider Dean's exact balance equation for the microscopic density of a system of interacting Brownian particles to obtain the basic equation of the dynamic density functional theory with noise. Our analysis demonstrates that on thermal averaging the dependence of the exact equations on the bare interaction potential is converted to dependence on the corresponding thermodynamic direct correlation functions in the coarse-grained equations.

Deterministic Role of Collision Cascade Density in Radiation Defect Dynamics in Si

NASA Astrophysics Data System (ADS)

Wallace, J. B.; Aji, L. B. Bayu; Shao, L.; Kucheyev, S. O.

2018-05-01

The formation of stable radiation damage in solids often proceeds via complex dynamic annealing (DA) processes, involving point defect migration and interaction. The dependence of DA on irradiation conditions remains poorly understood even for Si. Here, we use a pulsed ion beam method to study defect interaction dynamics in Si bombarded in the temperature range from ˜-30 ° C to 210 °C with ions in a wide range of masses, from Ne to Xe, creating collision cascades with different densities. We demonstrate that the complexity of the influence of irradiation conditions on defect dynamics can be reduced to a deterministic effect of a single parameter, the average cascade density, calculated by taking into account the fractal nature of collision cascades. For each ion species, the DA rate exhibits two well-defined Arrhenius regions where different DA mechanisms dominate. These two regions intersect at a critical temperature, which depends linearly on the cascade density. The low-temperature DA regime is characterized by an activation energy of ˜0.1 eV , independent of the cascade density. The high-temperature regime, however, exhibits a change in the dominant DA process for cascade densities above ˜0.04 at.%, evidenced by an increase in the activation energy. These results clearly demonstrate a crucial role of the collision cascade density and can be used to predict radiation defect dynamics in Si.

Deterministic Role of Collision Cascade Density in Radiation Defect Dynamics in Si.

PubMed

Wallace, J B; Aji, L B Bayu; Shao, L; Kucheyev, S O

2018-05-25

The formation of stable radiation damage in solids often proceeds via complex dynamic annealing (DA) processes, involving point defect migration and interaction. The dependence of DA on irradiation conditions remains poorly understood even for Si. Here, we use a pulsed ion beam method to study defect interaction dynamics in Si bombarded in the temperature range from ∼-30 °C to 210 °C with ions in a wide range of masses, from Ne to Xe, creating collision cascades with different densities. We demonstrate that the complexity of the influence of irradiation conditions on defect dynamics can be reduced to a deterministic effect of a single parameter, the average cascade density, calculated by taking into account the fractal nature of collision cascades. For each ion species, the DA rate exhibits two well-defined Arrhenius regions where different DA mechanisms dominate. These two regions intersect at a critical temperature, which depends linearly on the cascade density. The low-temperature DA regime is characterized by an activation energy of ∼0.1  eV, independent of the cascade density. The high-temperature regime, however, exhibits a change in the dominant DA process for cascade densities above ∼0.04 at.%, evidenced by an increase in the activation energy. These results clearly demonstrate a crucial role of the collision cascade density and can be used to predict radiation defect dynamics in Si.

Quantum dynamics modeled by interacting trajectories

NASA Astrophysics Data System (ADS)

Cruz-Rodríguez, L.; Uranga-Piña, L.; Martínez-Mesa, A.; Meier, C.

2018-03-01

We present quantum dynamical simulations based on the propagation of interacting trajectories where the effect of the quantum potential is mimicked by effective pseudo-particle interactions. The method is applied to several quantum systems, both for bound and scattering problems. For the bound systems, the quantum ground state density and zero point energy are shown to be perfectly obtained by the interacting trajectories. In the case of time-dependent quantum scattering, the Eckart barrier and uphill ramp are considered, with transmission coefficients in very good agreement with standard quantum calculations. Finally, we show that via wave function synthesis along the trajectories, correlation functions and energy spectra can be obtained based on the dynamics of interacting trajectories.

Domain size polydispersity effects on the structural and dynamical properties in lipid monolayers with phase coexistence

NASA Astrophysics Data System (ADS)

Rufeil-Fiori, Elena; Banchio, Adolfo J.

Lipid monolayers with phase coexistence are a frequently used model for lipid membranes. In these systems, domains of the liquid-condensed phase always present size polydispersity. However, very few theoretical works consider size distribution effects on the monolayer properties. Because of the difference in surface densities, domains have excess dipolar density with respect to the surrounding liquid expanded phase, originating a dipolar inter-domain interaction. This interaction depends on the domain area, and hence the presence of a domain size distribution is associated with interaction polydispersity. Inter-domain interactions are fundamental to understanding the structure and dynamics of the monolayer. For this reason, it is expected that polydispersity significantly alters monolayer properties. By means of Brownian dynamics simulations, we study the radial distribution function (RDF), the average mean square displacement and the average time-dependent self-diffusion coefficient, D(t), of lipid monolayers with normal distributed size domains. It was found that polydispersity strongly affects the value of the interaction strength obtained, which is greatly underestimated if polydispersity is not considered. However, within a certain range of parameters, the RDF obtained from a polydisperse model can be well approximated by that of a monodisperse model, suitably fitting the interaction strength, even for 40% polydispersities. For small interaction strengths or small polydispersities, the polydisperse systems obtained from fitting the experimental RDF have an average mean square displacement and D(t) in good agreement with that of the monodisperse system.

Optical phonon effect in quasi-one-dimensional semiconductor quantum wires: Band-gap renormalization

NASA Astrophysics Data System (ADS)

Dan, Nguyen Trung; Bechstedt, F.

1996-02-01

We present theoretical studies of dynamical screening in quasi-one-dimensional semiconductor quantum wires including electron-electron and electron-LO-phonon interactions. Within the random-phase approximation we obtain analytical expressions for screened interaction potentials. These expressions can be used to calculate the band-gap renormalization of quantum wires, which depends on the free-carrier density and temperature. We find that the optical phonon interaction effect plays a significant role in band-gap renormalization of quantum wires. The numerical results are compared with some recent experiment measurements as well as available theories.

Fluctuation-driven anisotropy in effective pair interactions between nanoparticles: Thiolated gold nanoparticles in ethane

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

Jabes, B. Shadrack; Yadav, Hari O. S.; Chakravarty, Charusita, E-mail: charus@chemistry.iitd.ac.in

2014-10-21

Fluctuations within the ligand shell of a nanoparticle give rise to a significant degree of anisotropy in effective pair interactions for low grafting densities [B. Bozorgui, D. Meng, S. K. Kumar, C. Chakravarty, and A. Cacciuto, Nano Lett. 13, 2732 (2013)]. Here, we examine the corresponding fluctuation-driven anisotropy for gold nanocrystals densely passivated with short ligands. In particular, we consider gold nanocrystals capped by alkylthiols, both in vacuum and in ethane solvent at high density. As in the preceding study, we show that the anisotropy in the nanoparticle pair potential can be quantified by an angle-dependent correction term to themore » isotropic potential of mean force (PMF). We find that the anisotropy of the ligand shells is distance dependent, and strongly influenced by ligand interdigitation effects as well as expulsion of ligand chains from the interparticle region at short distances. Such fluctuation-driven anisotropy can be significant for alkylthiol-coated gold nanoparticles, specially for longer chain lengths, under good solvent conditions. The consequences of such anisotropy for self-assembly, specially as a function of grafting density, solvent quality and at interfaces, should provide some interesting insights in future work. Our results clearly show that an isotropic two-body PMF cannot adequately describe the thermodynamics and assembly behavior of nanoparticles in this dense grafting regime and inclusion of anisotropic effects, as well as possibly many-body interactions, is necessary. Extensions of this approach to other passivated nanoparticle systems and implications for self-assembly are considered.« less

Predictive of the quantum capacitance effect on the excitation of plasma waves in graphene transistors with scaling limit

NASA Astrophysics Data System (ADS)

Wang, Lin; Chen, Xiaoshuang; Hu, Yibin; Wang, Shao-Wei; Lu, Wei

2015-04-01

Plasma waves in graphene field-effect transistors (FETs) and nano-patterned graphene sheets have emerged as very promising candidates for potential terahertz and infrared applications in myriad areas including remote sensing, biomedical science, military, and many other fields with their electrical tunability and strong interaction with light. In this work, we study the excitations and propagation properties of plasma waves in nanometric graphene FETs down to the scaling limit. Due to the quantum-capacitance effect, the plasma wave exhibits strong correlation with the distribution of density of states (DOS). It is indicated that the electrically tunable plasma resonance has a power-dependent V0.8TG relation on the gate voltage, which originates from the linear dependence of density of states (DOS) on the energy in pristine graphene, in striking difference to those dominated by classical capacitance with only V0.5TG dependence. The results of different transistor sizes indicate the potential application of nanometric graphene FETs in highly-efficient electro-optic modulation or detection of terahertz or infrared radiation. In addition, we highlight the perspectives of plasma resonance excitation in probing the many-body interaction and quantum matter state in strong correlation electron systems. This study reveals the key feature of plasma waves in decorated/nanometric graphene FETs, and paves the way to tailor plasma band-engineering and expand its application in both terahertz and mid-infrared regions.Plasma waves in graphene field-effect transistors (FETs) and nano-patterned graphene sheets have emerged as very promising candidates for potential terahertz and infrared applications in myriad areas including remote sensing, biomedical science, military, and many other fields with their electrical tunability and strong interaction with light. In this work, we study the excitations and propagation properties of plasma waves in nanometric graphene FETs down to the scaling limit. Due to the quantum-capacitance effect, the plasma wave exhibits strong correlation with the distribution of density of states (DOS). It is indicated that the electrically tunable plasma resonance has a power-dependent V0.8TG relation on the gate voltage, which originates from the linear dependence of density of states (DOS) on the energy in pristine graphene, in striking difference to those dominated by classical capacitance with only V0.5TG dependence. The results of different transistor sizes indicate the potential application of nanometric graphene FETs in highly-efficient electro-optic modulation or detection of terahertz or infrared radiation. In addition, we highlight the perspectives of plasma resonance excitation in probing the many-body interaction and quantum matter state in strong correlation electron systems. This study reveals the key feature of plasma waves in decorated/nanometric graphene FETs, and paves the way to tailor plasma band-engineering and expand its application in both terahertz and mid-infrared regions. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr07689c

How habitat-modifying organisms structure the food web of two coastal ecosystems

PubMed Central

van der Zee, Els M.; Angelini, Christine; Govers, Laura L.; Christianen, Marjolijn J. A.; Altieri, Andrew H.; van der Reijden, Karin J.; Silliman, Brian R.; van de Koppel, Johan; van der Geest, Matthijs; van Gils, Jan A.; van der Veer, Henk W.; Piersma, Theunis; de Ruiter, Peter C.; Olff, Han; van der Heide, Tjisse

2016-01-01

The diversity and structure of ecosystems has been found to depend both on trophic interactions in food webs and on other species interactions such as habitat modification and mutualism that form non-trophic interaction networks. However, quantification of the dependencies between these two main interaction networks has remained elusive. In this study, we assessed how habitat-modifying organisms affect basic food web properties by conducting in-depth empirical investigations of two ecosystems: North American temperate fringing marshes and West African tropical seagrass meadows. Results reveal that habitat-modifying species, through non-trophic facilitation rather than their trophic role, enhance species richness across multiple trophic levels, increase the number of interactions per species (link density), but decrease the realized fraction of all possible links within the food web (connectance). Compared to the trophic role of the most highly connected species, we found this non-trophic effects to be more important for species richness and of more or similar importance for link density and connectance. Our findings demonstrate that food webs can be fundamentally shaped by interactions outside the trophic network, yet intrinsic to the species participating in it. Better integration of non-trophic interactions in food web analyses may therefore strongly contribute to their explanatory and predictive capacity. PMID:26962135

How habitat-modifying organisms structure the food web of two coastal ecosystems.

PubMed

van der Zee, Els M; Angelini, Christine; Govers, Laura L; Christianen, Marjolijn J A; Altieri, Andrew H; van der Reijden, Karin J; Silliman, Brian R; van de Koppel, Johan; van der Geest, Matthijs; van Gils, Jan A; van der Veer, Henk W; Piersma, Theunis; de Ruiter, Peter C; Olff, Han; van der Heide, Tjisse

2016-03-16

The diversity and structure of ecosystems has been found to depend both on trophic interactions in food webs and on other species interactions such as habitat modification and mutualism that form non-trophic interaction networks. However, quantification of the dependencies between these two main interaction networks has remained elusive. In this study, we assessed how habitat-modifying organisms affect basic food web properties by conducting in-depth empirical investigations of two ecosystems: North American temperate fringing marshes and West African tropical seagrass meadows. Results reveal that habitat-modifying species, through non-trophic facilitation rather than their trophic role, enhance species richness across multiple trophic levels, increase the number of interactions per species (link density), but decrease the realized fraction of all possible links within the food web (connectance). Compared to the trophic role of the most highly connected species, we found this non-trophic effects to be more important for species richness and of more or similar importance for link density and connectance. Our findings demonstrate that food webs can be fundamentally shaped by interactions outside the trophic network, yet intrinsic to the species participating in it. Better integration of non-trophic interactions in food web analyses may therefore strongly contribute to their explanatory and predictive capacity. © 2016 The Author(s).

Testing fundamental ecological concepts with a Pythium-Prunus pathosystem

USDA-ARS?s Scientific Manuscript database

The study of plant-pathogen interactions has enabled tests of basic ecological concepts on plant community assembly (Janzen-Connell Hypothesis) and plant invasion (Enemy Release Hypothesis). We used a field experiment to (#1) test whether Pythium effects depended on host (seedling) density and/or d...

Directional Dependence of Hydrogen Bonds: a Density-based Energy Decomposition Analysis and Its Implications on Force Field Development

PubMed Central

Lu, Zhenyu; Zhou, Nengjie; Wu, Qin; Zhang, Yingkai

2011-01-01

One well-known shortcoming of widely-used biomolecular force fields is the description of the directional dependence of hydrogen bonding (HB). Here we aim to better understand the origin of this difficulty and thus provide some guidance for further force field development. Our theoretical approaches center on a novel density-based energy decomposition analysis (DEDA) method [J. Chem. Phys., 131, 164112 (2009)], in which the frozen density energy is variationally determined through constrained search. This unique and most significant feature of DEDA enables us to find that the frozen density interaction term is the key factor in determining the HB orientation, while the sum of polarization and charge-transfer components shows very little HB directional dependence. This new insight suggests that the difficulty for current non-polarizable force fields to describe the HB directional dependence is not due to the lack of explicit polarization or charge-transfer terms. Using the DEDA results as reference, we further demonstrate that the main failure coming from the atomic point charge model can be overcome largely by introducing extra charge sites or higher order multipole moments. Among all the electrostatic models explored, the smeared charge distributed multipole model (up to quadrupole), which also takes account of charge penetration effects, gives the best agreement with the corresponding DEDA results. Meanwhile, our results indicate that the van der Waals interaction term needs to be further improved to better model directional hydrogen bonding. PMID:22267958

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

USGS Publications Warehouse

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

2015-01-01

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 potential 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.

Anharmonic Damping of Terahertz Acoustic Waves in a Network Glass and Its Effect on the Density of Vibrational States

NASA Astrophysics Data System (ADS)

Baldi, G.; Giordano, V. M.; Ruta, B.; Dal Maschio, R.; Fontana, A.; Monaco, G.

2014-03-01

We report the observation, by means of high-resolution inelastic x-ray scattering, of an unusually large temperature dependence of the sound attenuation of a network glass at terahertz frequency, an unprecedentedly observed phenomenon. The anharmonicity can be ascribed to the interaction between the propagating acoustic wave and the bath of thermal vibrations. At low temperatures the sound attenuation follows a Rayleigh-Gans scattering law. As the temperature is increased the anharmonic process sets in, resulting in an almost quadratic frequency dependence of the damping in the entire frequency range. We show that the temperature variation of the sound damping accounts quantitatively for the temperature dependence of the density of vibrational states.

Effective atomic numbers and electron densities of bioactive glasses for photon interaction

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

Shantappa, Anil, E-mail: anilmalipatil@yahoo.co.in; Hanagodimath, S. M., E-mail: smhmath@rediffmail.com

2015-08-28

This work was carried out to study the nature of mass attenuation coefficient of bioactive glasses for gamma rays. Bioactive glasses are a group of synthetic silica-based bioactive materials with unique bone bonding properties. In the present study, we have calculated the effective atomic number, electron density for photon interaction of some selected bioactive glasses viz., SiO{sub 2}-Na{sub 2}O, SiO{sub 2}-Na{sub 2}O-CaO and SiO{sub 2}-Na{sub 2}O-P{sub 2}O{sub 5} in the energy range 1 keV to 100 MeV. We have also computed the single valued effective atomic number by using XMuDat program. It is observed that variation in effective atomic number (Z{submore » PI,} {sub eff}) depends also upon the weight fractions of selected bioactive glasses and range of atomic numbers of the elements. The results shown here on effective atomic number, electron density will be more useful in the medical dosimetry for the calculation of absorbed dose and dose rate.« less

Crowding of Interacting Fluid Particles in Porous Media through Molecular Dynamics: Breakdown of Universality for Soft Interactions.

PubMed

Schnyder, Simon K; Horbach, Jürgen

2018-02-16

Molecular dynamics simulations of interacting soft disks confined in a heterogeneous quenched matrix of soft obstacles show dynamics which is fundamentally different from that of hard disks. The interactions between the disks can enhance transport when their density is increased, as disks cooperatively help each other over the finite energy barriers in the matrix. The system exhibits a transition from a diffusive to a localized state, but the transition is strongly rounded. Effective exponents in the mean-squared displacement can be observed over three decades in time but depend on the density of the disks and do not correspond to asymptotic behavior in the vicinity of a critical point, thus, showing that it is incorrect to relate them to the critical exponents in the Lorentz model scenario. The soft interactions are, therefore, responsible for a breakdown of the universality of the dynamics.

Crowding of Interacting Fluid Particles in Porous Media through Molecular Dynamics: Breakdown of Universality for Soft Interactions

NASA Astrophysics Data System (ADS)

Schnyder, Simon K.; Horbach, Jürgen

2018-02-01

Molecular dynamics simulations of interacting soft disks confined in a heterogeneous quenched matrix of soft obstacles show dynamics which is fundamentally different from that of hard disks. The interactions between the disks can enhance transport when their density is increased, as disks cooperatively help each other over the finite energy barriers in the matrix. The system exhibits a transition from a diffusive to a localized state, but the transition is strongly rounded. Effective exponents in the mean-squared displacement can be observed over three decades in time but depend on the density of the disks and do not correspond to asymptotic behavior in the vicinity of a critical point, thus, showing that it is incorrect to relate them to the critical exponents in the Lorentz model scenario. The soft interactions are, therefore, responsible for a breakdown of the universality of the dynamics.

Stocking density affects the growth performance of broilers in a sex-dependent fashion.

PubMed

Zuowei, S; Yan, L; Yuan, L; Jiao, H; Song, Z; Guo, Y; Lin, H

2011-07-01

The effects of stocking density, sex, and dietary ME concentration on live performance, footpad burns, and leg weakness of broilers were investigated. A total of 876 male and 1,020 female 1-d-old chicks were placed in 24 pens to simulate final stocking density treatments of 26 kg (LSD; 10 males or 12 females/m(2)) and 42 kg (HSD; 16 males or 18 females/m(2)) of BW/m(2) floor space. Two series of experimental diets with a 150 kcal/kg difference in ME concentration (2,800, 2,900, and 3,000 or 2,950, 3,050, and 3,150 kcal of ME/kg) were compared in a 3-phase feeding program. The HSD treatment significantly decreased BW gain and feed conversion ratio (FCR). The HSD chickens consumed less feed by 35 d of age; thereafter, the reverse was true. Male chickens had significantly higher feed intake (FI), BW gain, and FCR compared with females. A significant interaction was found of stocking density and age for FI, BW gain, and FCR. Compared with LSD treatment, HSD broilers had a higher FI and a lower FCR from 36 to 42 d of age. Stocking density, sex, and age had a significant interaction for BW gain and FCR. Female broilers had worse BW gain and FCR when stocked at high density from 36 to 42 d of age. Stocking density had no significant influence on breast, thigh, or abdominal fat yield. Female broilers had significantly higher breast yield and abdominal fat. Male broilers and HSD treatment had high footpad burn and gait scores. A low ME diet increased footpad burn score but had no effect on gait score. The result indicated that stocking density had a more severe effect on the growth of male broilers before 35 d of age. Female broilers need more space than males at similar BW per square meter near marketing age. The incidence and severity of leg weakness are associated with sex, diet, and stocking density. This result suggests that the deteriorated effect of high stocking density is sex and age dependent.

Density, Viscosity and Surface Tension of Binary Mixtures of 1-Butyl-1-Methylpyrrolidinium Tricyanomethanide with Benzothiophene.

PubMed

Domańska, Urszula; Królikowska, Marta; Walczak, Klaudia

2014-01-01

The effects of temperature and composition on the density and viscosity of pure benzothiophene and ionic liquid (IL), and those of the binary mixtures containing the IL 1-butyl-1-methylpyrrolidynium tricyanomethanide ([BMPYR][TCM] + benzothiophene), are reported at six temperatures (308.15, 318.15, 328.15, 338.15, 348.15 and 358.15) K and ambient pressure. The temperature dependences of the density and viscosity were represented by an empirical second-order polynomial and by the Vogel-Fucher-Tammann equation, respectively. The density and viscosity variations with compositions were described by polynomials. Excess molar volumes and viscosity deviations were calculated and correlated by Redlich-Kister polynomial expansions. The surface tensions of benzothiophene, pure IL and binary mixtures of ([BMPYR][TCM] + benzothiophene) were measured at atmospheric pressure at four temperatures (308.15, 318.15, 328.15 and 338.15) K. The surface tension deviations were calculated and correlated by a Redlich-Kister polynomial expansion. The temperature dependence of the interfacial tension was used to evaluate the surface entropy, the surface enthalpy, the critical temperature, the surface energy and the parachor for pure IL. These measurements have been provided to complete information of the influence of temperature and composition on physicochemical properties for the selected IL, which was chosen as a possible new entrainer in the separation of sulfur compounds from fuels. A qualitative analysis on these quantities in terms of molecular interactions is reported. The obtained results indicate that IL interactions with benzothiophene are strongly dependent on packing effects and hydrogen bonding of this IL with the polar solvent.

Non-Linear Interactions between Consumers and Flow Determine the Probability of Plant Community Dominance on Maine Rocky Shores

PubMed Central

Silliman, Brian R.; McCoy, Michael W.; Trussell, Geoffrey C.; Crain, Caitlin M.; Ewanchuk, Patrick J.; Bertness, Mark D.

2013-01-01

Although consumers can strongly influence community recovery from disturbance, few studies have explored the effects of consumer identity and density and how they may vary across abiotic gradients. On rocky shores in Maine, recent experiments suggest that recovery of plant- or animal- dominated community states is governed by rates of water movement and consumer pressure. To further elucidate the mechanisms of consumer control, we examined the species-specific and density-dependent effects of rocky shore consumers (crabs and snails) on community recovery under both high (mussel dominated) and low flow (plant dominated) conditions. By partitioning the direct impacts of predators (crabs) and grazers (snails) on community recovery across a flow gradient, we found that grazers, but not predators, are likely the primary agent of consumer control and that their impact is highly non-linear. Manipulating snail densities revealed that herbivorous and bull-dozing snails (Littorina littorea) alone can control recovery of high and low flow communities. After ∼1.5 years of recovery, snail density explained a significant amount of the variation in macroalgal coverage at low flow sites and also mussel recovery at high flow sites. These density-dependent grazer effects were were both non-linear and flow-dependent, with low abundance thresholds needed to suppress plant community recovery, and much higher levels needed to control mussel bed development. Our study suggests that consumer density and identity are key in regulating both plant and animal community recovery and that physical conditions can determine the functional forms of these consumer effects. PMID:23940510

Surface force and vibrational spectroscopic analyses of interfacial water molecules in the vicinity of methoxy-tri(ethylene glycol)-terminated monolayers: mechanisms underlying the effect of lateral packing density on bioinertness.

PubMed

Sekine, Taito; Asatyas, Syifa; Sato, Chikako; Morita, Shigeaki; Tanaka, Masaru; Hayashi, Tomohiro

Unequivocal dependence of bioinertness of self-assembled monolayers of methoxy-tri(ethylene glycol)-terminated alkanethiol (EG3-OMe SAMs) on their packing density has been a mystery for more than two decades. We tackled this long-standing question by performing surface force and surface-enhanced infrared absorption (SEIRA) spectroscopic measurements. Our surface force measurements revealed a physical barrier of interfacial water in the vicinity of the Au-supported EG3-OMe SAM (low packing density), whereas the Ag-supported one (high packing density) did not possess such interfacial water. In addition, the results of SEIRA measurements clearly exhibited that hydrogen bonding states of the interfacial water differ depending on the substrates. We also characterized the bioinertness of these SAMs by protein adsorption tests and adhesion assays of platelet and human umbilical vein endothelial cells. The hydrogen bonding states of the interfacial water and water-induced interaction clearly correlated with the bioinertness of the SAMs, suggesting that the interfacial water plays an important role determining the interaction of the SAMs with biomolecules and cells.

Effect of culture density on biomass production and light utilization efficiency of Synechocystis sp. PCC 6803.

PubMed

Straka, Levi; Rittmann, Bruce E

2018-02-01

The viability of large-scale microalgae cultivation depends on providing optimal growth conditions, for which a key operational parameter is culture density. Using Synechocystis sp. PCC 6803, we conducted a series of fixed-density, steady-state experiments and one batch-growth experiment to investigate the role of culture density on biomass production and light utilization efficiency. In all cases, the fixed-density, steady-state experiments and batch-growth experiment showed good agreement. The highest biomass production rates (260 mg L -1  d -1 ) and efficiency for converting light energy to biomass (0.80 μg (μmol photons) -1 ) occurred together at a culture density near 760 mg L -1 , which approximately corresponded to the lowest culture density where almost all incident light was absorbed. The ratio of OD 680 /OD 735 increased with culture density up to the point of maximum productivity, where it plateaued (at a value of 2.4) for higher culture densities. This change in OD 680 /OD 735 indicates a photoacclimation effect that depended on culture density. Very high culture densities led to a sharp decline in efficiency of biomass production per photons absorbed, likely due to a combination of increased decay relative to growth, metabolic changes due to cell-cell interactions, and photodamage due to mixing between regions with high light intensity and zero light intensity. © 2017 Wiley Periodicals, Inc.

Estimating peer density effects on oral health for community-based older adults.

PubMed

Chakraborty, Bibhas; Widener, Michael J; Mirzaei Salehabadi, Sedigheh; Northridge, Mary E; Kum, Susan S; Jin, Zhu; Kunzel, Carol; Palmer, Harvey D; Metcalf, Sara S

2017-12-29

As part of a long-standing line of research regarding how peer density affects health, researchers have sought to understand the multifaceted ways that the density of contemporaries living and interacting in proximity to one another influence social networks and knowledge diffusion, and subsequently health and well-being. This study examined peer density effects on oral health for racial/ethnic minority older adults living in northern Manhattan and the Bronx, New York, NY. Peer age-group density was estimated by smoothing US Census data with 4 kernel bandwidths ranging from 0.25 to 1.50 mile. Logistic regression models were developed using these spatial measures and data from the ElderSmile oral and general health screening program that serves predominantly racial/ethnic minority older adults at community centers in northern Manhattan and the Bronx. The oral health outcomes modeled as dependent variables were ordinal dentition status and binary self-rated oral health. After construction of kernel density surfaces and multiple imputation of missing data, logistic regression analyses were performed to estimate the effects of peer density and other sociodemographic characteristics on the oral health outcomes of dentition status and self-rated oral health. Overall, higher peer density was associated with better oral health for older adults when estimated using smaller bandwidths (0.25 and 0.50 mile). That is, statistically significant relationships (p < 0.01) between peer density and improved dentition status were found when peer density was measured assuming a more local social network. As with dentition status, a positive significant association was found between peer density and fair or better self-rated oral health when peer density was measured assuming a more local social network. This study provides novel evidence that the oral health of community-based older adults is affected by peer density in an urban environment. To the extent that peer density signifies the potential for social interaction and support, the positive significant effects of peer density on improved oral health point to the importance of place in promoting social interaction as a component of healthy aging. Proximity to peers and their knowledge of local resources may facilitate utilization of community-based oral health care.

Structure of neutron star crusts from new Skyrme effective interactions constrained by chiral effective field theory

NASA Astrophysics Data System (ADS)

Lim, Yeunhwan; Holt, Jeremy W.

2017-06-01

We investigate the structure of neutron star crusts, including the crust-core boundary, based on new Skyrme mean field models constrained by the bulk-matter equation of state from chiral effective field theory and the ground-state energies of doubly-magic nuclei. Nuclear pasta phases are studied using both the liquid drop model as well as the Thomas-Fermi approximation. We compare the energy per nucleon for each geometry (spherical nuclei, cylindrical nuclei, nuclear slabs, cylindrical holes, and spherical holes) to obtain the ground state phase as a function of density. We find that the size of the Wigner-Seitz cell depends strongly on the model parameters, especially the coefficients of the density gradient interaction terms. We employ also the thermodynamic instability method to check the validity of the numerical solutions based on energy comparisons.

Electron-phonon coupling and superconductivity in the (4/3)-monolayer of Pb on Si(111): Role of spin-orbit interaction

NASA Astrophysics Data System (ADS)

Sklyadneva, I. Yu.; Heid, R.; Bohnen, K.-P.; Echenique, P. M.; Chulkov, E. V.

2018-05-01

The effect of spin-orbit coupling on the electron-phonon interaction in a (4/3)-monolayer of Pb on Si(111) is investigated within the density-functional theory and linear-response approach in the mixed-basis pseudopotential representation. We show that the spin-orbit interaction produces a large weakening of the electron-phonon coupling strength, which appears to be strongly overestimated in the scalar relativistic calculations. The effect of spin-orbit interaction is largely determined by the induced modification of Pb electronic bands and a stiffening of the low-energy part of phonon spectrum, which favor a weakening of the electron-phonon coupling strength. The state-dependent strength of the electron-phonon interaction in occupied Pb electronic bands varies depending on binding energy rather than electronic momentum. It is markedly larger than the value averaged over electron momentum because substrate electronic bands make a small contribution to the phonon-mediated scattering and agrees well with the experimental data.

Interactions between environmental variables determine immunity in the Indian meal moth Plodia interpunctella.

PubMed

Triggs, Alison; Knell, Robert J

2012-03-01

1. Animals raised in good environmental conditions are expected to have more resources to invest in immunity than those raised in poor conditions. Variation in immune activity and parasite resistance in response to changes in environmental temperature, population density and food quality have been shown in many invertebrate species. 2. Almost all studies to date have examined the effects of individual variables in isolation. The aim of this study was to address whether environmental factors interact to produce synergistic effects on phenoloxidase (PO) activity and haemocyte count, both indicators of immune system activity. Temperature, food quality and density were varied in a fully factorial design for a total of eight treatment combinations. 3. Strong interactions between the three environmental variables led to the magnitude and in some cases the direction of the effect of most variables changing as the other environmental factors were altered. Overall, food quality had the most important and consistent influence, larvae raised on a good-quality diet having substantially higher PO activity in every case and substantially higher haemocyte counts in all treatments except unheated/low density. 4. When food quality was good, the larvae showed 'density-dependent prophylaxis': raising their investment in immunity when population density is high. When food quality was poor and the temperature low, however, those larvae raised at high densities invested less in immunity. 5. Increased temperature is often thought to lead to increased immune reactivity in ectotherms, but we found that the effect of temperature was strongly dependent on the values of other environmental variables. PO activity increased with temperature when larvae were raised on good food or when density was high, but when food was poor and density low, a higher temperature led to reduced PO activity. A higher temperature led to higher haemocyte counts when density was high and food quality was poor, but in all other cases, the effect of increased temperature was either close to zero or somewhat negative. 6. Although PO activity and haemocyte count were weakly correlated across the whole data set, there were a number of treatments where the two measures responded in different ways to environmental change. Overall, effect sizes for PO activity were substantially higher than those for haemocyte count, indicating that the different components of the immune system vary in their sensitivity to environmental change. 7. Predictions of the effect of environmental or population change on immunity and disease dynamics based on laboratory experiments that only investigate the effects of single variable are likely to be inaccurate or even entirely wrong. © 2011 The Authors. Journal of Animal Ecology © 2011 British Ecological Society.

Solar wind/local interstellar medium interaction including charge exchange with neural hydrogen

NASA Technical Reports Server (NTRS)

Pauls, H. Louis; Zank, Gary P.

1995-01-01

We present results from a hydrodynamic model of the interaction of the solar wind with the local interstellar medium (LISM), self-consistently taking into account the effects of charge exchange between the plasma component and the interstellar neutrals. The simulation is fully time dependent, and is carried out in two or three dimensions, depending on whether the helio-latitudinal dependence of the solar wind speed and number density (both giving rise to three dimensional effects) are included. As a first approximation it is assumed that the neutral component of the flow can be described by a single, isotropic fluid. Clearly, this is not the actual situation, since charge exchange with the supersonic solar wind plasma in the region of the nose results in a 'second' neutral fluid propagating in the opposite direction as that of the LISM neutrals.

Symmetry lowering of pentacene molecular states interacting with a Cu surface

NASA Astrophysics Data System (ADS)

Baldacchini, Chiara; Mariani, Carlo; Betti, Maria Grazia; Vobornik, Ivana; Fujii, Jun; Annese, Emilia; Rossi, Giorgio; Ferretti, Andrea; Calzolari, Arrigo; di Felice, Rosa; Ruini, Alice; Molinari, Elisa

2007-12-01

Pentacene adsorbed on the Cu(119) vicinal surface forms long-range ordered chain structures. Photoemission spectroscopy measurements and ab initio density functional theory simulations provide consistent evidences that pentacene molecular orbitals mix with the copper bands, giving rise to interaction states localized at the interface. Angular-resolved and polarization dependent photoemission spectroscopy shows that most of the pentacene derived intensity is strongly dichroic. The symmetry of the molecular states of the free pentacene molecules is reduced upon adsorption on Cu(119), as a consequence of the molecule-metal interaction. Theoretical results show a redistribution of the charge density in π molecular states close to the Fermi level, consistent with the photoemission intensities (density of states) and polarization dependence (orbital symmetry).

Influence of soil pathogens on early regeneration success of tropical trees varies between forest edge and interior.

PubMed

Krishnadas, Meghna; Comita, Liza S

2018-01-01

Soil fungi are key mediators of negative density-dependent mortality in seeds and seedlings, and the ability to withstand pathogens in the shaded understory of closed-canopy forests could reinforce light gradient partitioning by tree species. For four species of tropical rainforest trees-two shade-tolerant and two shade-intolerant-we conducted a field experiment to examine the interactive effects of fungal pathogens, light, and seed density on germination and early seedling establishment. In a fully factorial design, seeds were sown into 1 m 2 plots containing soil collected from underneath conspecific adult trees, with plots assigned to forest edge (high light) or shaded understory, high or low density, and fungicide or no fungicide application. We monitored total seed germination and final seedling survival over 15 weeks. Shade-intolerant species were strongly constrained by light; their seedlings survived only at the edge. Fungicide application significantly improved seedling emergence and/or survival for three of the four focal species. There were no significant interactions between fungicide and seed density, suggesting that pathogen spread with increased aggregation of seeds and seedlings did not contribute to pathogen-mediated mortality. Two species experienced significant edge-fungicide interactions, but fungicide effects in edge vs. interior forest varied with species and recruitment stage. Our results suggest that changes to plant-pathogen interactions could affect plant recruitment in human-impacted forests subject to fragmentation and edge-effects.

Modelling interactions of toxicants and density dependence in wildlife populations

USGS Publications Warehouse

Schipper, Aafke M.; Hendriks, Harrie W.M.; Kauffman, Matthew J.; Hendriks, A. Jan; Huijbregts, Mark A.J.

2013-01-01

1. A major challenge in the conservation of threatened and endangered species is to predict population decline and design appropriate recovery measures. However, anthropogenic impacts on wildlife populations are notoriously difficult to predict due to potentially nonlinear responses and interactions with natural ecological processes like density dependence. 2. Here, we incorporated both density dependence and anthropogenic stressors in a stage-based matrix population model and parameterized it for a density-dependent population of peregrine falcons Falco peregrinus exposed to two anthropogenic toxicants [dichlorodiphenyldichloroethylene (DDE) and polybrominated diphenyl ethers (PBDEs)]. Log-logistic exposure–response relationships were used to translate toxicant concentrations in peregrine falcon eggs to effects on fecundity. Density dependence was modelled as the probability of a nonbreeding bird acquiring a breeding territory as a function of the current number of breeders. 3. The equilibrium size of the population, as represented by the number of breeders, responded nonlinearly to increasing toxicant concentrations, showing a gradual decrease followed by a relatively steep decline. Initially, toxicant-induced reductions in population size were mitigated by an alleviation of the density limitation, that is, an increasing probability of territory acquisition. Once population density was no longer limiting, the toxicant impacts were no longer buffered by an increasing proportion of nonbreeders shifting to the breeding stage, resulting in a strong decrease in the equilibrium number of breeders. 4. Median critical exposure concentrations, that is, median toxicant concentrations in eggs corresponding with an equilibrium population size of zero, were 33 and 46 μg g−1 fresh weight for DDE and PBDEs, respectively. 5. Synthesis and applications. Our modelling results showed that particular life stages of a density-limited population may be relatively insensitive to 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.

Effect of the collective motions of molecules inside a condensed phase on fluctuations in the density of small bodies

NASA Astrophysics Data System (ADS)

Tovbin, Yu. K.

2017-11-01

An approach to calculating the effects of fluctuations in density that considers the collective motions of molecules in small condensed phases (e.g., droplets, microcrystals, adsorption at microcrystal faces) is proposed. Statistical sums of the vibrational, rotational, and translational motions of molecules are of a collective character expressed in the dependences of these statistical sums on the local configurations of neighboring molecules. This changes their individual contributions to the free energy and modifies fluctuations in density in the inner homogeneous regions of small bodies. Interactions between nearest neighbors are considered in a quasi-chemical approximation that reflects the effects of short-range direct correlations. Expressions for isotherms relating the densities of mixture components to the chemical potentials in a thermostat are obtained, along with equations for pair distribution functions.

Time-dependent density functional theory for the charging kinetics of electric double layer containing room-temperature ionic liquids

DOE PAGES

Lian, Cheng; Univ. of California, Riverside, CA; Zhao, Shuangliang; ...

2016-11-29

Understanding the charging kinetics of electric double layers is of fundamental importance for the design and development of novel electrochemical devices such as supercapacitors and field-effect transistors. In this paper, we study the dynamic behavior of room-temperature ionic liquids using a classical time-dependent density functional theory that accounts for the molecular excluded volume effects, the electrostatic correlations, and the dispersion forces. While the conventional models predict a monotonic increase of the surface charge with time upon application of an electrode voltage, our results show that dispersion between ions results in a non-monotonic increase of the surface charge with the durationmore » of charging. Finally and furthermore, we investigate the effects of van der Waals attraction between electrode/ionic-liquid interactions on the charging processes.« less

Strong-field ionization of Li and Be: a time-dependent density functional theory with self-interaction correction

NASA Astrophysics Data System (ADS)

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

2011-11-01

In the framework of the time-dependent density functional theory, we have performed 3D calculations of multiphoton ionization of Li and Be atoms by strong near-infrared laser fields. The results for the intensity-dependent probabilities of single and double ionization are presented. We make use of the time-dependent Krieger-Li-Iafrate exchange-correlation potential with self-interaction correction (TD-KLI-SIC). Such a potential possesses an integer discontinuity which improves description of the ionization process. However, we have found that the discontinuity of the TD-KLI-SIC potential is not sufficient to reproduce characteristic feature of double ionization.

Subsystem real-time time dependent density functional theory.

PubMed

Krishtal, Alisa; Ceresoli, Davide; Pavanello, Michele

2015-04-21

We present the extension of Frozen Density Embedding (FDE) formulation of subsystem Density Functional Theory (DFT) to real-time Time Dependent Density Functional Theory (rt-TDDFT). FDE is a DFT-in-DFT embedding method that allows to partition a larger Kohn-Sham system into a set of smaller, coupled Kohn-Sham systems. Additional to the computational advantage, FDE provides physical insight into the properties of embedded systems and the coupling interactions between them. The extension to rt-TDDFT is done straightforwardly by evolving the Kohn-Sham subsystems in time simultaneously, while updating the embedding potential between the systems at every time step. Two main applications are presented: the explicit excitation energy transfer in real time between subsystems is demonstrated for the case of the Na4 cluster and the effect of the embedding on optical spectra of coupled chromophores. In particular, the importance of including the full dynamic response in the embedding potential is demonstrated.

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

PubMed

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

2008-09-01

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

Improving the assessment of predator functional responses by considering alternate prey and predator interactions.

PubMed

Chan, K; Boutin, S; Hossie, T J; Krebs, C J; O'Donoghue, M; Murray, D L

2017-07-01

To improve understanding of the complex and variable patterns of predator foraging behavior in natural systems, it is critical to determine how density-dependent predation and predator hunting success are mediated by alternate prey or predator interference. Despite considerable theory and debate seeking to place predator-prey interactions in a more realistic context, few empirical studies have quantified the role of alternate prey or intraspecific interactions on predator-prey dynamics. We assessed functional responses of two similarly sized, sympatric carnivores, lynx (Lynx canadensis) and coyotes (Canis latrans), foraging on common primary (snowshoe hares; Lepus americanus) and alternate (red squirrels; Tamiasciurus hudsonicus) prey in a natural system. Lynx exhibited a hyperbolic prey-dependent response to changes in hare density, which is characteristic of predators relying primarily on a single prey species. In contrast, the lynx-squirrel response was found to be linear ratio dependent, or inversely dependent on hare density. The coyote-hare and coyote-squirrel interactions also were linear and influenced by predator density. We explain these novel results by apparent use of spatial and temporal refuges by prey, and the likelihood that predators commonly experience interference and lack of satiation when foraging. Our study provides empirical support from a natural predator-prey system that (1) predation rate may not be limited at high prey densities when prey are small or rarely captured; (2) interference competition may influence the predator functional response; and (3) predator interference has a variable role across different prey types. Ultimately, distinct functional responses of predators to different prey types illustrates the complexity associated with predator-prey interactions in natural systems and highlights the need to investigate predator behavior and predation rate in relation to the broader ecological community. © 2017 by the Ecological Society of America.

A Finite-Difference Time-Domain Model of Artificial Ionospheric Modification

NASA Astrophysics Data System (ADS)

Cannon, Patrick; Honary, Farideh; Borisov, Nikolay

Experiments in the artificial modification of the ionosphere via a radio frequency pump wave have observed a wide range of non-linear phenomena near the reflection height of an O-mode wave. These effects exhibit a strong aspect-angle dependence thought to be associated with the process by which, for a narrow range of off-vertical launch angles, the O-mode pump wave can propagate beyond the standard reflection height at X=1 as a Z-mode wave and excite additional plasma activity. A numerical model based on Finite-Difference Time-Domain method has been developed to simulate the interaction of the pump wave with an ionospheric plasma and investigate different non-linear processes involved in modification experiments. The effects on wave propagation due to plasma inhomogeneity and anisotropy are introduced through coupling of the Lorentz equation of motion for electrons and ions to Maxwell’s wave equations in the FDTD formulation, leading to a model that is capable of exciting a variety of plasma waves including Langmuir and upper-hybrid waves. Additionally, discretized equations describing the time-dependent evolution of the plasma fluid temperature and density are included in the FDTD update scheme. This model is used to calculate the aspect angle dependence and angular size of the radio window for which Z-mode excitation occurs, and the results compared favourably with both theoretical predictions and experimental observations. The simulation results are found to reproduce the angular dependence on electron density and temperature enhancement observed experimentally. The model is used to investigate the effect of different initial plasma density conditions on the evolution of non-linear effects, and demonstrates that the inclusion of features such as small field-aligned density perturbations can have a significant influence on wave propagation and the magnitude of temperature and density enhancements.

Self-consistent description of the SHFB equations for 112Sn

NASA Astrophysics Data System (ADS)

Ghafouri, M.; Sadeghi, H.; Torkiha, M.

2018-03-01

The Hartree-Fock (HF) method is an excellent approximation of the closed shell magic nuclei. Pair correlation is essential for the description of open shell nuclei and has been derived for even-even, odd-odd and even-odd nuclei. These effects are reported by Hartree-Fock with BCS (HFBCS) or Hartree-Fock-Bogolyubov (HFB). These issues have been investigated, especially in the nuclear charts, and such studies have been compared with the observed information. We compute observations such as total binding energy, charge radius, densities, separation energies, pairing gaps and potential energy surfaces for neutrons and protons, and compare them with experimental data and the result of the spherical codes. In spherical even-even neutron-rich nuclei are considered in the Skyrme-Hartree-Fock-Bogolyubov (SHFB) method with density-dependent pairing interaction. Zero-range density-dependent interactions is used in the pairing channel. We solve SHF or SHFB equations in the spatial coordinates with spherical symmetry for tin isotopes such as 112Sn. The numerical accuracy of solving equations in the coordinate space is much greater than the fundamental extensions, which yields almost precise results.

Skyrme interaction to second order in nuclear matter

NASA Astrophysics Data System (ADS)

Kaiser, N.

2015-09-01

Based on the phenomenological Skyrme interaction various density-dependent nuclear matter quantities are calculated up to second order in many-body perturbation theory. The spin-orbit term as well as two tensor terms contribute at second order to the energy per particle. The simultaneous calculation of the isotropic Fermi-liquid parameters provides a rigorous check through the validity of the Landau relations. It is found that published results for these second order contributions are incorrect in most cases. In particular, interference terms between s-wave and p-wave components of the interaction can contribute only to (isospin or spin) asymmetry energies. Even with nine adjustable parameters, one does not obtain a good description of the empirical nuclear matter saturation curve in the low density region 0\\lt ρ \\lt 2{ρ }0. The reason for this feature is the too strong density-dependence {ρ }8/3 of several second-order contributions. The inclusion of the density-dependent term \\frac{1}{6}{t}3{ρ }1/6 is therefore indispensable for a realistic description of nuclear matter in the Skyrme framework.

Effects of prey density, temperature and predator diversity on nonconsumptive predator-driven mortality in a freshwater food web.

PubMed

Veselý, Lukáš; Boukal, David S; Buřič, Miloš; Kozák, Pavel; Kouba, Antonín; Sentis, Arnaud

2017-12-22

Nonconsumptive predator-driven mortality (NCM), defined as prey mortality due to predation that does not result in prey consumption, is an underestimated component of predator-prey interactions with possible implications for population dynamics and ecosystem functioning. However, the biotic and abiotic factors influencing this mortality component remain largely unexplored, leaving a gap in our understanding of the impacts of environmental change on ecological communities. We investigated the effects of temperature, prey density, and predator diversity and density on NCM in an aquatic food web module composed of dragonfly larvae (Aeshna cyanea) and marbled crayfish (Procambarus fallax f. virginalis) preying on common carp (Cyprinus carpio) fry. We found that NCM increased with prey density and depended on the functional diversity and density of the predator community. Warming significantly reduced NCM only in the dragonfly larvae but the magnitude depended on dragonfly larvae density. Our results indicate that energy transfer across trophic levels is more efficient due to lower NCM in functionally diverse predator communities, at lower resource densities and at higher temperatures. This suggests that environmental changes such as climate warming and reduced resource availability could increase the efficiency of energy transfer in food webs only if functionally diverse predator communities are conserved.

A comparison of shock-cloud and wind-cloud interactions: effect of increased cloud density contrast on cloud evolution

NASA Astrophysics Data System (ADS)

Goldsmith, K. J. A.; Pittard, J. M.

2018-05-01

The similarities, or otherwise, of a shock or wind interacting with a cloud of density contrast χ = 10 were explored in a previous paper. Here, we investigate such interactions with clouds of higher density contrast. We compare the adiabatic hydrodynamic interaction of a Mach 10 shock with a spherical cloud of χ = 103 with that of a cloud embedded in a wind with identical parameters to the post-shock flow. We find that initially there are only minor morphological differences between the shock-cloud and wind-cloud interactions, compared to when χ = 10. However, once the transmitted shock exits the cloud, the development of a turbulent wake and fragmentation of the cloud differs between the two simulations. On increasing the wind Mach number, we note the development of a thin, smooth tail of cloud material, which is then disrupted by the fragmentation of the cloud core and subsequent `mass-loading' of the flow. We find that the normalized cloud mixing time (tmix) is shorter at higher χ. However, a strong Mach number dependence on tmix and the normalized cloud drag time, t_{drag}^' }, is not observed. Mach-number-dependent values of tmix and t_{drag}^' } from comparable shock-cloud interactions converge towards the Mach-number-independent time-scales of the wind-cloud simulations. We find that high χ clouds can be accelerated up to 80-90 per cent of the wind velocity and travel large distances before being significantly mixed. However, complete mixing is not achieved in our simulations and at late times the flow remains perturbed.

Ordering nanoparticles with polymer brushes

NASA Astrophysics Data System (ADS)

Cheng, Shengfeng; Stevens, Mark J.; Grest, Gary S.

2017-12-01

Ordering nanoparticles into a desired super-structure is often crucial for their technological applications. We use molecular dynamics simulations to study the assembly of nanoparticles in a polymer brush randomly grafted to a planar surface as the solvent evaporates. Initially, the nanoparticles are dispersed in a solvent that wets the polymer brush. After the solvent evaporates, the nanoparticles are either inside the brush or adsorbed at the surface of the brush, depending on the strength of the nanoparticle-polymer interaction. For strong nanoparticle-polymer interactions, a 2-dimensional ordered array is only formed when the brush density is finely tuned to accommodate a single layer of nanoparticles. When the brush density is higher or lower than this optimal value, the distribution of nanoparticles shows large fluctuations in space and the packing order diminishes. For weak nanoparticle-polymer interactions, the nanoparticles order into a hexagonal array on top of the polymer brush as long as the grafting density is high enough to yield a dense brush. An interesting healing effect is observed for a low-grafting-density polymer brush that can become more uniform in the presence of weakly adsorbed nanoparticles.

Molecular dynamics simulation study of the structure of poly(ethylene oxide) brushes on nonpolar surfaces in aqueous solution.

PubMed

Bedrov, Dmitry; Smith, Grant D

2006-07-04

The structure of poly(ethylene oxide) (PEO, M(w) = 526) brushes of various grafting density (sigma) on nonpolar graphite and hydrophobic (oily) surfaces in aqueous solution has been studied using atomistic molecular dynamics simulations. Additionally, the influence of PEO-surface interactions on the brush structure was investigated by systematically reducing the strength of the (dispersion) attraction between PEO and the surfaces. PEO chains were found to adsorb strongly to the graphite surface due primarily to the relative strength of dispersion interactions between PEO and the atomically dense graphite compared to those between water and graphite. For the oily surface, PEO-surface and water-surface dispersion interactions are much weaker, greatly reducing the energetic driving force for PEO adsorption. This reduction is mediated to some extent by a hydrophobic driving force for PEO adsorption on the oily surface. Reduction in the strength of PEO-surface attraction results in reduced adsorption of PEO for both surfaces, with the effect being much greater for the graphite surface where the strong PEO-surface dispersion interactions dominate. At high grafting density (sigma approximately 1/R(g)(2)), the PEO density profiles exhibited classical brush behavior and were largely independent of the strength of the PEO-surface interaction. With decreasing grafting density (sigma < 1/R(g)(2)), coverage of the surface by PEO requires an increasingly large fraction of PEO segments resulting in a strong dependence of the PEO density profile on the nature of the PEO-surface interaction.

Increased consumer density reduces the strength of neighborhood effects in a model system.

PubMed

Merwin, Andrew C; Underwood, Nora; Inouye, Brian D

2017-11-01

An individual's susceptibility to attack can be influenced by conspecific and heterospecifics neighbors. Predicting how these neighborhood effects contribute to population-level processes such as competition and evolution requires an understanding of how the strength of neighborhood effects is modified by changes in the abundances of both consumers and neighboring resource species. We show for the first time that consumer density can interact with the density and frequency of neighboring organisms to determine the magnitude of neighborhood effects. We used the bean beetle, Callosobruchus maculatus, and two of its host beans, Vigna unguiculata and V. radiata, to perform a response-surface experiment with a range of resource densities and three consumer densities. At low beetle density, damage to beans was reduced with increasing conspecific density (i.e., resource dilution) and damage to the less preferred host, V. unguiculata, was reduced with increasing V. radiata frequency (i.e., frequency-dependent associational resistance). As beetle density increased, however, neighborhood effects were reduced; at the highest beetle densities neither focal nor neighboring resource density nor frequency influenced damage. These findings illustrate the importance of consumer density in mediating indirect effects among resources, and suggest that accounting for consumer density may improve our ability to predict population-level outcomes of neighborhood effects and our use of them in applications such as mixed-crop pest management. © 2017 by the Ecological Society of America.

Effects of charge density waves on flux dynamics in weak-pinning single crystals of NbSe2 : free flux flow, flux-core size effects, and unexpected doubling of Jc(H) `peak effect'

NASA Astrophysics Data System (ADS)

Favreau, Peter; Gapud, Albert A.; Moraes, Sunhee; Delong, Lance; Reyes, Arneil P.; Thompson, James R.; Christen, David K.

2010-03-01

The interaction of two different ordering schemes -- charge density waves (CDWs) and superconductivity -- is studied in high-quality samples of NbSe2, particularly in the motion of magnetic flux quanta. More specifically, the study is on the effect of ``switching off'' the CDW phase -- effected by doping with Ta -- on the magnetic-field H dependence of: (i) the Lorentz-force-driven free flux flow (FFF) resistivity ρf associated with the ordered motion of vortices, and (ii) critical current density Jc. FFF is achieved for the first time in this material. The field dependence of ρf deviates from traditional Bardeen-Stephen flux flow and is more consistent with effects of flux core size as predicted by Kogan and Zelezhina. However, the suppression of CDW's seems to have no significant effect on these properties. On the other hand, Jc(H) shows a surprising double peak for the CDW-suppressed sample --contrary to previous studies in which the Jc peak was shown to disappear. Possible mechanisms are discussed.

Lateral Membrane Diffusion Modulated by a Minimal Actin Cortex

PubMed Central

Heinemann, Fabian; Vogel, Sven K.; Schwille, Petra

2013-01-01

Diffusion of lipids and proteins within the cell membrane is essential for numerous membrane-dependent processes including signaling and molecular interactions. It is assumed that the membrane-associated cytoskeleton modulates lateral diffusion. Here, we use a minimal actin cortex to directly study proposed effects of an actin meshwork on the diffusion in a well-defined system. The lateral diffusion of a lipid and a protein probe at varying densities of membrane-bound actin was characterized by fluorescence correlation spectroscopy (FCS). A clear correlation of actin density and reduction in mobility was observed for both the lipid and the protein probe. At high actin densities, the effect on the protein probe was ∼3.5-fold stronger compared to the lipid. Moreover, addition of myosin filaments, which contract the actin mesh, allowed switching between fast and slow diffusion in the minimal system. Spot variation FCS was in accordance with a model of fast microscopic diffusion and slower macroscopic diffusion. Complementing Monte Carlo simulations support the analysis of the experimental FCS data. Our results suggest a stronger interaction of the actin mesh with the larger protein probe compared to the lipid. This might point toward a mechanism where cortical actin controls membrane diffusion in a strong size-dependent manner. PMID:23561523

Domain size polydispersity effects on the structural and dynamical properties in lipid monolayers with phase coexistence.

PubMed

Rufeil-Fiori, Elena; Banchio, Adolfo J

2018-03-07

In lipid monolayers with phase coexistence, domains of the liquid-condensed phase always present size polydispersity. However, very few theoretical works consider size distribution effects on the monolayer properties. Because of the difference in surface densities, domains have excess dipolar density with respect to the surrounding liquid expanded phase, originating a dipolar inter-domain interaction. This interaction depends on the domain area, and hence the presence of a domain size distribution is associated with interaction polydispersity. Inter-domain interactions are fundamental to understanding the structure and dynamics of the monolayer. For this reason, it is expected that polydispersity significantly alters monolayer properties. By means of Brownian dynamics simulations, we study the radial distribution function (RDF), the average mean square displacement and the average time-dependent self-diffusion coefficient, D(t), of lipid monolayers with normally distributed size domains. For this purpose, we vary the relevant system parameters, polydispersity and interaction strength, within a range of experimental interest. We also analyze the consequences of using a monodisperse model to determine the interaction strength from an experimental RDF. We find that polydispersity strongly affects the value of the interaction strength, which is greatly underestimated if polydispersity is not considered. However, within a certain range of parameters, the RDF obtained from a polydisperse model can be well approximated by that of a monodisperse model, by suitably fitting the interaction strength, even for 40% polydispersities. For small interaction strengths or small polydispersities, the polydisperse systems obtained from fitting the experimental RDF have an average mean square displacement and D(t) in good agreement with that of the monodisperse system.

Dielectric properties of classical and quantized ionic fluids.

PubMed

Høye, Johan S

2010-06-01

We study time-dependent correlation functions of classical and quantum gases using methods of equilibrium statistical mechanics for systems of uniform as well as nonuniform densities. The basis for our approach is the path integral formalism of quantum mechanical systems. With this approach the statistical mechanics of a quantum mechanical system becomes the equivalent of a classical polymer problem in four dimensions where imaginary time is the fourth dimension. Several nontrivial results for quantum systems have been obtained earlier by this analogy. Here, we will focus upon the presence of a time-dependent electromagnetic pair interaction where the electromagnetic vector potential that depends upon currents, will be present. Thus both density and current correlations are needed to evaluate the influence of this interaction. Then we utilize that densities and currents can be expressed by polarizations by which the ionic fluid can be regarded as a dielectric one for which a nonlocal susceptibility is found. This nonlocality has as a consequence that we find no contribution from a possible transverse electric zero-frequency mode for the Casimir force between metallic plates. Further, we establish expressions for a leading correction to ab initio calculations for the energies of the quantized electrons of molecules where now retardation effects also are taken into account.

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

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

Yokogawa, D., E-mail: d.yokogawa@chem.nagoya-u.ac.jp; Institute of Transformative Bio-Molecules

2016-09-07

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

The nature of three-body interactions in DFT: Exchange and polarization effects

NASA Astrophysics Data System (ADS)

Hapka, Michał; Rajchel, Łukasz; Modrzejewski, Marcin; Schäffer, Rainer; Chałasiński, Grzegorz; Szcześniak, Małgorzata M.

2017-08-01

We propose a physically motivated decomposition of density functional theory (DFT) 3-body nonadditive interaction energies into the exchange and density-deformation (polarization) components. The exchange component represents the effect of the Pauli exclusion in the wave function of the trimer and is found to be challenging for density functional approximations (DFAs). The remaining density-deformation nonadditivity is less dependent upon the DFAs. Numerical demonstration is carried out for rare gas atom trimers, Ar2-HX (X = F, Cl) complexes, and small hydrogen-bonded and van der Waals molecular systems. None of the tested semilocal, hybrid, and range-separated DFAs properly accounts for the nonadditive exchange in dispersion-bonded trimers. By contrast, for hydrogen-bonded systems, range-separated DFAs achieve a qualitative agreement to within 20% of the reference exchange energy. A reliable performance for all systems is obtained only when the monomers interact through the Hartree-Fock potential in the dispersion-free Pauli blockade scheme. Additionally, we identify the nonadditive second-order exchange-dispersion energy as an important but overlooked contribution in force-field-like dispersion corrections. Our results suggest that range-separated functionals do not include this component, although semilocal and global hybrid DFAs appear to imitate it in the short range.

Fermi orbital derivatives in self-interaction corrected density functional theory: Applications to closed shell atoms

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

Pederson, Mark R., E-mail: mark.pederson@science.doe.gov

2015-02-14

A recent modification of the Perdew-Zunger self-interaction-correction to the density-functional formalism has provided a framework for explicitly restoring unitary invariance to the expression for the total energy. The formalism depends upon construction of Löwdin orthonormalized Fermi-orbitals which parametrically depend on variational quasi-classical electronic positions. Derivatives of these quasi-classical electronic positions, required for efficient minimization of the self-interaction corrected energy, are derived and tested, here, on atoms. Total energies and ionization energies in closed-shell singlet atoms, where correlation is less important, using the Perdew-Wang 1992 Local Density Approximation (PW92) functional, are in good agreement with experiment and non-relativistic quantum-Monte-Carlo results albeitmore » slightly too low.« less

NEW HYPERON EQUATIONS OF STATE FOR SUPERNOVAE AND NEUTRON STARS IN DENSITY-DEPENDENT HADRON FIELD THEORY

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

Banik, Sarmistha; Hempel, Matthias; Bandyopadhyay, Debades

2014-10-01

We develop new hyperon equation of state (EoS) tables for core-collapse supernova simulations and neutron stars. These EoS tables are based on a density-dependent relativistic hadron field theory where baryon-baryon interaction is mediated by mesons, using the parameter set DD2 for nucleons. Furthermore, light and heavy nuclei along with interacting nucleons are treated in the nuclear statistical equilibrium model of Hempel and Schaffner-Bielich which includes excluded volume effects. Of all possible hyperons, we consider only the contribution of Λs. We have developed two variants of hyperonic EoS tables: in the npΛφ case the repulsive hyperon-hyperon interaction mediated by the strangemore » φ meson is taken into account, and in the npΛ case it is not. The EoS tables for the two cases encompass a wide range of densities (10{sup –12} to ∼1 fm{sup –3}), temperatures (0.1 to 158.48 MeV), and proton fractions (0.01 to 0.60). The effects of Λ hyperons on thermodynamic quantities such as free energy per baryon, pressure, or entropy per baryon are investigated and found to be significant at higher densities. The cold, β-equilibrated EoS (with the crust included self-consistently) results in a 2.1 M {sub ☉} maximum mass neutron star for the npΛφ case, whereas that for the npΛ case is 1.95 M {sub ☉}. The npΛφ EoS represents the first supernova EoS table involving hyperons that is directly compatible with the recently measured 2 M {sub ☉} neutron stars.« less

Numerical band structure calculations of plasma metamaterials

NASA Astrophysics Data System (ADS)

Pederson, Dylan; Kourtzanidis, Konstantinos; Raja, Laxminarayan

2015-09-01

Metamaterials (MM) are materials engineered to display negative macroscopic permittivity and permeability. These materials allow for designed control over electromagnetic energy flow, especially at frequencies where natural materials do not interact. Plasmas have recently found application in MM as a negative permittivity component. The permittivity of a plasma depends on its electron density, which can be controlled by an applied field. This means that plasmas can be used in MM to actively control the transmission or reflection of incident waves. This work focuses on a plasma MM geometry in which microplasmas are generated in perforations in a metal plate. We characterizethis material by its band structure, which describes its interaction with incident waves. The plasma-EM interactions are obtained by coupling Maxwell's equations to a simplified plasma momentum equation. A plasma density profile is prescribed, and its effect on the band structure is investigated. The band structure calculations are typically done for static structures, whereas our current density responds to the incident waves. The resulting band structures are compared with experimental results.

Heating rates in collisionally opaque alkali-metal atom traps: Role of secondary collisions

NASA Astrophysics Data System (ADS)

Beijerinck, H. C. W.

2000-12-01

Grazing collisions with background gas are the major cause of trap loss and trap heating in atom traps. To first order, these effects do not depend on the trap density. In collisionally opaque trapped atom clouds, however, scattered atoms with an energy E larger than the effective trap depth Eeff, which are destined to escape from the atom cloud, will have a finite probability for a secondary collision. This results in a contribution to the heating rate that depends on the column density of the trapped atoms, i.e., the product of density and characteristic size of the trap. For alkali-metal atom traps, secondary collisions are quite important due to the strong long-range interaction with like atoms. We derive a simple analytical expression for the secondary heating rate, showing a dependency proportional to E1/2eff. When extrapolating to a vanishing column density, only primary collisions with the background gas will contribute to the heating rate. This contribution is rather small, due to the weak long-range interaction of the usual background gas species in an ultrahigh-vacuum system-He, Ne, or Ar-with the trapped alkali-metal atoms. We conclude that the transition between trap-loss collisions and heating collisions is determined by a cutoff energy 200 μK<=Eeff<=400 μK, much smaller than the actual trap depth E in most magnetic traps. Atoms with an energy Eeff

Effects of Interactions among Heterodera glycines, Meloidogyne incognita, and Host Genotype on Soybean Yield and Nematode Population Densities

PubMed Central

Niblack, T. L.; Hussey, R. S.; Boerma, H. R.

1986-01-01

The effects of host genotype and initial nematode population densities (Pi) on yield of soybean and soil population densities of Heterodera glycines (Hg) race 3 and Meloidogyne incognita (Mi) race 3 were studied in a greenhouse and field microplots in 1983 and 1984. Centennial (resistant to Hg and Mi), Braxton (resistant to Mi, susceptible to Hg), and Coker 237 (susceptible to Hg and Mi) were planted in soil infested with 0, 31, or 124 eggs of Hg and Mi, individually and in all combinations, per 100 cm³ soil. Yield responses of the soybean cultivars to individual and combined infestations of Hg and Mi were primarily dependent on soybean resistance or susceptibility to each species separately. Yield of Centennial was stimulated or unaffected by nematode treatments, yield of Braxton was suppressed by Hg only, and yield suppressions caused by Hg and Mi were additive and dependent on Pi for Coker 237. Other plant responses to nematodes were also dependent on host resistance or susceptibility. Population densities of Mi second-stage juveniles (J2) in soil were related to Mi Pi and remained constant in the presence of Hg for all three cultivars. Population densities of Hg J2 on the two Hg-susceptible Cultivars, Braxton and Coker 237, were suppressed in the presence of Mi at low Hg Pi. PMID:19294208

Potential misuse of avian density as a conservation metric

USGS Publications Warehouse

Skagen, Susan K.; Yackel Adams, Amy A.

2011-01-01

Effective conservation metrics are needed to evaluate the success of management in a rapidly changing world. Reproductive rates and densities of breeding birds (as a surrogate for reproductive rate) have been used to indicate the quality of avian breeding habitat, but the underlying assumptions of these metrics rarely have been examined. When birds are attracted to breeding areas in part by the presence of conspecifics and when breeding in groups influences predation rates, the effectiveness of density and reproductive rate as indicators of habitat quality is reduced. It is beneficial to clearly distinguish between individual- and population-level processes when evaluating habitat quality. We use the term reproductive rate to refer to both levels and further distinguish among levels by using the terms per capita fecundity (number of female offspring per female per year, individual level) and population growth rate (the product of density and per capita fecundity, population level). We predicted how density and reproductive rate interact over time under density-independent and density-dependent scenarios, assuming the ideal free distribution model of how birds settle in breeding habitats. We predicted population density of small populations would be correlated positively with both per capita fecundity and population growth rate due to the Allee effect. For populations in the density-dependent growth phase, we predicted no relation between density and per capita fecundity (because individuals in all patches will equilibrate to the same success rate) and a positive relation between density and population growth rate. Several ecological theories collectively suggest that positive correlations between density and per capita fecundity would be difficult to detect. We constructed a decision tree to guide interpretation of positive, neutral, nonlinear, and negative relations between density and reproductive rates at individual and population levels. ?? 2010 Society for Conservation Biology.

Data analysis on physical and mechanical properties of cassava pellets.

PubMed

Oguntunde, Pelumi E; Adejumo, Oluyemisi A; Odetunmibi, Oluwole A; Okagbue, Hilary I; Adejumo, Adebowale O

2018-02-01

In this data article, laboratory experimental investigation results carried out at National Centre for Agricultural Mechanization (NCAM) on moisture content, machine speed, die diameter of the rig, and the outputs (hardness, durability, bulk density, and unit density of the pellets) at different levels of cassava pellets were observed. Analysis of variance using randomized complete block design with factorial was used to perform analysis for each of the outputs: hardness, durability, bulk density, and unit density of the pellets. A clear description on each of these outputs was considered separately using tables and figures. It was observed that for all the output with the exception of unit density, their main factor effects as well as two and three ways interactions is significant at 5% level. This means that the hardness, bulk density and durability of cassava pellets respectively depend on the moisture content of the cassava dough, the machine speed, the die diameter of the extrusion rig and the combinations of these factors in pairs as well as the three altogether. Higher machine speeds produced more quality pellets at lower die diameters while lower machine speed is recommended for higher die diameter. Also the unit density depends on die diameter and the three-way interaction only. Unit density of cassava pellets is neither affected by machine parameters nor moisture content of the cassava dough. Moisture content of cassava dough, speed of the machine and die diameter of the extrusion rig are significant factors to be considered in pelletizing cassava to produce pellets. Increase in moisture content of cassava dough increase the quality of cassava pellets.

Effect of Sequence Blockiness on the Morphologies of Surface-grafted Elastin-like Polypeptides

NASA Astrophysics Data System (ADS)

Albert, Julie; Sintavanon, Kornkanok; Mays, Robin; MacEwan, Sarah; Chilkoti, Ashutosh; Genzer, Jan

2014-03-01

The inter- and intra- molecular interactions among monomeric units of copolymers and polypeptides depend strongly on monomer sequence distribution and dictate the phase behavior of these species both in solution and on surfaces. To study the relationship between sequence and phase behavior, we have designed a series of elastin-like polypeptides (ELPs) with controlled monomer sequences that mimic copolymers with various co-monomer sequence distributions and attached them covalently to silicon substrates from buffer solutions at temperatures below and above the bulk ELPs' lower critical solution temperatures (LCSTs). The dependence of ELP grafting density on solution temperature was examined by ellipsometry and the resultant surface morphologies were examined in air and under water with atomic force microscopy. Depositions performed above the LCST resulted in higher grafting densities and greater surface roughness of ELPs relative to depositions carried out below the LCST. In addition, we are using gradient substrates to examine the effect of ELP grafting density on temperature responsiveness.

Electron quantum dynamics in atom-ion interaction

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

Sabzyan, H., E-mail: sabzyan@sci.ui.ac.ir; Jenabi, M. J.

2016-04-07

Electron transfer (ET) process and its dependence on the system parameters are investigated by solving two-dimensional time-dependent Schrödinger equation numerically using split operator technique. Evolution of the electron wavepacket occurs from the one-electron species hydrogen atom to another bare nucleus of charge Z > 1. This evolution is quantified by partitioning the simulation box and defining regional densities belonging to the two nuclei of the system. It is found that the functional form of the time-variations of these regional densities and the extent of ET process depend strongly on the inter-nuclear distance and relative values of the nuclear charges, whichmore » define the potential energy surface governing the electron wavepacket evolution. Also, the initial electronic state of the single-electron atom has critical effect on this evolution and its consequent (partial) electron transfer depending on its spreading extent and orientation with respect to the inter-nuclear axis.« less

Density-dependent effects of omnivorous stream crayfish on benthic trophic dynamics

USGS Publications Warehouse

Ludlam, J.P.; Banks, B. T.; Magoulick, Daniel D.

2015-01-01

Crayfish are abundant and important consumers in aquatic food webs and crayfish invasions have demonstrated strong effects of crayfish on multiple trophic levels. Density may be an important factor determining the role of omnivorous crayfish in benthic communities, especially if density alters the strength of trophic interactions. The effect of crayfish density on a simple benthic food web using ceramic tiles was examined in three treatments (crayfish exclusion cage, cage control (open to crayfish), and exposed ceramic tiles) in mesocosms stocked with 6, 12, or 18 crayfish·m-2. We hypothesized that at low densities crayfish consumption of herbivorous chironomids would increase algal abundance, but at high densities crayfish would reduce both periphyton and invertebrates. In the experiment, periphyton and chironomid abundance increased with declining crayfish biomass on day 30 but not day 15. The magnitude of crayfish effects on day 15 periphyton chlorophyll a abundance increased with crayfish biomass, but crayfish effects on day 30 periphyton chlorophyll a or chironomid biomass did not increase with crayfish biomass. In this experiment there was little evidence for a trophic cascade at low crayfish densities and strong omnivory by crayfish dominated trophic dynamics.

Systematic analysis of hot Yb* isotopes using the energy density formalism

NASA Astrophysics Data System (ADS)

Jain, Deepika; Sharma, Manoj K.; Rajni; Kumar, Raj; Gupta, Raj K.

2014-10-01

A systematic study of the spin-orbit density interaction potential is carried out, with spherical as well as deformed choices of nuclei, for a variety of near-symmetric and asymmetric colliding nuclei leading to various isotopes of the compound nucleus Yb*, using the semiclassical extended Thomas-Fermi formulation (ETF) of the Skyrme energy density formalism (SEDF). We observe that the spin-orbit density interaction barrier height ( and barrier position ( increase systematically with the increase in number of neutrons in both the projectile and target, for spherical systems. On allowing deformation effects with optimum orientations, the barrier-height increases by a large order of magnitude, as compared to the spherical case, in going from 156Yb* to 172Yb* nuclear systems formed via near-symmetric Ni+Mo or asymmetric O+Sm colliding nuclei, except that for the oblate-shaped nuclei, the is the highest and shifts towards a smaller (compact) interaction radius. The temperature does not change the behavior of spin-orbit density dependent ( and independent ( interaction potentials, except for some minor changes in the magnitude. The orientation degree of freedom also plays an important role in modifying the barrier characteristics and hence produces a large effect on the fusion cross section. The fusion excitation function of the compound nuclei 160, 164Yb* formed in different incoming channels, show clearly that the new forces GSkI and KDE0v1 respond better than the old SIII force. Among the first two, KDE0v1 seems to perform better. The fusion cross-sections are also predicted for a few other isotopes of Yb*.

Congested Aggregation via Newtonian Interaction

NASA Astrophysics Data System (ADS)

Craig, Katy; Kim, Inwon; Yao, Yao

2018-01-01

We consider a congested aggregation model that describes the evolution of a density through the competing effects of nonlocal Newtonian attraction and a hard height constraint. This provides a counterpoint to existing literature on repulsive-attractive nonlocal interaction models, where the repulsive effects instead arise from an interaction kernel or the addition of diffusion. We formulate our model as the Wasserstein gradient flow of an interaction energy, with a penalization to enforce the constraint on the height of the density. From this perspective, the problem can be seen as a singular limit of the Keller-Segel equation with degenerate diffusion. Two key properties distinguish our problem from previous work on height constrained equations: nonconvexity of the interaction kernel (which places the model outside the scope of classical gradient flow theory) and nonlocal dependence of the velocity field on the density (which causes the problem to lack a comparison principle). To overcome these obstacles, we combine recent results on gradient flows of nonconvex energies with viscosity solution theory. We characterize the dynamics of patch solutions in terms of a Hele-Shaw type free boundary problem and, using this characterization, show that in two dimensions patch solutions converge to a characteristic function of a disk in the long-time limit, with an explicit rate on the decay of the energy. We believe that a key contribution of the present work is our blended approach, combining energy methods with viscosity solution theory.

Pressure effect on the energy structure and superexchange interaction in undoped orthorhombic La2CuO4

NASA Astrophysics Data System (ADS)

Gavrichkov, Vladimir A.; Pchelkina, Zlata V.; Nekrasov, Igor A.; Ovchinnikov, Sergey G.

2016-09-01

We studied the pressure dependences of the electronic structure and superexchange interaction J(P) = JA - JB (where JA and JB are antiferromagnetic (AFM) and ferromagnetic (FM) contributions) in antiferromagnetic La214 under hydrostatic, uniaxial (along c-axial) 3% compressions and 1% in-plane compressions by the local density approximation with generalized tight-binding method (LDA + GTB cell approach). The changes in J(P) correlated with the experimentally known TC(P) dependence are in accordance with the relation dTC/dP = (∂TC/∂J)(∂J/∂P), where ∂TC/∂J ˜ 0.1. The in-plane pressure more effectively stabilizes the ground singlet two-hole state A1 than the simple hydrostatic pressure, its effect on J and TC is the largest. Within the same cell approach together with the superexchange interaction J(P), the valence band structure was calculated. Its changes with pressure clearly reproduce the k-distribution of the singlet and triplet quasi-particles over the Brillouin zone (BZ).

Mean-field study of hot β -stable protoneutron star matter: Impact of the symmetry energy and nucleon effective mass

NASA Astrophysics Data System (ADS)

Tan, Ngo Hai; Loan, Doan Thi; Khoa, Dao T.; Margueron, Jerome

2016-03-01

A consistent Hartree-Fock study of the equation of state (EOS) of asymmetric nuclear matter at finite temperature has been performed using realistic choices of the effective, density-dependent nucleon-nucleon (NN ) interaction, which were successfully used in different nuclear structure and reaction studies. Given the importance of the nuclear symmetry energy in the neutron star formation, EOSs associated with different behaviors of the symmetry energy were used to study hot asymmetric nuclear matter. The slope of the symmetry energy and nucleon effective mass with increasing baryon density was found to affect the thermal properties of nuclear matter significantly. Different density-dependent NN interactions were further used to study the EOS of hot protoneutron star (PNS) matter of the n p e μ ν composition in β equilibrium. The hydrostatic configurations of PNS in terms of the maximal gravitational mass Mmax and radius, central density, pressure, and temperature at the total entropy per baryon S /A =1 ,2 , and 4 have been determined in both the neutrino-free and neutrino-trapped scenarios. The obtained results show consistently a strong impact of the symmetry energy and nucleon effective mass on thermal properties and composition of hot PNS matter. Mmax values obtained for the (neutrino-free) β -stable PNS at S /A =4 were used to assess time tBH of the collapse of a 40 M⊙ protoneutron progenitor to a black hole, based on a correlation between tBH and Mmax found from the hydrodynamic simulation by Hempel et al. [Astrophys. J. 748, 70 (2012), 10.1088/0004-637X/748/1/70].

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

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

Brémond, Éric; Corminboeuf, Clémence, E-mail: clemence.corminboeuf@epfl.ch; Golubev, Nikolay

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 pointmore » 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.« less

Effect of Culverts on Predator-Prey Interactions in a Tropical Stream.

NASA Astrophysics Data System (ADS)

Hein, C. L.; Kikkert, D. A.; Crowl, T. A.

2005-05-01

As part of a biocomplexity project in Puerto Rico, we use river and road networks as a platform to understand the interactions between stream biota, the physical environment, and human activity. Specifically, we ask if humans affect aquatic organisms through road building and recreational activities. Culverts have been documented to impede or slow migration of aquatic biota. This is especially important in these streams because all of the freshwater, stream species have diadramous life cycles. If culverts do act as bottlenecks to shrimp migrations, we expect altered predator-prey interactions downstream through density-dependent predation dynamics. In order to determine how roads may affect predation rates on upstream migrating shrimp, we parameterized functional response curves for mountain mullet (Agonostomus monticola) consuming shrimp (Xiphocaris sp.) using artificial mesocosm experiments. We then used data obtained from underwater videography to determine how culverts decrease the rate and number of shrimp moving upstream. These data were combined in a predator-prey model to quantify the effects of culverts on localized shrimp densities and fish predation.

Orthogonal fitness benefits of nitrogen and ants for nitrogen-limited plants in the presence of herbivores.

PubMed

Pringle, Elizabeth G; Ableson, Ian; Kerber, Jennifer; Vannette, Rachel L; Tao, Leiling

2017-12-01

Predictable effects of resource availability on plant growth-defense strategies provide a unifying theme in theories of direct anti-herbivore defense, but it is less clear how resource availability modulates plant indirect defense. Ant-plant-hemipteran interactions produce mutualistic trophic cascades when hemipteran-tending ants reduce total herbivory, and these interactions are a key component of plant indirect defense in most terrestrial ecosystems. Here we conducted an experiment to test how ant-plant-hemipteran interactions depend on nitrogen (N) availability by manipulating the presence of ants and aphids under different N fertilization treatments. Ants increased plant flowering success by decreasing the densities of herbivores, and the effects of ants on folivores were positively related to the density of aphids. Unexpectedly, N fertilization produced no changes in plant N concentrations. Plants grown in higher N grew and flowered more, but aphid honeydew chemistry stayed the same, and neither the density of aphids nor the rate of ant attraction per aphid changed with N addition. The positive effects of ants and N addition on plant fitness were thus independent of one another. We conclude that N was the plant's limiting nutrient and propose that addition of the limiting nutrient is unlikely to alter the strength of mutualistic trophic cascades. © 2017 by the Ecological Society of America.

Pollinator-mediated interactions in experimental arrays vary with neighbor identity.

PubMed

Ha, Melissa K; Ivey, Christopher T

2017-02-01

Local ecological conditions influence the impact of species interactions on evolution and community structure. We investigated whether pollinator-mediated interactions between coflowering plants vary with plant density, coflowering neighbor identity, and flowering season. We conducted a field experiment in which flowering time and floral neighborhood were manipulated in a factorial design. Early- and late-flowering Clarkia unguiculata plants were placed into arrays with C. biloba neighbors, noncongeneric neighbors, additional conspecific plants, or no additional plants as a density control. We compared whole-plant pollen limitation of seed set, pollinator behavior, and pollen deposition among treatments. Interactions mediated by shared pollinators depended on the identity of the neighbor and possibly changed through time, although flowering-season comparisons were compromised by low early-season plant survival. Interactions with conspecific neighbors were likely competitive late in the season. Interactions with C. biloba appeared to involve facilitation or neutral interactions. Interactions with noncongeners were more consistently competitive. The community composition of pollinators varied among treatment combinations. Pollinator-mediated interactions involved competition and likely facilitation, depending on coflowering neighbor. Experimental manipulation helped to reveal context-dependent variation in indirect biotic interactions. © 2017 Botanical Society of America.

Interaction Between New Anti-cancer Drug Syndros and CNT(6,6-6) Nanotube for Medical Applications: Geometry Optimization, Molecular Structure, Spectroscopic (NMR, UV/Vis, Excited state), FMO, MEP and HOMO-LUMO Investigation

NASA Astrophysics Data System (ADS)

Sheikhi, Masoome; Shahab, Siyamak; Khaleghian, Mehrnoosh; Kumar, Rakesh

2018-03-01

In the present work, Density Functional Theory (DFT) was first time employed to investigate the interaction between new drug (6aR,10aR)-6,6,9-trimethyl-3-pentyl-6a,7,8,10a-tetrahydrobenzo[c]chromen-1-ol (Syndros) and the CNT(6,6-6) Nanotube in the gaseous phase. The interaction effects of compounds Syndros and CNT (6,6-6) nanotube on the electronic properties, chemical shift tensors and natural charge was also determined and discussed. The electronic spectra of the Syndros and the complex CNT(6,6-6)/Syndros in the gas phase were calculated by Time Dependent Density Functional Theory (TD-DFT) for the formation of adsorption effect on maximum wavelength of the Syndros. Nucleus-Independent Chemical Shifts (NICS) calculations have also been carried out for the compound Syndors and the complex CNT(6,6-6)/Syndros and the aromaticity of the compound Syndors before and after interaction with the CNT(6,6-6) Nanotube was investigated.

Spatial dynamics of the 1918 influenza pandemic in England, Wales and the United States.

PubMed

Eggo, Rosalind M; Cauchemez, Simon; Ferguson, Neil M

2011-02-06

There is still limited understanding of key determinants of spatial spread of influenza. The 1918 pandemic provides an opportunity to elucidate spatial determinants of spread on a large scale. To better characterize the spread of the 1918 major wave, we fitted a range of city-to-city transmission models to mortality data collected for 246 population centres in England and Wales and 47 cities in the US. Using a gravity model for city-to-city contacts, we explored the effect of population size and distance on the spread of disease and tested assumptions regarding density dependence in connectivity between cities. We employed Bayesian Markov Chain Monte Carlo methods to estimate parameters of the model for population, infectivity, distance and density dependence. We inferred the most likely transmission trees for both countries. For England and Wales, a model that estimated the degree of density dependence in connectivity between cities was preferable by deviance information criterion comparison. Early in the major wave, long distance infective interactions predominated, with local infection events more likely as the epidemic became widespread. For the US, with fewer more widely dispersed cities, statistical power was lacking to estimate population size dependence or the degree of density dependence, with the preferred model depending on distance only. We find that parameters estimated from the England and Wales dataset can be applied to the US data with no likelihood penalty.

Spatial dynamics of the 1918 influenza pandemic in England, Wales and the United States

PubMed Central

Eggo, Rosalind M.; Cauchemez, Simon; Ferguson, Neil M.

2011-01-01

There is still limited understanding of key determinants of spatial spread of influenza. The 1918 pandemic provides an opportunity to elucidate spatial determinants of spread on a large scale. To better characterize the spread of the 1918 major wave, we fitted a range of city-to-city transmission models to mortality data collected for 246 population centres in England and Wales and 47 cities in the US. Using a gravity model for city-to-city contacts, we explored the effect of population size and distance on the spread of disease and tested assumptions regarding density dependence in connectivity between cities. We employed Bayesian Markov Chain Monte Carlo methods to estimate parameters of the model for population, infectivity, distance and density dependence. We inferred the most likely transmission trees for both countries. For England and Wales, a model that estimated the degree of density dependence in connectivity between cities was preferable by deviance information criterion comparison. Early in the major wave, long distance infective interactions predominated, with local infection events more likely as the epidemic became widespread. For the US, with fewer more widely dispersed cities, statistical power was lacking to estimate population size dependence or the degree of density dependence, with the preferred model depending on distance only. We find that parameters estimated from the England and Wales dataset can be applied to the US data with no likelihood penalty. PMID:20573630

Peculiarities of magnetic and spin effects in a biradical/stable radical complex (three-spin system). Theory and comparison with experiment.

PubMed

Magin, Ilya M; Purtov, Petr A; Kruppa, Alexander I; Leshina, Tatiana V

2005-08-25

The field dependencies of biradical recombination probability in the presence of paramagnetic species with spins S(3) = 1 and S(3) = (1)/(2) have been calculated in the framework of the density matrix formalism. To describe the effect of the "third" spin on the spin evolution in biradical, we have also considered the spin exchange interaction between the added spin and one of the paramagnetic biradical centers. A characteristic feature of the calculated field dependencies is the existence of several extrema with positions and magnitudes depending on the signs and values of the exchange integrals in the system. The method proposed can be used to describe the effect of spin catalysis. It is shown that for the system with the third spin S(3) = 1 spin catalysis manifests itself stronger than in the case of spin S(3) = (1)/(2). The dependence of spin catalysis efficiency on the exchange interaction with the third spin has an extremum with position independent of the value of the spin added.

Interaction between Water and Wind as a Driver of Passive Dispersal in Mangroves

PubMed Central

Van der Stocken, Tom; Vanschoenwinkel, Bram; De Ryck, Dennis J. R.; Bouma, Tjeerd J.; Dahdouh-Guebas, Farid; Koedam, Nico

2015-01-01

Although knowledge on dispersal patterns is essential for predicting long-term population dynamics, critical information on the modalities of passive dispersal and potential interactions between vectors is often missing. Here, we use mangrove propagules with a wide variety of morphologies to investigate the interaction between water and wind as a driver of passive dispersal. We imposed 16 combinations of wind and hydrodynamic conditions in a flume tank, using propagules of six important mangrove species (and genera), resulting in a set of dispersal morphologies that covers most variation present in mangrove propagules worldwide. Additionally, we discussed the broader implications of the outcome of this flume study on the potential of long distance dispersal for mangrove propagules in nature, applying a conceptual model to a natural mangrove system in Gazi Bay (Kenya). Overall, the effect of wind on dispersal depended on propagule density (g l-1). The low-density Heritiera littoralis propagules were most affected by wind, while the high-density vertically floating propagules of Ceriops tagal and Bruguiera gymnorrhiza were least affected. Avicennia marina, and horizontally floating Rhizophora mucronata and C. tagal propagules behaved similarly. Morphological propagule traits, such as the dorsal sail of H. littoralis, explained another part of the interspecific differences. Within species, differences in dispersal velocities can be explained by differences in density and for H. littoralis also by variations in the shape of the dorsal sail. Our conceptual model illustrates that different propagule types have a different likelihood of reaching the open ocean depending on prevailing water and wind currents. Results suggest that in open water, propagule traits (density, morphology, and floating orientation) appear to determine the effect of water and wind currents on dispersal dynamics. This has important implications for inter- and intraspecific variation in dispersal patterns and the likelihood of reaching suitable habitat patches within a propagule's viable period. PMID:25811191

Two-body contributions to the effective mass in nuclear effective interactions

NASA Astrophysics Data System (ADS)

Davesne, D.; Navarro, J.; Meyer, J.; Bennaceur, K.; Pastore, A.

2018-04-01

Starting from general expressions of well-chosen symmetric nuclear matter quantities derived for both zero- and finite-range effective theories, we derive some universal relations between them. We first show that, independently of the range, the two-body contribution is enough to describe correctly the saturation mechanism but gives an effective mass value around m*/m ≃0.4 when the other properties of the saturation point are set near their generally accepted values. Then, we show that a more elaborated interaction (for instance, an effective two-body density-dependent term on top of the pure two-body term) is needed to reach the accepted value m*/m ≃0.7 -0.8 .

Global analysis of Skyrme forces with higher-order density dependencies

NASA Astrophysics Data System (ADS)

Zuo, Zhi-Wei; Pei, Jun-Chen; Xiong, Xue-Yu; Zhu, Yi

2018-05-01

The density-dependent term in Skyrme forces is essential to simulate three-body and many-body correlations beyond the low-momentum two-body interaction. We speculate that a single density term may be insufficient and a higher-order density dependent term is added. The present work investigates the influence of higher-order density dependencies based on extended UNEDF0 and SkM* forces. Global descriptions of nuclear masses and charge radii are presented. The extended UNEDF0 force gives a global rms error on binding energies of 1.29 MeV. The influence on fission barriers and equation of state are also investigated. Perspectives to improve Skyrme forces are discussed, including global center-of-mass corrections and Lipkin-Nogami pairing corrections. Supported by National Natural Science Foundation of China (11522538)

The correlation between fragility, density, and atomic interaction in glass-forming liquids

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

Wang, Lijin; Guan, Pengfei, E-mail: pguan@csrc.ac.cn; Wang, W. H.

2016-07-21

The fragility that controls the temperature-dependent viscous properties of liquids as the glass transition is approached, in various glass-forming liquids with different softness of the repulsive part of atomic interactions at different densities, is investigated by molecular dynamic simulations. We show that the landscape of fragility in purely repulsive systems can be separated into three regions denoted as R{sub I,} R{sub II}, and R{sub III}, respectively, with qualitatively disparate dynamic behaviors: R{sub I} which can be described by “softness makes strong glasses,” R{sub II} where fragility is independent of softness and can only be tuned by density, and R{sub III}more » with constant fragility, suggesting that density plays an unexpected role for understanding the repulsive softness dependence of fragility. What is more important is that we unify the long-standing inconsistence with respect to the repulsive softness dependence of fragility by observing that a glass former can be tuned more fragile if nonperturbative attraction is added into it. Moreover, we find that the vastly dissimilar influences of attractive interaction on fragility could be estimated from the structural properties of related zero-temperature glasses.« less

Molecular electrostatic potential and "atoms-in-molecules" analyses of the interplay between π-hole and lone pair···π/X-H···π/metal···π interactions.

PubMed

Bauzá, Antonio; Seth, Saikat Kumar; Frontera, Antonio

2018-04-05

Using ab initio calculations, we analyze the interplay between π-hole interactions involving the nitro group of 1,4-dinitrobenzene and lone pair···π (lp···π), C-H···π or metal(M)···π noncovalent interactions. Moreover, we have also used 1,4-phenylenebis(phosphine dioxide) for comparison purposes. Interesting cooperativity effects are found when π-hole (F···N,P) and lp···π/C-H···π/M···π interactions coexist in the same supramolecular assembly. These effects are studied theoretically in terms of energetic and geometric features of the complexes, which are computed by ab initio methods (RI-MP2/def2-TZVP). A charge density analysis using the Bader's theory of "atoms in molecules" is carried out to characterize the interactions and to analyze their strengthening or weakening depending on the variation of charge density at critical points. The importance of electrostatic effects on the mutual influence of the interaction is studied by means of molecular electrostatic potential calculations. By taking advantage of these computational tools, the present study examines interplay of these interactions. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Intercohort density dependence drives brown trout habitat selection

NASA Astrophysics Data System (ADS)

Ayllón, Daniel; Nicola, Graciela G.; Parra, Irene; Elvira, Benigno; Almodóvar, Ana

2013-01-01

Habitat selection can be viewed as an emergent property of the quality and availability of habitat but also of the number of individuals and the way they compete for its use. Consequently, habitat selection can change across years due to fluctuating resources or to changes in population numbers. However, habitat selection predictive models often do not account for ecological dynamics, especially density dependent processes. In stage-structured population, the strength of density dependent interactions between individuals of different age classes can exert a profound influence on population trajectories and evolutionary processes. In this study, we aimed to assess the effects of fluctuating densities of both older and younger competing life stages on the habitat selection patterns (described as univariate and multivariate resource selection functions) of young-of-the-year, juvenile and adult brown trout Salmo trutta. We observed all age classes were selective in habitat choice but changed their selection patterns across years consistently with variations in the densities of older but not of younger age classes. Trout of an age increased selectivity for positions highly selected by older individuals when their density decreased, but this pattern did not hold when the density of younger age classes varied. It suggests that younger individuals are dominated by older ones but can expand their range of selected habitats when density of competitors decreases, while older trout do not seem to consider the density of younger individuals when distributing themselves even though they can negatively affect their final performance. Since these results may entail critical implications for conservation and management practices based on habitat selection models, further research should involve a wider range of river typologies and/or longer time frames to fully understand the patterns of and the mechanisms underlying the operation of density dependence on brown trout habitat selection.

Analytical nuclear gradients for the range-separated many-body dispersion model of noncovalent interactions.

PubMed

Blood-Forsythe, Martin A; Markovich, Thomas; DiStasio, Robert A; Car, Roberto; Aspuru-Guzik, Alán

2016-03-01

An accurate treatment of the long-range electron correlation energy, including van der Waals (vdW) or dispersion interactions, is essential for describing the structure, dynamics, and function of a wide variety of systems. Among the most accurate models for including dispersion into density functional theory (DFT) is the range-separated many-body dispersion (MBD) method [A. Ambrosetti et al. , J. Chem. Phys. , 2014, 140 , 18A508], in which the correlation energy is modeled at short-range by a semi-local density functional and at long-range by a model system of coupled quantum harmonic oscillators. In this work, we develop analytical gradients of the MBD energy with respect to nuclear coordinates, including all implicit coordinate dependencies arising from the partitioning of the charge density into Hirshfeld effective volumes. To demonstrate the efficiency and accuracy of these MBD gradients for geometry optimizations of systems with intermolecular and intramolecular interactions, we optimized conformers of the benzene dimer and isolated small peptides with aromatic side-chains. We find excellent agreement with the wavefunction theory reference geometries of these systems (at a fraction of the computational cost) and find that MBD consistently outperforms the popular TS and D3(BJ) dispersion corrections. To demonstrate the performance of the MBD model on a larger system with supramolecular interactions, we optimized the C 60 @C 60 H 28 buckyball catcher host-guest complex. In our analysis, we also find that neglecting the implicit nuclear coordinate dependence arising from the charge density partitioning, as has been done in prior numerical treatments, leads to an unacceptable error in the MBD forces, with relative errors of ∼20% (on average) that can extend well beyond 100%.

DENSITY-DEPENDENT EVOLUTION OF LIFE-HISTORY TRAITS IN DROSOPHILA MELANOGASTER.

PubMed

Bierbaum, Todd J; Mueller, Laurence D; Ayala, Francisco J

1989-03-01

Populations of Drosophila melanogaster were maintained for 36 generations in r- and K-selected environments in order to test the life-history predictions of theories on density-dependent selection. In the r-selection environment, populations were reduced to low densities by density-independent adult mortality, whereas populations in the K-selection environment were maintained at their carrying capacity. Some of the experimental results support the predictions or r- and K-selection theory; relative to the r-selected populations, the K-selected populations evolved an increased larval-to-adult viability, larger body size, and longer development time at high larval densities. Mueller and Ayala (1981) found that K-selected populations also have a higher rate of population growth at high densities. Other predictions of the thoery are contradicted by the lack of differences between the r and K populations in adult longevity and fecundity and a slower rate of development for r-selected individuals at low densities. The differences between selected populations in larval survivorship, larval-to-adult development time, and adult body size are strongly dependent on larval density, and there is a significant interaction between populations and larval density for each trait. This manifests an inadequacy of the theory on r- and K-selection, which does not take into account such interactions between genotypes and environments. We describe mechanisms that may explain the evolution of preadult life-history traits in our experiment and discuss the need for changes in theories of density-dependent selection. © 1989 The Society for the Study of Evolution.

Time-dependent i-DFT exchange-correlation potentials with memory: applications to the out-of-equilibrium Anderson model

NASA Astrophysics Data System (ADS)

Kurth, Stefan; Stefanucci, Gianluca

2018-06-01

We have recently put forward a steady-state density functional theory (i-DFT) to calculate the transport coefficients of quantum junctions. Within i-DFT it is possible to obtain the steady density on and the steady current through an interacting junction using a fictitious noninteracting junction subject to an effective gate and bias potential. In this work we extend i-DFT to the time domain for the single-impurity Anderson model. By a reverse engineering procedure we extract the exchange-correlation (xc) potential and xc bias at temperatures above the Kondo temperature T K. The derivation is based on a generalization of a recent paper by Dittmann et al. [N. Dittmann et al., Phys. Rev. Lett. 120, 157701 (2018)]. Interestingly the time-dependent (TD) i-DFT potentials depend on the system's history only through the first time-derivative of the density. We perform numerical simulations of the early transient current and investigate the role of the history dependence. We also empirically extend the history-dependent TD i-DFT potentials to temperatures below T K. For this purpose we use a recently proposed parametrization of the i-DFT potentials which yields highly accurate results in the steady state.

Refractive index and solubility control of para-cymene solutions for index-matched fluid-structure interaction studies

NASA Astrophysics Data System (ADS)

Fort, Charles; Fu, Christopher D.; Weichselbaum, Noah A.; Bardet, Philippe M.

2015-12-01

To deploy optical diagnostics such as particle image velocimetry or planar laser-induced fluorescence (PLIF) in complex geometries, it is beneficial to use index-matched facilities. A binary mixture of para-cymene and cinnamaldehyde provides a viable option for matching the refractive index of acrylic, a common material for scaled models and test sections. This fluid is particularly appropriate for large-scale facilities and when a low-density and low-viscosity fluid is sought, such as in fluid-structure interaction studies. This binary solution has relatively low kinematic viscosity and density; its use enables the experimentalist to select operating temperature and to increase fluorescence signal in PLIF experiments. Measurements of spectral and temperature dependence of refractive index, density, and kinematic viscosity are reported. The effect of the binary mixture on solubility control of Rhodamine 6G is also characterized.

Resolution-of-identity stochastic time-dependent configuration interaction for dissipative electron dynamics in strong fields.

PubMed

Klinkusch, Stefan; Tremblay, Jean Christophe

2016-05-14

In this contribution, we introduce a method for simulating dissipative, ultrafast many-electron dynamics in intense laser fields. The method is based on the norm-conserving stochastic unraveling of the dissipative Liouville-von Neumann equation in its Lindblad form. The N-electron wave functions sampling the density matrix are represented in the basis of singly excited configuration state functions. The interaction with an external laser field is treated variationally and the response of the electronic density is included to all orders in this basis. The coupling to an external environment is included via relaxation operators inducing transition between the configuration state functions. Single electron ionization is represented by irreversible transition operators from the ionizing states to an auxiliary continuum state. The method finds its efficiency in the representation of the operators in the interaction picture, where the resolution-of-identity is used to reduce the size of the Hamiltonian eigenstate basis. The zeroth-order eigenstates can be obtained either at the configuration interaction singles level or from a time-dependent density functional theory reference calculation. The latter offers an alternative to explicitly time-dependent density functional theory which has the advantage of remaining strictly valid for strong field excitations while improving the description of the correlation as compared to configuration interaction singles. The method is tested on a well-characterized toy system, the excitation of the low-lying charge transfer state in LiCN.

Resolution-of-identity stochastic time-dependent configuration interaction for dissipative electron dynamics in strong fields

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

Klinkusch, Stefan; Tremblay, Jean Christophe

In this contribution, we introduce a method for simulating dissipative, ultrafast many-electron dynamics in intense laser fields. The method is based on the norm-conserving stochastic unraveling of the dissipative Liouville-von Neumann equation in its Lindblad form. The N-electron wave functions sampling the density matrix are represented in the basis of singly excited configuration state functions. The interaction with an external laser field is treated variationally and the response of the electronic density is included to all orders in this basis. The coupling to an external environment is included via relaxation operators inducing transition between the configuration state functions. Single electronmore » ionization is represented by irreversible transition operators from the ionizing states to an auxiliary continuum state. The method finds its efficiency in the representation of the operators in the interaction picture, where the resolution-of-identity is used to reduce the size of the Hamiltonian eigenstate basis. The zeroth-order eigenstates can be obtained either at the configuration interaction singles level or from a time-dependent density functional theory reference calculation. The latter offers an alternative to explicitly time-dependent density functional theory which has the advantage of remaining strictly valid for strong field excitations while improving the description of the correlation as compared to configuration interaction singles. The method is tested on a well-characterized toy system, the excitation of the low-lying charge transfer state in LiCN.« less

Evolution of the characteristics of Parametric X-ray Radiation from textured polycrystals under different observation angles

NASA Astrophysics Data System (ADS)

Alekseev, V. I.; Eliseyev, A. N.; Irribarra, E.; Kishin, I. A.; Klyuev, A. S.; Kubankin, A. S.; Nazhmudinov, R. M.; Zhukova, P. N.

2018-02-01

The Parametric X-Ray radiation (PXR) spectra and yield dependencies on the orientation angle are measured during the interaction of 7 MeV electrons with a tungsten textured polycrystalline foil for different observation angles. The effects of PXR spectral density increase and PXR yield orientation dependence broadening in the backward direction is shown experimentally for the first time. The experimental results are compared with PXR kinematical theories for both mosaic crystals and polycrystals.

Emergence of Lévy walks in systems of interacting individuals

NASA Astrophysics Data System (ADS)

Fedotov, Sergei; Korabel, Nickolay

2017-03-01

We propose a model of superdiffusive Lévy walk as an emergent nonlinear phenomenon in systems of interacting individuals. The aim is to provide a qualitative explanation of recent experiments [G. Ariel et al., Nat. Commun. 6, 8396 (2015), 10.1038/ncomms9396] revealing an intriguing behavior: swarming bacteria fundamentally change their collective motion from simple diffusion into a superdiffusive Lévy walk dynamics. We introduce microscopic mean-field kinetic equations in which we combine two key ingredients: (1) alignment interactions between individuals and (2) non-Markovian effects. Our interacting run-and-tumble model leads to the superdiffusive growth of the mean-squared displacement and the power-law distribution of run length with infinite variance. The main result is that the superdiffusive behavior emerges as a cooperative effect without using the standard assumption of the power-law distribution of run distances from the inception. At the same time, we find that the collision and repulsion interactions lead to the density-dependent exponential tempering of power-law distributions. This qualitatively explains the experimentally observed transition from superdiffusion to the diffusion of mussels as their density increases [M. de Jager et al., Proc. R. Soc. B 281, 20132605 (2014), 10.1098/rspb.2013.2605].

Dependence of interfacial Dzyaloshinskii-Moriya interaction and perpendicular magnetic anisotropy on the thickness of the heavy-metal layer

NASA Astrophysics Data System (ADS)

Kim, Nam-Hui; Han, Dong-Soo; Jung, Jinyong; Park, Kwonjin; Swagten, Henk J. M.; Kim, June-Seo; You, Chun-Yeol

2017-10-01

The interfacial Dzyaloshinskii-Moriya interaction (iDMI) and the interfacial perpendicular magnetic anisotropy (iPMA) between a heavy metal and ferromagnet are investigated by employing Brillouin light scattering. With increasing thickness of the heavy-metal (Pt) layer, the iDMI and iPMA energy densities are rapidly enhanced and they saturate for a Pt thickness of 2.4 nm. Since these two individual magnetic properties show the same Pt thickness dependence, this is evidence that the iDMI and iPMA at the interface between the heavy metal and ferromagnet, the physical origin of these phenomena, are effectively enhanced upon increasing the thickness of the heavy-metal layer.

Effects of density on growth, metamorphosis, and survivorship in tadpoles of Scaphiopus holbrooki

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

Semlitsch, R.D.; Caldwell, J.P.

1982-08-01

Density-dependent aspects of growth, metamorphosis, and survivorship of Scaphiopus holbrooki tadpoles were examined in the laboratory under two experimental regimes. In the first density experiment, the growth index (W) of tadpoles decreased exponentially with density. Mean growth rate varied from 0.023 mL/d at the lowest density to 0.006 mL/d at the highest density. The mean number of days to metamorphic climax was positively associated with the initial density treatment: 27 d at the lowest density to 86 d at the highest density. The body size of tadpoles at metamorphosis showed a concave curvilinear relationship to initial density, indicating tadpoles atmore » the highest densities are apparently capable to growth recovery once released from density stress. The survival of tadpoles decreased exponentially with initial density, from 90% at the lowest density to 20% at the highest initial density. In the second experiment a cross-classified design was used to examine the effects of density and duration of treatment (time) on growth and metamorphosis. Density and time had significant effects on body size at metamorphosis and days to metamorphosis. There was no significant interaction between density and time. These results indicate that the inhibitory effect of density stress varies with the duration of the stress. Scaphiopus holbrooki tadpoles exhibit developmental traits (rapid growth, short larval period, small body size at metamorphosis) that should be favored by natural selection in high density habitats. Dispersability may be a mechanism whereby S. holbrooki can minimize the detrimental effects of density stress.« less

Universal Low-energy Behavior in a Quantum Lorentz Gas with Gross-Pitaevskii Potentials

NASA Astrophysics Data System (ADS)

Basti, Giulia; Cenatiempo, Serena; Teta, Alessandro

2018-06-01

We consider a quantum particle interacting with N obstacles, whose positions are independently chosen according to a given probability density, through a two-body potential of the form N 2 V ( N x) (Gross-Pitaevskii potential). We show convergence of the N dependent one-particle Hamiltonian to a limiting Hamiltonian where the quantum particle experiences an effective potential depending only on the scattering length of the unscaled potential and the density of the obstacles. In this sense our Lorentz gas model exhibits a universal behavior for N large. Moreover we explicitely characterize the fluctuations around the limit operator. Our model can be considered as a simplified model for scattering of slow neutrons from condensed matter.

Can time-dependent density functional theory predict intersystem crossing in organic chromophores? A case study on benzo(bis)-X-diazole based donor-acceptor-donor type molecules.

PubMed

Tam, Teck Lip Dexter; Lin, Ting Ting; Chua, Ming Hui

2017-06-21

Here we utilized new diagnostic tools in time-dependent density functional theory to explain the trend of intersystem crossing in benzo(bis)-X-diazole based donor-acceptor-donor type molecules. These molecules display a wide range of fluorescence quantum yields and triplet yields, making them excellent candidates for testing the validity of these diagnostic tools. We believe that these tools are cost-effective and can be applied to structurally similar organic chromophores to predict/explain the trends of intersystem crossing, and thus fluorescence quantum yields and triplet yields without the use of complex and expensive multireference configuration interaction or multireference pertubation theory methods.

Capturing contextual effects in spectro-temporal receptive fields.

PubMed

Westö, Johan; May, Patrick J C

2016-09-01

Spectro-temporal receptive fields (STRFs) are thought to provide descriptive images of the computations performed by neurons along the auditory pathway. However, their validity can be questioned because they rely on a set of assumptions that are probably not fulfilled by real neurons exhibiting contextual effects, that is, nonlinear interactions in the time or frequency dimension that cannot be described with a linear filter. We used a novel approach to investigate how a variety of contextual effects, due to facilitating nonlinear interactions and synaptic depression, affect different STRF models, and if these effects can be captured with a context field (CF). Contextual effects were incorporated in simulated networks of spiking neurons, allowing one to define the true STRFs of the neurons. This, in turn, made it possible to evaluate the performance of each STRF model by comparing the estimations with the true STRFs. We found that currently used STRF models are particularly poor at estimating inhibitory regions. Specifically, contextual effects make estimated STRFs dependent on stimulus density in a contrasting fashion: inhibitory regions are underestimated at lower densities while artificial inhibitory regions emerge at higher densities. The CF was found to provide a solution to this dilemma, but only when it is used together with a generalized linear model. Our results therefore highlight the limitations of the traditional STRF approach and provide useful recipes for how different STRF models and stimuli can be used to arrive at reliable quantifications of neural computations in the presence of contextual effects. The results therefore push the purpose of STRF analysis from simply finding an optimal stimulus toward describing context-dependent computations of neurons along the auditory pathway. Copyright © 2016 Elsevier B.V. All rights reserved.

Native Contact Density and Nonnative Hydrophobic Effects in the Folding of Bacterial Immunity Proteins

PubMed Central

Chen, Tao; Chan, Hue Sun

2015-01-01

The bacterial colicin-immunity proteins Im7 and Im9 fold by different mechanisms. Experimentally, at pH 7.0 and 10°C, Im7 folds in a three-state manner via an intermediate but Im9 folding is two-state-like. Accordingly, Im7 exhibits a chevron rollover, whereas the chevron arm for Im9 folding is linear. Here we address the biophysical basis of their different behaviors by using native-centric models with and without additional transferrable, sequence-dependent energies. The Im7 chevron rollover is not captured by either a pure native-centric model or a model augmented by nonnative hydrophobic interactions with a uniform strength irrespective of residue type. By contrast, a more realistic nonnative interaction scheme that accounts for the difference in hydrophobicity among residues leads simultaneously to a chevron rollover for Im7 and an essentially linear folding chevron arm for Im9. Hydrophobic residues identified by published experiments to be involved in nonnative interactions during Im7 folding are found to participate in the strongest nonnative contacts in this model. Thus our observations support the experimental perspective that the Im7 folding intermediate is largely underpinned by nonnative interactions involving large hydrophobics. Our simulation suggests further that nonnative effects in Im7 are facilitated by a lower local native contact density relative to that of Im9. In a one-dimensional diffusion picture of Im7 folding with a coordinate- and stability-dependent diffusion coefficient, a significant chevron rollover is consistent with a diffusion coefficient that depends strongly on native stability at the conformational position of the folding intermediate. PMID:26016652

Ordering nanoparticles with polymer brushes

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

Cheng, Shengfeng; Stevens, Mark J.; Grest, Gary S.

Ordering nanoparticles into a desired super-structure is often crucial for their technological applications. We use molecular dynamics simulations to study the assembly of nanoparticles in a polymer brush randomly grafted to a planar surface as the solvent evaporates. Initially, the nanoparticles are dispersed in a solvent that wets the polymer brush. After the solvent evaporates, the nanoparticles are either inside the brush or adsorbed at the surface of the brush, depending on the strength of the nanoparticle-polymer interaction. For strong nanoparticle-polymer interactions, a 2-dimensional ordered array is only formed when the brush density is finely tuned to accommodate a singlemore » layer of nanoparticles. When the brush density is higher or lower than this optimal value, the distribution of nanoparticles shows large fluctuations in space and the packing order diminishes. For weak nanoparticle-polymer interactions, the nanoparticles order into a hexagonal array on top of the polymer brush as long as the grafting density is high enough to yield a dense brush. As a result, an interesting healing effect is observed for a low-grafting-density polymer brush that can become more uniform in the presence of weakly adsorbed nanoparticles.« less

Ordering nanoparticles with polymer brushes

DOE PAGES

Cheng, Shengfeng; Stevens, Mark J.; Grest, Gary S.

2017-12-08

Ordering nanoparticles into a desired super-structure is often crucial for their technological applications. We use molecular dynamics simulations to study the assembly of nanoparticles in a polymer brush randomly grafted to a planar surface as the solvent evaporates. Initially, the nanoparticles are dispersed in a solvent that wets the polymer brush. After the solvent evaporates, the nanoparticles are either inside the brush or adsorbed at the surface of the brush, depending on the strength of the nanoparticle-polymer interaction. For strong nanoparticle-polymer interactions, a 2-dimensional ordered array is only formed when the brush density is finely tuned to accommodate a singlemore » layer of nanoparticles. When the brush density is higher or lower than this optimal value, the distribution of nanoparticles shows large fluctuations in space and the packing order diminishes. For weak nanoparticle-polymer interactions, the nanoparticles order into a hexagonal array on top of the polymer brush as long as the grafting density is high enough to yield a dense brush. As a result, an interesting healing effect is observed for a low-grafting-density polymer brush that can become more uniform in the presence of weakly adsorbed nanoparticles.« less

Dynamical role of predators in population cycles of a forest insect: an experimental test.

Treesearch

P. Turchin; A.D. Taylor; J.D. Reeve

1999-01-01

Population cycles occur frequently in forest insects.Time-series analysis of fluctuations in one such insect, the southern pine beetle (Dendroctonus frontalis), suggests that beetle dynamics are dominated by an ecological process acting in a delayed density-dependent manner.The hypothesis that delayed density-dependence in this insect results from its interaction with...

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

PubMed

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

2016-02-01

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

Spatially nonrandom tree mortality and ingrowth maintain equilibrium pattern in an old-growth Pseudotsuga-Tsuga forest.

PubMed

Lutz, James A; Larson, Andrew J; Furniss, Tucker J; Donato, Daniel C; Freund, James A; Swanson, Mark E; Bible, Kenneth J; Chen, Jiquan; Franklin, Jerry F

2014-08-01

Mortality processes in old-growth forests are generally assumed to be driven by gap-scale disturbance, with only a limited role ascribed to density-dependent mortality, but these assumptions are rarely tested with data sets incorporating repeated measurements. Using a 12-ha spatially explicit plot censused 13 years apart in an approximately 500-year-old Pseudotsuga-Tsuga forest, we demonstrate significant density-dependent mortality and spatially aggregated tree recruitment. However, the combined effect of these strongly nonrandom demographic processes was to maintain tree patterns in a state of dynamic equilibrium. Density-dependent mortality was most pronounced for the dominant late-successional species, Tsuga heterophylla. The long-lived, early-seral Pseudotsuga menziesii experienced an annual stem mortality rate of 0.84% and no new recruitment. Late-seral species Tsuga and Abies amabilis had nearly balanced demographic rates of ingrowth and mortality. The 2.34% mortality rate for Taxus brevifolia was higher than expected, notably less than ingrowth, and strongly affected by proximity to Tsuga. Large-diameter Tsuga structured both the regenerating conspecific and heterospecific cohorts with recruitment of Tsuga and Abies unlikely in neighborhoods crowded with large-diameter competitors (P < 0.001). Density-dependent competitive interactions strongly shape forest communities even five centuries after stand initiation, underscoring the dynamic nature of even equilibrial old-growth forests.

Biophotonic patterns of optical interactions between fish eggs and embryos.

PubMed

Beloussov, L V; Burlakov, A B; Louchinskaia, N N

2003-05-01

The optical (non-substantial) interactions between various biological samples have been evident in a number of cases mainly by the effects on their functional activity and developmental patterns. However, the mechanisms of these interactions have remained obscure. Effect of optical interaction has been observed on the intensity and Fourier patterns of biophoton emission of fish embryos. We demonstrate that: (1) the short-term optical interactions are accompanied by a gradual decrease of a total emission intensity of the interacting batches; (2) this effect is spread laterally to that part of a batch which does not have any direct optical contacts with its partner; and (3) the long-term optical contacts lead to a mutual exchange of spectral characteristics of interacting batches in which the total spectral density values are reversed (often with an overshoot). The reversal rate depends upon the developmental distance between the optical partners and the initial differences of their spectral characteristics. The results are discussed in terms of a sub-radiance and Le Chatelier principle.

Two-leg ladder systems with dipole–dipole Fermion interactions

NASA Astrophysics Data System (ADS)

Mosadeq, Hamid; Asgari, Reza

2018-05-01

The ground-state phase diagram of a two-leg fermionic dipolar ladder with inter-site interactions is studied using density matrix renormalization group (DMRG) techniques. We use a state-of-the-art implementation of the DMRG algorithm and finite size scaling to simulate large system sizes with high accuracy. We also consider two different model systems and explore stable phases in half and quarter filling factors. We find that in the half filling, the charge and spin gaps emerge in a finite value of the dipole–dipole and on-site interactions. In the quarter filling case, s-wave superconducting state, charge density wave, homogenous insulating and phase separation phases occur depend on the interaction values. Moreover, in the dipole–dipole interaction, the D-Mott phase emerges when the hopping terms along the chain and rung are the same, whereas, this phase has been only proposed for the anisotropic Hubbard model. In the half filling case, on the other hand, there is either charge-density wave or charged Mott order phase depends on the orientation of the dipole moments of the particles with respect to the ladder geometry.

Particle Trapping Mechanisms Are Different in Spatially Ordered and Disordered Interacting Gels.

PubMed

Hansing, Johann; Netz, Roland R

2018-06-05

Using stochastic simulations, we study the influence of spatial disorder on the diffusion of a single particle through a gel that consists of rigid, straight fibers. The interaction between the particle and the gel fibers consists of an invariant short-range repulsion, the steric part, and an interaction part that can be attractive or repulsive and of varying range. The effect that spatial disorder of the gel structure has on the particle diffusivity depends crucially on the presence of nonsteric interactions. For attractive interactions, disorder slows down diffusion, because in disordered gels, the particle becomes strongly trapped in regions of locally increased fiber density. For repulsive interactions, the diffusivity is minimal for intermediate disorder strength, because highly disordered lattices exhibit abundant passageways of locally low fiber density. The comparison with experimental data on protein and fluorophore diffusion through various hydrogels is favorable. Our findings shed light on particle-diffusion mechanisms in biogels and thus on biological barrier properties, which can be helpful for the optimal design of synthetic diffusors as well as synthetic mucus constructs. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Optical conductivity of an interacting Weyl liquid in the collisionless regime

NASA Astrophysics Data System (ADS)

Roy, Bitan; Juričić, Vladimir

2017-10-01

Optical conductivity (OC) can serve as a measure of correlation effects in a wide range of condensed-matter systems. We show that the long-range tail of the Coulomb interaction yields a universal correction to the OC in a three-dimensional Weyl semimetal σ (Ω ) =σ0(Ω ) [1 +1/N +1 ] , where σ0(Ω ) =N e02Ω /(12 h v ) is the OC in the noninteracting system, with v as the actual (renormalized) Fermi velocity of Weyl quasiparticles at frequency Ω , and e0 is the electron charge in vacuum. Such universal enhancement of OC, which depends only on the number of Weyl nodes near the Fermi level (N ), is a remarkable consequence of an intriguing conspiracy among the quantum-critical nature of an interacting Weyl liquid, marginal irrelevance of the long-range Coulomb interaction, and violation of hyperscaling in three dimensions, and can directly be measured in recently discovered Weyl as well as Dirac materials. By contrast, a local density-density interaction produces a nonuniversal correction to the OC, stemming from the nonrenormalizable nature of the corresponding interacting field theory.

Self-interaction-corrected time-dependent density-functional-theory calculations of x-ray-absorption spectra

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

Tu, Guangde; Rinkevicius, Zilvinas; Vahtras, Olav

We outline an approach within time-dependent density functional theory that predicts x-ray spectra on an absolute scale. The approach rests on a recent formulation of the resonant-convergent first-order polarization propagator [P. Norman et al., J. Chem. Phys. 123, 194103 (2005)] and corrects for the self-interaction energy of the core orbital. This polarization propagator approach makes it possible to directly calculate the x-ray absorption cross section at a particular frequency without explicitly addressing the excited-state spectrum. The self-interaction correction for the employed density functional accounts for an energy shift of the spectrum, and fully correlated absolute-scale x-ray spectra are thereby obtainedmore » based solely on optimization of the electronic ground state. The procedure is benchmarked against experimental spectra of a set of small organic molecules at the carbon, nitrogen, and oxygen K edges.« less

Effect of Interaction on the Majorana Zero Modes in the Kitaev Chain at Half Filling

NASA Astrophysics Data System (ADS)

Li, Zhidan; Han, Qiang

2018-04-01

The one dimension interacting Kitaev chain at half filling is studied. The symmetry of the Hamiltonian is examined by dual transformations and various physical quantities as functions of the fermion-fermion interaction $U$ are calculated systematically using the density matrix renormalization group method. A special value of interaction $U_p$ is revealed in the topological region of the phase diagram. We show that at $U_p$ the ground states are strictly two-fold degenerate even though the chain length is finite and the zero-energy peak due to the Majorana zero modes is maximally enhanced and exactly localized at the end sites. $U_p$ may be attractive or repulsive depending on other system parameters. We also give a qualitative understanding of the effect of interaction under the self-consistent mean field framework.

The ‘cutting away’ of potential secondary electron tracks explains the effects of beam size and detector wall density in small-field photon dosimetry

NASA Astrophysics Data System (ADS)

Khee Looe, Hui; Delfs, Björn; Poppinga, Daniela; Jiang, Ping; Harder, Dietrich; Poppe, Björn

2018-01-01

The well-known field-size dependent overresponse in small-field photon-beam dosimetry of solid-state detectors equipped with very thin sensitive volumes, such as the PTW microDiamond, cannot be caused by the photon and electron interactions within these sensitive layers because they are only a few micrometers thick. The alternative explanation is that their overresponse is caused by the combination of two effects, the modification of the secondary electron fluence profile (i) by a field size too small to warrant lateral secondary electron equilibrium and (ii) by the density-dependent electron ranges in the structural detector materials placed in front of or backing the sensitive layer. The present study aims at the numerical demonstration and visualization of this combined mechanism. The lateral fluence profiles of the secondary electrons hitting a 1 µm thick scoring layer were Monte-Carlo simulated by modelling their generation and transport in the upstream or downstream adjacent layers of thickness 0.6 mm and densities from 0.0012 to 3 g cm-3, whose atomic composition was constantly kept water-like. The scoring layer/adjacent layer sandwich was placed in an infinite water phantom irradiated by circular 60Co, 6 MV and 15 MV photon beams with diameters from 3 to 40 mm. The interpretation starts from the ideal case of lateral secondary electron equilibrium, where the Fano theorem excludes any density effect. If the field size is then reduced, electron tracks potentially originating from source points outside the field border will then be numerically ‘cut away’. This geometrical effect reduces the secondary electron fluence at the field center, but the magnitude of this reduction also varies with the density-dependent electron ranges in the adjacent layers. This combined mechanism, which strongly depends on the photon spectrum, explains the field size and material density effect on the response of detectors with very thin sensitive layers used in small-field photon-beam dosimetry.

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

Rebolini, Elisa, E-mail: rebolini@lct.jussieu.fr; Toulouse, Julien, E-mail: julien.toulouse@upmc.fr; Savin, Andreas, E-mail: savin@lct.jussieu.fr

We present a study of the variation of total energies and excitation energies along a range-separated adiabatic connection. This connection links the non-interacting Kohn–Sham electronic system to the physical interacting system by progressively switching on the electron–electron interactions whilst simultaneously adjusting a one-electron effective potential so as to keep the ground-state density constant. The interactions are introduced in a range-dependent manner, first introducing predominantly long-range, and then all-range, interactions as the physical system is approached, as opposed to the conventional adiabatic connection where the interactions are introduced by globally scaling the standard Coulomb interaction. Reference data are reported for themore » He and Be atoms and the H{sub 2} molecule, obtained by calculating the short-range effective potential at the full configuration-interaction level using Lieb's Legendre-transform approach. As the strength of the electron–electron interactions increases, the excitation energies, calculated for the partially interacting systems along the adiabatic connection, offer increasingly accurate approximations to the exact excitation energies. Importantly, the excitation energies calculated at an intermediate point of the adiabatic connection are much better approximations to the exact excitation energies than are the corresponding Kohn–Sham excitation energies. This is particularly evident in situations involving strong static correlation effects and states with multiple excitation character, such as the dissociating H{sub 2} molecule. These results highlight the utility of long-range interacting reference systems as a starting point for the calculation of excitation energies and are of interest for developing and analyzing practical approximate range-separated density-functional methodologies.« less

Heterotypic interactions regulate cell shape and density during color pattern formation in zebrafish.

PubMed

Mahalwar, Prateek; Singh, Ajeet Pratap; Fadeev, Andrey; Nüsslein-Volhard, Christiane; Irion, Uwe

2016-11-15

The conspicuous striped coloration of zebrafish is produced by cell-cell interactions among three different types of chromatophores: black melanophores, orange/yellow xanthophores and silvery/blue iridophores. During color pattern formation xanthophores undergo dramatic cell shape transitions and acquire different densities, leading to compact and orange xanthophores at high density in the light stripes, and stellate, faintly pigmented xanthophores at low density in the dark stripes. Here, we investigate the mechanistic basis of these cell behaviors in vivo, and show that local, heterotypic interactions with dense iridophores regulate xanthophore cell shape transition and density. Genetic analysis reveals a cell-autonomous requirement of gap junctions composed of Cx41.8 and Cx39.4 in xanthophores for their iridophore-dependent cell shape transition and increase in density in light-stripe regions. Initial melanophore-xanthophore interactions are independent of these gap junctions; however, subsequently they are also required to induce the acquisition of stellate shapes in xanthophores of the dark stripes. In summary, we conclude that, whereas homotypic interactions regulate xanthophore coverage in the skin, their cell shape transitions and density is regulated by gap junction-mediated, heterotypic interactions with iridophores and melanophores. © 2016. Published by The Company of Biologists Ltd.

Thermal effects in supernova matter

NASA Astrophysics Data System (ADS)

Constantinou, Constantinos

A crucial ingredient in simulations of core collapse supernova (SN) explosions is the equation of state (EOS) of nucleonic matter for densities extending from 10-7 fm-3 to 1 ffm-3, temperatures up to 50 MeV, and proton-to-baryon fraction in the range 0 to 1/2. SN explosions release 99% of the progenitor star's gravitational potential energy in the form of neutrinos and, additionally, they are responsible for populating the universe with elements heavier than 56Fe. Therefore, the importance of understanding this phenomenon cannot be overstated as it could shed light onto the underlying nuclear and neutrino physics. A realistic EOS of SN matter must incorporate the nucleon-nucleon interaction in a many-body environment. We treat this problem with a non-relativistic potential model as well as relativistic mean-field theoretical one. In the former approach, we employ the Skyrme-like Hamiltonian density constructed by Akmal, Pandharipande, and Ravenhall which takes into account the long scattering lengths of nucleons that determine the low density characteristics. In the latter, we use a Walecka-like Lagrangian density supplemented by non-linear interactions involving scalar, vector, and isovector meson exchanges, calibrated so that known properties of nuclear matter are reproduced. We focus on the bulk homogeneous phase and calculate its thermodynamic properties as functions of baryon density, temperature, and proton-to-baryon ratio. The exact numerical results are then compared to those in the degenerate and non-degenerate limits for which analytical formulae have been derived. We find that the two models bahave similarly for densities up to nuclear saturation but exhibit differences at higher densities most notably in the isospin susceptibilities, the chemical potentials, and the pressure. The importance of the correct momentum dependence in the single particle potential that fits optical potentials of nucleon-nucleus scattering was highlighted in the context of intermediate energy heavy-ion collisions. To explore the effect momentum-dependent interactions have on the thermal properties of dense matter we study a schematic model constructed by Welke et al. in which the appropriate momentum dependence that fits optical potential data is built through finite-range exchange forces of the Yukawa type. We look into the finite-temperature properties of this model in the context of infinite, isospin-symmetric nucleonic matter. The exact numerical results are compared to analytical ones in the quantum regime where we rely on Landau's Fermi-Liquid Theory, and in the classical regime where the state variables are obtained through a steepest descent calculation. Detailed comparisons with similarly calibrated Skyrme models are also performed. We find that the high-density behavior of the thermal pressure is once again a differentiating feature. We attribute this to the temperature dependence of the energy spectrum of the finite-range and the meson-exchange models which leads to a higher specific heat and thus a lower pressure.

Does interspecific competition have a moderating effect on Taenia solium transmission dynamics in Southeast Asia?

PubMed

Conlan, James V; Vongxay, Khamphouth; Fenwick, Stanley; Blacksell, Stuart D; Thompson, R C Andrew

2009-09-01

It is well understood that sociocultural practices strongly influence Taenia solium transmission; however, the extent to which interspecific parasite competition moderates Taenia transmission has yet to be determined. This is certainly the case in Southeast Asia where T. solium faces competition in both the definitive host (people) and the intermediate host (pigs). In people, adult worms of T. solium, T. saginata and T. asiatica compete through density-dependent crowding mechanisms. In pigs, metacestodes of T. solium, T. hydatigena and T. asiatica compete through density-dependent immune-mediated interactions. Here, we describe the biological and epidemiological implications of Taenia competition and propose that interspecific competition has a moderating effect on the transmission dynamics of T. solium in the region. Furthermore, we argue that this competitive ecological scenario should be considered in future research and surveillance activities examining T. solium cysticercosis and taeniasis in Southeast Asia.

Protein-ligand interaction energies with dispersion corrected density functional theory and high-level wave function based methods.

PubMed

Antony, Jens; Grimme, Stefan; Liakos, Dimitrios G; Neese, Frank

2011-10-20

With dispersion-corrected density functional theory (DFT-D3) intermolecular interaction energies for a diverse set of noncovalently bound protein-ligand complexes from the Protein Data Bank are calculated. The focus is on major contacts occurring between the drug molecule and the binding site. Generalized gradient approximation (GGA), meta-GGA, and hybrid functionals are used. DFT-D3 interaction energies are benchmarked against the best available wave function based results that are provided by the estimated complete basis set (CBS) limit of the local pair natural orbital coupled-electron pair approximation (LPNO-CEPA/1) and compared to MP2 and semiempirical data. The size of the complexes and their interaction energies (ΔE(PL)) varies between 50 and 300 atoms and from -1 to -65 kcal/mol, respectively. Basis set effects are considered by applying extended sets of triple- to quadruple-ζ quality. Computed total ΔE(PL) values show a good correlation with the dispersion contribution despite the fact that the protein-ligand complexes contain many hydrogen bonds. It is concluded that an adequate, for example, asymptotically correct, treatment of dispersion interactions is necessary for the realistic modeling of protein-ligand binding. Inclusion of the dispersion correction drastically reduces the dependence of the computed interaction energies on the density functional compared to uncorrected DFT results. DFT-D3 methods provide results that are consistent with LPNO-CEPA/1 and MP2, the differences of about 1-2 kcal/mol on average (<5% of ΔE(PL)) being on the order of their accuracy, while dispersion-corrected semiempirical AM1 and PM3 approaches show a deviating behavior. The DFT-D3 results are found to depend insignificantly on the choice of the short-range damping model. We propose to use DFT-D3 as an essential ingredient in a QM/MM approach for advanced virtual screening approaches of protein-ligand interactions to be combined with similarly "first-principle" accounts for the estimation of solvation and entropic effects.

Exchange-Correlation Effects for Noncovalent Interactions in Density Functional Theory.

PubMed

Otero-de-la-Roza, A; DiLabio, Gino A; Johnson, Erin R

2016-07-12

In this article, we develop an understanding of how errors from exchange-correlation functionals affect the modeling of noncovalent interactions in dispersion-corrected density-functional theory. Computed CCSD(T) reference binding energies for a collection of small-molecule clusters are decomposed via a molecular many-body expansion and are used to benchmark density-functional approximations, including the effect of semilocal approximation, exact-exchange admixture, and range separation. Three sources of error are identified. Repulsion error arises from the choice of semilocal functional approximation. This error affects intermolecular repulsions and is present in all n-body exchange-repulsion energies with a sign that alternates with the order n of the interaction. Delocalization error is independent of the choice of semilocal functional but does depend on the exact exchange fraction. Delocalization error misrepresents the induction energies, leading to overbinding in all induction n-body terms, and underestimates the electrostatic contribution to the 2-body energies. Deformation error affects only monomer relaxation (deformation) energies and behaves similarly to bond-dissociation energy errors. Delocalization and deformation errors affect systems with significant intermolecular orbital interactions (e.g., hydrogen- and halogen-bonded systems), whereas repulsion error is ubiquitous. Many-body errors from the underlying exchange-correlation functional greatly exceed in general the magnitude of the many-body dispersion energy term. A functional built to accurately model noncovalent interactions must contain a dispersion correction, semilocal exchange, and correlation components that minimize the repulsion error independently and must also incorporate exact exchange in such a way that delocalization error is absent.

Stopping power beyond the adiabatic approximation

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

Caro, M.; Correa, A. A.; Artacho, E.

2017-06-01

Energetic ions traveling in solids deposit energy in a variety of ways, being nuclear and electronic stopping the two avenues in which dissipation is usually treated. This separation between electrons and ions relies on the adiabatic approximation in which ions interact via forces derived from the instantaneous electronic ground state. In a more detailed view, in which non-adiabatic effects are explicitly considered, electronic excitations alter the atomic bonding, which translates into changes in the interatomic forces. In this work, we use time dependent density functional theory and forces derived from the equations of Ehrenfest dynamics that depend instantaneously on themore » time-dependent electronic density. With them we analyze how the inter-ionic forces are affected by electronic excitations in a model of a Ni projectile interacting with a Ni target, a metallic system with strong electronic stopping and shallow core level states. We find that the electronic excitations induce substantial modifications to the inter-ionic forces, which translate into nuclear stopping power well above the adiabatic prediction. Particularly, we observe that most of the alteration of the adiabatic potential in early times comes from the ionization of the core levels of the target ions, not readily screened by the valence electrons.« less

Pressure dependence of effective Coulomb interaction parameters in BaFe2As2 by first-principle calculation

NASA Astrophysics Data System (ADS)

Aghajani, M.; Hadipour, H.; Akhavan, M.

2018-05-01

Pressure dependence of the onsite Coulomb interactions of the BaFe2As2 has been studied by employing the constrained random phase approximation within first-principle calculations. Analyzing total and projected density of states, a pseudogap is found for dxy band at the energy roughly 0.25 eV higher than the Fermi level. Also, by applying pressure the spectral weight of the dxy orbital vanishes while other orbitals remain metallic. The different screening channels, as discussed in four different models, affect significantly on the Hubbard U while the Hund J remains almost unchanged. The average onsite bare and partially and fully screened Coulomb interactions increase with different rates upon compression. These different rates can be explained by competition between the electronic screening and reduction of bond lengths.

The non-linear, interactive effects of population density and climate drive the geographical patterns of waterfowl survival

USGS Publications Warehouse

Zhao, Qing; Boomer, G. Scott; Kendall, William L.

2018-01-01

On-going climate change has major impacts on ecological processes and patterns. Understanding the impacts of climate on the geographical patterns of survival can provide insights to how population dynamics respond to climate change and provide important information for the development of appropriate conservation strategies at regional scales. It is challenging to understand the impacts of climate on survival, however, due to the fact that the non-linear relationship between survival and climate can be modified by density-dependent processes. In this study we extended the Brownie model to partition hunting and non-hunting mortalities and linked non-hunting survival to covariates. We applied this model to four decades (1972–2014) of waterfowl band-recovery, breeding population survey, and precipitation and temperature data covering multiple ecological regions to examine the non-linear, interactive effects of population density and climate on waterfowl non-hunting survival at a regional scale. Our results showed that the non-linear effect of temperature on waterfowl non-hunting survival was modified by breeding population density. The concave relationship between non-hunting survival and temperature suggested that the effects of warming on waterfowl survival might be multifaceted. Furthermore, the relationship between non-hunting survival and temperature was stronger when population density was higher, suggesting that high-density populations may be less buffered against warming than low-density populations. Our study revealed distinct relationships between waterfowl non-hunting survival and climate across and within ecological regions, highlighting the importance of considering different conservation strategies according to region-specific population and climate conditions. Our findings and associated novel modelling approach have wide implications in conservation practice.

The trans-generational impact of population density signals on host-parasite interactions.

PubMed

Michel, Jessica; Ebert, Dieter; Hall, Matthew D

2016-11-25

The density of a host population is a key parameter underlying disease transmission, but it also has implications for the expression of disease through its effect on host physiology. In response to higher densities, individuals are predicted to either increase their immune investment in response to the elevated risk of parasitism, or conversely to decrease their immune capacity as a consequence of the stress of a crowded environment. However, an individual's health is shaped by many different factors, including their genetic background, current environmental conditions, and maternal effects. Indeed, population density is often sensed through the presence of info-chemicals in the environment, which may influence a host's interaction with parasites, and also those of its offspring. All of which may alter the expression of disease, and potentially uncouple the presumed link between changes in host density and disease outcomes. In this study, we used the water flea Daphnia magna and its obligate bacterial parasite Pasteuria ramosa, to investigate how signals of high host density impact on host-parasite interactions over two consecutive generations. We found that the chemical signals from crowded treatments induced phenotypic changes in both the parental and offspring generations. In the absence of a pathogen, life-history changes were genotype-specific, but consistent across generations, even when the signal of density was removed. In contrast, the influence of density on infected animals depended on the trait and generation of exposure. When directly exposed to signals of high-density, host genotypes responded differently in how they minimised the severity of disease. Yet, in the subsequent generation, the influence of density was rarely genotype-specific and instead related to ability of the host to minimise the onset of infection. Our findings reveal that population level correlations between host density and infection capture only part of the complex relationship between crowding and the severity of disease. We suggest that besides its role in horizontal transmission, signals of density can influence parasite epidemiology by modifying mechanisms of resistance across multiple generations, and elevating variability via genotype-by-environment interactions. Our results help resolve why some studies are able to find a positive correlation between high density and resistance, while others uncover a negative correlation, or even no direct relationship at all.

Gas-surface interactions using accommodation coefficients for a dilute and a dense gas in a micro- or nanochannel: heat flux predictions using combined molecular dynamics and Monte Carlo techniques.

PubMed

Nedea, S V; van Steenhoven, A A; Markvoort, A J; Spijker, P; Giordano, D

2014-05-01

The influence of gas-surface interactions of a dilute gas confined between two parallel walls on the heat flux predictions is investigated using a combined Monte Carlo (MC) and molecular dynamics (MD) approach. The accommodation coefficients are computed from the temperature of incident and reflected molecules in molecular dynamics and used as effective coefficients in Maxwell-like boundary conditions in Monte Carlo simulations. Hydrophobic and hydrophilic wall interactions are studied, and the effect of the gas-surface interaction potential on the heat flux and other characteristic parameters like density and temperature is shown. The heat flux dependence on the accommodation coefficient is shown for different fluid-wall mass ratios. We find that the accommodation coefficient is increasing considerably when the mass ratio is decreased. An effective map of the heat flux depending on the accommodation coefficient is given and we show that MC heat flux predictions using Maxwell boundary conditions based on the accommodation coefficient give good results when compared to pure molecular dynamics heat predictions. The accommodation coefficients computed for a dilute gas for different gas-wall interaction parameters and mass ratios are transferred to compute the heat flux predictions for a dense gas. Comparison of the heat fluxes derived using explicit MD, MC with Maxwell-like boundary conditions based on the accommodation coefficients, and pure Maxwell boundary conditions are discussed. A map of the heat flux dependence on the accommodation coefficients for a dense gas, and the effective accommodation coefficients for different gas-wall interactions are given. In the end, this approach is applied to study the gas-surface interactions of argon and xenon molecules on a platinum surface. The derived accommodation coefficients are compared with values of experimental results.

Plant diversity increases with the strength of negative density dependence at the global scale

Treesearch

Joseph A. LaManna; Scott A. Mangan; Alfonso Alonso; Norman A. Bourg; Warren Y. Brockelman; Sarayudh Bunyavejchewin; Li-Wan Chang; Jyh-Min Chiang; George B. Chuyong; Keith Clay; Richard Condit; Susan Cordell; Stuart J. Davies; Tucker J. Furniss; Christian P. Giardina; I. A. U. Nimal Gunatilleke; C. V. Savitri Gunatilleke; Fangliang He; Robert W. Howe; Stephen P. Hubbell; Chang-Fu Hsieh; Faith M. Inman-Narahari; David Janík; Daniel J. Johnson; David Kenfack; Lisa Korte; Kamil Král; Andrew J. Larson; James A. Lutz; Sean M. McMahon; William J. McShea; Hervé R. Memiaghe; Anuttara Nathalang; Vojtech Novotny; Perry S. Ong; David A. Orwig; Rebecca Ostertag; Geoffrey G. Parker; Richard P. Phillips; Lawren Sack; I-Fang Sun; J. Sebastián Tello; Duncan W. Thomas; Benjamin L. Turner; Dilys M. Vela Díaz; Tomáš Vrška; George D. Weiblen; Amy Wolf; Sandra Yap; Jonathan A. Myers

2017-01-01

Theory predicts that higher biodiversity in the tropics is maintained by specialized interactions among plants and their natural enemies that result in conspecific negative density dependence (CNDD). By using more than 3000 species and nearly 2.4 million trees across 24 forest plots worldwide, we show that global patterns in tree species diversity reflect not only...

Predictive of the quantum capacitance effect on the excitation of plasma waves in graphene transistors with scaling limit.

PubMed

Wang, Lin; Chen, Xiaoshuang; Hu, Yibin; Wang, Shao-Wei; Lu, Wei

2015-04-28

Plasma waves in graphene field-effect transistors (FETs) and nano-patterned graphene sheets have emerged as very promising candidates for potential terahertz and infrared applications in myriad areas including remote sensing, biomedical science, military, and many other fields with their electrical tunability and strong interaction with light. In this work, we study the excitations and propagation properties of plasma waves in nanometric graphene FETs down to the scaling limit. Due to the quantum-capacitance effect, the plasma wave exhibits strong correlation with the distribution of density of states (DOS). It is indicated that the electrically tunable plasma resonance has a power-dependent V0.8 TG relation on the gate voltage, which originates from the linear dependence of density of states (DOS) on the energy in pristine graphene, in striking difference to those dominated by classical capacitance with only V0.5 TG dependence. The results of different transistor sizes indicate the potential application of nanometric graphene FETs in highly-efficient electro-optic modulation or detection of terahertz or infrared radiation. In addition, we highlight the perspectives of plasma resonance excitation in probing the many-body interaction and quantum matter state in strong correlation electron systems. This study reveals the key feature of plasma waves in decorated/nanometric graphene FETs, and paves the way to tailor plasma band-engineering and expand its application in both terahertz and mid-infrared regions.

Light-Cone and Diffusive Propagation of Correlations in a Many-Body Dissipative System.

PubMed

Bernier, Jean-Sébastien; Tan, Ryan; Bonnes, Lars; Guo, Chu; Poletti, Dario; Kollath, Corinna

2018-01-12

We analyze the propagation of correlations after a sudden interaction change in a strongly interacting quantum system in contact with an environment. In particular, we consider an interaction quench in the Bose-Hubbard model, deep within the Mott-insulating phase, under the effect of dephasing. We observe that dissipation effectively speeds up the propagation of single-particle correlations while reducing their coherence. In contrast, for two-point density correlations, the initial ballistic propagation regime gives way to diffusion at intermediate times. Numerical simulations, based on a time-dependent matrix product state algorithm, are supplemented by a quantitatively accurate fermionic quasiparticle approach providing an intuitive description of the initial dynamics in terms of holon and doublon excitations.

Communication: A combined periodic density functional and incremental wave-function-based approach for the dispersion-accounting time-resolved dynamics of ⁴He nanodroplets on surfaces: ⁴He/graphene.

PubMed

de Lara-Castells, María Pilar; Stoll, Hermann; Civalleri, Bartolomeo; Causà, Mauro; Voloshina, Elena; Mitrushchenkov, Alexander O; Pi, Martí

2014-10-21

In this work we propose a general strategy to calculate accurate He-surface interaction potentials. It extends the dispersionless density functional approach recently developed by Pernal et al. [Phys. Rev. Lett. 103, 263201 (2009)] to adsorbate-surface interactions by including periodic boundary conditions. We also introduce a scheme to parametrize the dispersion interaction by calculating two- and three-body dispersion terms at coupled cluster singles and doubles and perturbative triples (CCSD(T)) level via the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)]. The performance of the composite approach is tested on (4)He/graphene by determining the energies of the low-lying selective adsorption states, finding an excellent agreement with the best available theoretical data. Second, the capability of the approach to describe dispersionless correlation effects realistically is used to extract dispersion effects in time-dependent density functional simulations on the collision of (4)He droplets with a single graphene sheet. It is found that dispersion effects play a key role in the fast spreading of the (4)He nanodroplet, the evaporation-like process of helium atoms, and the formation of solid-like helium structures. These characteristics are expected to be quite general and highly relevant to explain experimental measurements with the newly developed helium droplet mediated deposition technique.

Nuclear half-lives for {alpha}-radioactivity of elements with 100 {<=} Z {<=} 130

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

Chowdhury, P. Roy; Samanta, C.; Physics Department, Gottwald Science Center, University of Richmond, Richmond, VA 23173

2008-11-15

Theoretical estimates for the half-lives of about 1700 isotopes of heavy elements with 100 {<=} Z {<=} 130 are tabulated using theoretical Q-values. The quantum mechanical tunneling probabilities are calculated within a WKB framework using microscopic nuclear potentials. The microscopic nucleus-nucleus potentials are obtained by folding the densities of interacting nuclei with a density-dependent M3Y effective nucleon-nucleon interaction. The {alpha}-decay half-lives calculated in this formalism using the experimental Q-values were found to be in good agreement over a wide range of experimental data spanning about 20 orders of magnitude. The theoretical Q-values used for the present calculations are extracted frommore » three different mass estimates viz. Myers-Swiatecki, Muntian-Hofmann-Patyk-Sobiczewski, and Koura-Tachibana-Uno-Yamada.« less

Exploring the origins of the Dzyaloshinskii-Moriya interaction in MnSi

DOE PAGES

Dhital, C.; DeBeer-Schmitt, L.; Zhang, Q.; ...

2017-12-19

By using magnetization and small-angle neutron scattering (SANS) measurements, we have investigated the magnetic behavior of the Mn 1-xIr xSi system to explore the effect of increased carrier density and spin-orbit interaction on the magnetic properties of MnSi. We determine estimates of the spin wave stiffness and the Dzyalloshinski-Moriya (DM) interaction strength and compare with Mn 1-xCo xSi and Mn 1-xFe xSi. Despite the large differences in atomic mass and size of the substituted elements, Mn 1-xCo xSi and Mn 1-xIr xSi show nearly identical variations in their magnetic properties with substitution. We find a systematic dependence of the transitionmore » temperature, the ordered moment, the helix period, and the DM interaction strength with electron count for Mn 1-xIr xSi, Mn 1-xCo xSi, and Mn 1-xFe xSi, indicating that the magnetic behavior is primarily dependent upon the additional carrier density, rather than on the mass or size of the substituting species. This indicates that the variation in magnetic properties, including the DM interaction strength, is primarily controlled by the electronic structure, as Co and Ir are isovalent. Our work suggests that although the rigid band model of electronic structure, along with Moriya’s model of weak itinerant magnetism, describes this system surprisingly well, phenomenological models for the DM interaction strength are not adequate to describe this system.« less

Hot and dense matter beyond relativistic mean field theory

NASA Astrophysics Data System (ADS)

Zhang, Xilin; Prakash, Madappa

2016-05-01

Properties of hot and dense matter are calculated in the framework of quantum hadrodynamics by including contributions from two-loop (TL) diagrams arising from the exchange of isoscalar and isovector mesons between nucleons. Our extension of mean field theory (MFT) employs the same five density-independent coupling strengths which are calibrated using the empirical properties at the equilibrium density of isospin-symmetric matter. Results of calculations from the MFT and TL approximations are compared for conditions of density, temperature, and proton fraction encountered in the study of core-collapse supernovae, young and old neutron stars, and mergers of compact binary stars. The TL results for the equation of state (EOS) of cold pure neutron matter at sub- and near-nuclear densities agree well with those of modern quantum Monte Carlo and effective field-theoretical approaches. Although the high-density EOS in the TL approximation for cold and β -equilibrated neutron-star matter is substantially softer than its MFT counterpart, it is able to support a 2 M⊙ neutron star required by recent precise determinations. In addition, radii of 1.4 M⊙ stars are smaller by ˜1 km than those obtained in MFT and lie in the range indicated by analysis of astronomical data. In contrast to MFT, the TL results also give a better account of the single-particle or optical potentials extracted from analyses of medium-energy proton-nucleus and heavy-ion experiments. In degenerate conditions, the thermal variables are well reproduced by results of Landau's Fermi-liquid theory in which density-dependent effective masses feature prominently. The ratio of the thermal components of pressure and energy density expressed as Γth=1 +(Pth/ɛth) , often used in astrophysical simulations, exhibits a stronger dependence on density than on proton fraction and temperature in both MFT and TL calculations. The prominent peak of Γth at supranuclear density found in MFT is, however, suppressed in TL calculations. This outcome is analogous to results of nonrelativistic models when exchange contributions from finite-range interactions are included in addition to those of contact interactions.

Potential misuse of avian density as a conservation metric.

PubMed

Skagen, Susan K; Yackel Adams, Amy A

2011-02-01

Effective conservation metrics are needed to evaluate the success of management in a rapidly changing world. Reproductive rates and densities of breeding birds (as a surrogate for reproductive rate) have been used to indicate the quality of avian breeding habitat, but the underlying assumptions of these metrics rarely have been examined. When birds are attracted to breeding areas in part by the presence of conspecifics and when breeding in groups influences predation rates, the effectiveness of density and reproductive rate as indicators of habitat quality is reduced. It is beneficial to clearly distinguish between individual- and population-level processes when evaluating habitat quality. We use the term reproductive rate to refer to both levels and further distinguish among levels by using the terms per capita fecundity (number of female offspring per female per year, individual level) and population growth rate (the product of density and per capita fecundity, population level). We predicted how density and reproductive rate interact over time under density-independent and density-dependent scenarios, assuming the ideal free distribution model of how birds settle in breeding habitats. We predicted population density of small populations would be correlated positively with both per capita fecundity and population growth rate due to the Allee effect. For populations in the density-dependent growth phase, we predicted no relation between density and per capita fecundity (because individuals in all patches will equilibrate to the same success rate) and a positive relation between density and population growth rate. Several ecological theories collectively suggest that positive correlations between density and per capita fecundity would be difficult to detect. We constructed a decision tree to guide interpretation of positive, neutral, nonlinear, and negative relations between density and reproductive rates at individual and population levels. Journal compilation ©2010 Society for Conservation Biology. No claim to original US government works.

Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models.

PubMed

Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob; Corni, Stefano; Frediani, Luca; Steindal, Arnfinn Hykkerud; Guido, Ciro A; Scalmani, Giovanni; Mennucci, Benedetta

2018-03-13

Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdW TS ) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdW TS expression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We explore transferable atom type-based parametrization strategies for the MM parameters, based on either vdW TS calculations performed on isolated fragments or on a direct estimation of the parameters from atomic polarizabilities taken from a polarizable force field. We investigate the performance of the implementation by computing self-consistent interaction energies for the S22 benchmark set, designed to represent typical noncovalent interactions in biological systems, in both equilibrium and out-of-equilibrium geometries. Overall, our results suggest that the present implementation is a promising strategy to include dispersion and repulsion in multiscale QM/MM models incorporating their explicit dependence on the electronic density.

On the temperature-dependent exchange splitting in the quasiparticle bandstructure of Ni

NASA Astrophysics Data System (ADS)

Borgiel, W.; Nolting, W.; Donath, M.

1989-11-01

A theoretical model for the bandferromagnet Ni is proposed, which takes into account the intraatomic electron interactions within the d band complex. After introducing effective spin operators the model-Hamiltonian consists of a one-particle part, an intraband interaction of Hubbard-type, and an interband exchange, formally describing electron magnon scattering (s-f model). The one particle energies are taken from a realistic bandstructure calculation for paramagnetic Ni. We use a many body procedure for a detailed inspection of the quasiparticle bandstructure in KX and XW directions, present the corresponding spectral densities, and compare the temperature dependent exchange splittings near the X and W point with recent results from spin resolved photoemission (PE) - and inverse photoemission (IPE) - experiments.

Use of Two-Body Correlated Basis Functions with van der Waals Interaction to Study the Shape-Independent Approximation for a Large Number of Trapped Interacting Bosons

NASA Astrophysics Data System (ADS)

Lekala, M. L.; Chakrabarti, B.; Das, T. K.; Rampho, G. J.; Sofianos, S. A.; Adam, R. M.; Haldar, S. K.

2017-05-01

We study the ground-state and the low-lying excitations of a trapped Bose gas in an isotropic harmonic potential for very small (˜ 3) to very large (˜ 10^7) particle numbers. We use the two-body correlated basis functions and the shape-dependent van der Waals interaction in our many-body calculations. We present an exhaustive study of the effect of inter-atomic correlations and the accuracy of the mean-field equations considering a wide range of particle numbers. We calculate the ground-state energy and the one-body density for different values of the van der Waals parameter C6. We compare our results with those of the modified Gross-Pitaevskii results, the correlated Hartree hypernetted-chain equations (which also utilize the two-body correlated basis functions), as well as of the diffusion Monte Carlo for hard sphere interactions. We observe the effect of the attractive tail of the van der Waals potential in the calculations of the one-body density over the truly repulsive zero-range potential as used in the Gross-Pitaevskii equation and discuss the finite-size effects. We also present the low-lying collective excitations which are well described by a hydrodynamic model in the large particle limit.

Astrophysical uncertainties on the local dark matter distribution and direct detection experiments

NASA Astrophysics Data System (ADS)

Green, Anne M.

2017-08-01

The differential event rate in weakly interacting massive particle (WIMP) direct detection experiments depends on the local dark matter density and velocity distribution. Accurate modelling of the local dark matter distribution is therefore required to obtain reliable constraints on the WIMP particle physics properties. Data analyses typically use a simple standard halo model which might not be a good approximation to the real Milky Way (MW) halo. We review observational determinations of the local dark matter density, circular speed and escape speed and also studies of the local dark matter distribution in simulated MW-like galaxies. We discuss the effects of the uncertainties in these quantities on the energy spectrum and its time and direction dependence. Finally, we conclude with an overview of various methods for handling these astrophysical uncertainties.

Combining Density Functional Theory and Green's Function Theory: Range-Separated, Nonlocal, Dynamic, and Orbital-Dependent Hybrid Functional.

PubMed

Kananenka, Alexei A; Zgid, Dominika

2017-11-14

We present a rigorous framework which combines single-particle Green's function theory with density functional theory based on a separation of electron-electron interactions into short- and long-range components. Short-range contribution to the total energy and exchange-correlation potential is provided by a density functional approximation, while the long-range contribution is calculated using an explicit many-body Green's function method. Such a hybrid results in a nonlocal, dynamic, and orbital-dependent exchange-correlation functional of a single-particle Green's function. In particular, we present a range-separated hybrid functional called srSVWN5-lrGF2 which combines the local-density approximation and the second-order Green's function theory. We illustrate that similarly to density functional approximations, the new functional is weakly basis-set dependent. Furthermore, it offers an improved description of the short-range dynamic correlation. The many-body contribution to the functional mitigates the many-electron self-interaction error present in many density functional approximations and provides a better description of molecular properties. Additionally, we illustrate that the new functional can be used to scale down the self-energy and, therefore, introduce an additional sparsity to the self-energy matrix that in the future can be exploited in calculations for large molecules or periodic systems.

Investigation of attractive and repulsive interactions associated with ketones in supercritical CO2, based on Raman spectroscopy and theoretical calculations.

PubMed

Kajiya, Daisuke; Saitow, Ken-ichi

2013-08-07

Carbonyl compounds are solutes that are highly soluble in supercritical CO2 (scCO2). Their solubility governs the efficiency of chemical reactions, and is significantly increased by changing a chromophore. To effectively use scCO2 as solvent, it is crucial to understand the high solubility of carbonyl compounds, the solvation structure, and the solute-solvent intermolecular interactions. We report Raman spectroscopic data, for three prototypical ketones dissolved in scCO2, and four theoretical analyses. The vibrational Raman spectra of the C=O stretching modes of ketones (acetone, acetophenone, and benzophenone) were measured in scCO2 along the reduced temperature Tr = T∕Tc = 1.02 isotherm as a function of the reduced density ρr = ρ∕ρc in the range 0.05-1.5. The peak frequencies of the C=O stretching modes shifted toward lower energies as the fluid density increased. The density dependence was analyzed by using perturbed hard-sphere theory, and the shift was decomposed into attractive and repulsive energy components. The attractive energy between the ketones and CO2 was up to nine times higher than the repulsive energy, and its magnitude increased in the following order: acetone < acetophenone < benzophenone. The Mulliken charges of the three solutes and CO2 molecules obtained by using quantum chemistry calculations described the order of the magnitude of the attractive energy and optimized the relative configuration between each solute and CO2. According to theoretical calculations for the dispersion energy, the dipole-induced-dipole interaction energy, and the frequency shift due to their interactions, the experimentally determined attractive energy differences in the three solutes were attributed to the dispersion energies that depended on a chromophore attached to the carbonyl groups. It was found that the major intermolecular interaction with the attractive shift varied from dipole-induced dipole to dispersion depending on the chromophore in the ketones in scCO2. As the common conclusion for the Raman spectral measurements and the four theoretical calculations, solute polarizability, modified by the chromophore, was at the core of the solute-solvent interactions of the ketones in scCO2.

Influence of the electron density on the characteristics of terahertz waves generated under laser–cluster interaction

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

Frolov, A. A., E-mail: frolov@ihed.ras.ru

2016-12-15

A theory of generation of terahertz radiation under laser–cluster interaction, developed earlier for an overdense cluster plasma [A. A. Frolov, Plasma Phys. Rep. 42. 637 (2016)], is generalized for the case of arbitrary electron density. The spectral composition of radiation is shown to substantially depend on the density of free electrons in the cluster. For an underdense cluster plasma, there is a sharp peak in the terahertz spectrum at the frequency of the quadrupole mode of a plasma sphere. As the electron density increases to supercritical values, this spectral line vanishes and a broad maximum at the frequency comparable withmore » the reciprocal of the laser pulse duration appears in the spectrum. The dependence of the total energy of terahertz radiation on the density of free electrons is analyzed. The radiation yield is shown to increase significantly under resonance conditions, when the laser frequency is close to the eigenfrequency of the dipole or quadrupole mode of a plasma sphere.« less

A drop in the pond: the effect of rapid mass-loss on the dynamics and interaction rate of collisionless particles

NASA Astrophysics Data System (ADS)

Penoyre, Zephyr; Haiman, Zoltán

2018-01-01

In symmetric gravitating systems experiencing rapid mass-loss, particle orbits change almost instantaneously, which can lead to the development of a sharply contoured density profile, including singular caustics for collisionless systems. This framework can be used to model a variety of dynamical systems, such as accretion discs following a massive black hole merger and dwarf galaxies following violent early star formation feedback. Particle interactions in the high-density peaks seem a promising source of observable signatures of these mass-loss events (i.e. a possible EM counterpart for black hole mergers or strong gamma-ray emission from dark matter annihilation around young galaxies), because the interaction rate depends on the square of the density. We study post-mass-loss density profiles, both analytic and numerical, in idealized cases and present arguments and methods to extend to any general system. An analytic derivation is presented for particles on Keplerian orbits responding to a drop in the central mass. We argue that this case, with initially circular orbits, gives the most sharply contoured profile possible. We find that despite the presence of a set of singular caustics, the total particle interaction rate is reduced compared to the unperturbed system; this is a result of the overall expansion of the system dominating over the steep caustics. Finally, we argue that this result holds more generally, and the loss of central mass decreases the particle interaction rate in any physical system.

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

USGS Publications Warehouse

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

2017-01-01

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

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

PubMed

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

2016-10-01

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

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

PubMed Central

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

2016-01-01

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

Density functional of a two-dimensional gas of dipolar atoms: Thomas-Fermi-Dirac treatment

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

Fang, Bess; Englert, Berthold-Georg

We derive the density functional for the ground-state energy of a two-dimensional, spin-polarized gas of neutral fermionic atoms with magnetic-dipole interaction, in the Thomas-Fermi-Dirac approximation. For many atoms in a harmonic trap, we give analytical solutions for the single-particle spatial density and the ground-state energy, in dependence on the interaction strength, and we discuss the weak-interaction limit that is relevant for experiments. We then lift the restriction of full spin polarization and account for a time-independent inhomogeneous external magnetic field. The field strength necessary to ensure full spin polarization is derived.

SIMULATIONS OF THE SYMBIOTIC RECURRENT NOVA V407 CYG. I. ACCRETION AND SHOCK EVOLUTIONS

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

Pan, Kuo-Chuan; Ricker, Paul M.; Taam, Ronald E., E-mail: kuo-chuan.pan@unibas.ch, E-mail: pmricker@illinois.edu, E-mail: r-taam@northwestern.edu, E-mail: taam@asiaa.sinica.edu.tw

2015-06-10

The shock interaction and evolution of nova ejecta with wind from a red giant (RG) star in a symbiotic binary system are investigated via three-dimensional hydrodynamics simulations. We specifically model the 2010 March outburst of the symbiotic recurrent nova V407 Cygni from its quiescent phase to its eruption phase. The circumstellar density enhancement due to wind–white-dwarf interaction is studied in detail. It is found that the density-enhancement efficiency depends on the ratio of the orbital speed to the RG wind speed. Unlike another recurrent nova, RS Ophiuchi, we do not observe a strong disk-like density enhancement, but instead observe anmore » aspherical density distribution with ∼20% higher density in the equatorial plane than at the poles. To model the 2010 outburst, we consider several physical parameters, including the RG mass-loss rate, nova eruption energy, and ejecta mass. A detailed study of the shock interaction and evolution reveals that the interaction of shocks with the RG wind generates strong Rayleigh–Taylor instabilities. In addition, the presence of the companion and circumstellar density enhancement greatly alter the shock evolution during the nova phase. Depending on the model, the ejecta speed after sweeping out most of the circumstellar medium decreases to ∼100–300 km s{sup −1}, which is consistent with the observed extended redward emission in [N ii] lines in 2011 April.« less

Interaction of a vortex and a premixed flame

NASA Technical Reports Server (NTRS)

Ferziger, Joel H.; Rutland, Christopher J.

1989-01-01

The interaction of a vortex structure and a premixed flame is studied. The presence of pressure gradients in the vortex and density gradients in the flame result in a complicated interaction. This interaction has been examined when the flame and vortex are fully coupled and in two special cases where they are decoupled: a frozen flame case and a frozen vortex case. In the frozen flame case the main effect of the flame on the vortex is through the barocline torque term. This has been modeled for high Damkoehler numbers. In the frozen vortex case the main effect, at moderate Damkoehler numbers, is to convect the flame around the vortex. At low Damkoehler numbers, depending on the length scales, pockets of unburned gas can form or the flame structure can be significantly changed. The two frozen cases provide a basis for understanding the full interaction.

Mesoscale spatiotemporal variability in a complex host-parasite system influenced by intermediate host body size.

PubMed

Rodríguez, Sara M; Valdivia, Nelson

2017-01-01

Parasites are essential components of natural communities, but the factors that generate skewed distributions of parasite occurrences and abundances across host populations are not well understood. Here, we analyse at a seascape scale the spatiotemporal relationships of parasite exposure and host body-size with the proportion of infected hosts (i.e., prevalence) and aggregation of parasite burden across ca. 150 km of the coast and over 22 months. We predicted that the effects of parasite exposure on prevalence and aggregation are dependent on host body-sizes. We used an indirect host-parasite interaction in which migratory seagulls, sandy-shore molecrabs, and an acanthocephalan worm constitute the definitive hosts, intermediate hosts, and endoparasite, respectively. In such complex systems, increments in the abundance of definitive hosts imply increments in intermediate hosts' exposure to the parasite's dispersive stages. Linear mixed-effects models showed a significant, albeit highly variable, positive relationship between seagull density and prevalence. This relationship was stronger for small (cephalothorax length >15 mm) than large molecrabs (<15 mm). Independently of seagull density, large molecrabs carried significantly more parasites than small molecrabs. The analysis of the variance-to-mean ratio of per capita parasite burden showed no relationship between seagull density and mean parasite aggregation across host populations. However, the amount of unexplained variability in aggregation was strikingly higher in larger than smaller intermediate hosts. This unexplained variability was driven by a decrease in the mean-variance scaling in heavily infected large molecrabs. These results show complex interdependencies between extrinsic and intrinsic population attributes on the structure of host-parasite interactions. We suggest that parasite accumulation-a characteristic of indirect host-parasite interactions-and subsequent increasing mortality rates over ontogeny underpin size-dependent host-parasite dynamics.

Double core-hole emissivity of transient aluminum plasmas produced in the interaction with ultra-intense x-ray laser pulse

NASA Astrophysics Data System (ADS)

Gao, Cheng; Zeng, Jiaolong; Yuan, Jianmin

2015-11-01

Emissivity of single core-hole (SCH) and double core-hole (DCH) states of aluminum plasmas produced in the interaction with ultra-intense x-ray laser pulse interaction are investigated systematically by solving the time-dependent rate equation implemented in the detailed level accounting approximation. We first demonstrated the plasma density effects on level populations and charge state distribution. Compared with recent experiments, it is shown that the plasma density effects play important roles in the evolution dynamics. Then we systematically investigated the emissivity of the transient aluminum plasmas produced by the x-ray laser pulses with a few photon energies above the threshold photon energy to create DCH states. For the laser photon energy where there are resonant absorptions (RA), 1s-np transitions with both full 1s and SCH 1s states play important roles in time evolution of the population and DCH emission spectroscopy. The significant RA effects are illustrated in detail for x-ray pulses, which creates the 1s-2p resonant absorption from the SCH states of Al VII. With the increase of the photon energy, the emissions from lower charge states become larger.

Structural changes induced by lattice-electron interactions: SiO2 stishovite and FeTiO3 ilmenite.

PubMed

Yamanaka, Takamitsu

2005-09-01

The bright source and highly collimated beam of synchrotron radiation offers many advantages for single-crystal structure analysis under non-ambient conditions. The structure changes induced by the lattice-electron interaction under high pressure have been investigated using a diamond anvil pressure cell. The pressure dependence of electron density distributions around atoms is elucidated by a single-crystal diffraction study using deformation electron density analysis and the maximum entropy method. In order to understand the bonding electrons under pressure, diffraction intensity measurements of FeTiO3 ilmenite and gamma-SiO2 stishovite single crystals at high pressures were made using synchrotron radiation. Both diffraction studies describe the electron density distribution including bonding electrons and provide the effective charge of the cations. In both cases the valence electrons are more localized around the cations with increasing pressure. This is consistent with molecular orbital calculations, proving that the bonding electron density becomes smaller with pressure. The thermal displacement parameters of both samples are reduced with increasing pressure.

Viscosity and thermal conductivity of moderately dense gas mixtures.

NASA Technical Reports Server (NTRS)

Wakeham, W. A.; Kestin, J.; Mason, E. A.; Sandler, S. I.

1972-01-01

Derivation of a simple, semitheoretical expression for the initial density dependence of the viscosity and thermal conductivity of gaseous mixtures in terms of the appropriate properties of the pure components and of their interaction quantities. The derivation is based on Enskog's theory of dense gases and yields an equation in which the composition dependence of the linear factor in the density expansion is explicit. The interaction quantities are directly related to those of the mixture extrapolated to zero density and to a universal function valid for all gases. The reliability of the formulation is assessed with respect to the viscosity of several binary mixtures. It is found that the calculated viscosities of binary mixtures agree with the experimental data with a precision which is comparable to that of the most precise measurements.

Density-dependent effects on physical condition and reproduction in North American elk: an experimental test.

Treesearch

Kelley M. Stewart; R. Terry Bowyer; Brian L. Dick; Bruce K. Johnson; John G. Kie

2005-01-01

Density dependence plays a key role in life-history characteristics and population ecology of large, herbivorous mammals. We designed a manipulative experiment to test hypotheses relating effects of density-dependent mechanisms on physical condition and fecundity of North American elk (Cervus elaphus) by creating populations at low and high density...

Irradiation-induced Ag nanocluster nucleation in silicate glasses: Analogy with photography

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

Espiau de Lamaestre, R.; Fontainebleau Research Center, Corning SA, 77210 Avon; Bea, H.

2007-11-15

The synthesis of Ag nanoclusters in soda lime silicate glasses and silica was studied by optical absorption and electron spin resonance experiments under both low (gamma ray) and high (MeV ion) deposited energy density irradiation conditions. Both types of irradiation create electrons and holes whose density and thermal evolution--notably via their interaction with defects--are shown to determine the clustering and growth rates of Ag nanocrystals. We thus establish the influence of redox interactions of defects and silver (poly)ions. The mechanisms are similar to the latent image formation in photography: Irradiation-induced photoelectrons are trapped within the glass matrix, notably on dissolvedmore » noble metal ions and defects, which are thus neutralized (reverse oxidation reactions are also shown to exist). Annealing promotes metal atom diffusion, which, in turn, leads to cluster nuclei formation. The cluster density depends not only on the irradiation fluence but also--and primarily--on the density of deposited energy and the redox properties of the glass. Ion irradiation (i.e., large deposited energy density) is far more effective in cluster formation, despite its lower neutralization efficiency (from Ag{sup +} to Ag{sup 0}) as compared to gamma photon irradiation.« less

Effect of Thermospheric Neutral Density upon Inner Trapped-belt Proton Flux

NASA Technical Reports Server (NTRS)

Wilson, Thomas L.; Lodhi, M. A. K.; Diaz, Abel B.

2007-01-01

We wish to point out that a secular change in the Earth's atmospheric neutral density alters charged-particle lifetime in the inner trapped radiation belts, in addition to the changes recently reported as produced by greenhouse gases. Heretofore, changes in neutral density have been of interest primarily because of their effect on the orbital drag of satellites. We extend this to include the orbital lifetime of charged particles in the lower radiation belts. It is known that the charged-belt population is coupled to the neutral density of the atmosphere through changes induced by solar activity, an effect produced by multiple scattering off neutral and ionized atoms along with ionization loss in the thermosphere where charged and neutral populations interact. It will be shown here that trapped-belt flux J is bivariant in energy E and thermospheric neutral density , as J(E,rho). One can conclude that proton lifetimes in these belts are also directly affected by secular changes in the neutral species populating the Earth s thermosphere. This result is a consequence of an intrinsic property of charged-particle flux, that flux is not merely a function of E but is dependent upon density rho when a background of neutrals is present.

The Effects of Density in a High-Rise Residence Hall on Helping Behavior and Social Interaction

ERIC Educational Resources Information Center

Stoner, Kenneth L.; Thurman, Christopher W.

1978-01-01

Focuses on the effects of high-density housing on the helping behaviors and social interactions of the residents living within such buildings. Concludes by recommending ways to overcome some of the negative effects of high-density housing. (Author)

Inoculum size-dependent interactive regulation of metabolism and stress response of Saccharomyces cerevisiae revealed by comparative metabolomics.

PubMed

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

2009-12-01

To investigate the metabolic regulation against inoculum density and stress response to high cell density, comparative metabolomic analysis was employed on Saccharomyces cerevisiae under fermentations with five different inoculum sizes by gas chromatography time-of-flight mass spectrometry. Samples from these fermentations were clearly distinguished by principal components analysis, indicating that inoculum size had a profound effect on the metabolism of S. cerevisiae. Potential biomarkers responsible for the discrimination were identified as glycerol, phosphoric acid, succinate, glycine, isoleucine, proline, palmitoleic acid, myo-inositol and ethanolamine. It indicated that enhanced stress protectants in glycerol biosynthesis and amino acid metabolism, depressed citric acid cycle intermediates, as well as decreased metabolites relating to membrane structure and function were involved as the inoculum size of yeast increased. Furthermore, significantly higher levels of glycerol and proline in yeast cells of higher inoculum size fermentation (40 g l(-1)) revealed that they played important roles in protecting yeast from stresses in high cell density fermentation. These findings provided new insights into characterizing the metabolic regulation and stress response depending on inoculum density during ethanol fermentation.

Structure of the first order reduced density matrix in three electron systems: A generalized Pauli constraints assisted study.

PubMed

Theophilou, Iris; Lathiotakis, Nektarios N; Helbig, Nicole

2018-03-21

We investigate the structure of the one-body reduced density matrix of three electron systems, i.e., doublet and quadruplet spin configurations, corresponding to the smallest interacting system with an open-shell ground state. To this end, we use configuration interaction (CI) expansions of the exact wave function in Slater determinants built from natural orbitals in a finite dimensional Hilbert space. With the exception of maximally polarized systems, the natural orbitals of spin eigenstates are generally spin dependent, i.e., the spatial parts of the up and down natural orbitals form two different sets. A measure to quantify this spin dependence is introduced and it is shown that it varies by several orders of magnitude depending on the system. We also study the ordering issue of the spin-dependent occupation numbers which has practical implications in reduced density matrix functional theory minimization schemes, when generalized Pauli constraints (GPCs) are imposed and in the form of the CI expansion in terms of the natural orbitals. Finally, we discuss the aforementioned CI expansion when there are GPCs that are almost "pinned."

The nuclear Thomas-Fermi model

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

Myers, W.D.; Swiatecki, W.J.

1994-08-01

The statistical Thomas-Fermi model is applied to a comprehensive survey of macroscopic nuclear properties. The model uses a Seyler-Blanchard effective nucleon-nucleon interaction, generalized by the addition of one momentum-dependent and one density-dependent term. The adjustable parameters of the interaction were fitted to shell-corrected masses of 1654 nuclei, to the diffuseness of the nuclear surface and to the measured depths of the optical model potential. With these parameters nuclear sizes are well reproduced, and only relatively minor deviations between measured and calculated fission barriers of 36 nuclei are found. The model determines the principal bulk and surface properties of nuclear mattermore » and provides estimates for the more subtle, Droplet Model, properties. The predicted energy vs density relation for neutron matter is in striking correspondence with the 1981 theoretical estimate of Friedman and Pandharipande. Other extreme situations to which the model is applied are a study of Sn isotopes from {sup 82}Sn to {sup 170}Sn, and the rupture into a bubble configuration of a nucleus (constrained to spherical symmetry) which takes place when Z{sup 2}/A exceeds about 100.« less

The Nuclear Thomas-Fermi Model

DOE R&D Accomplishments Database

Myers, W. D.; Swiatecki, W. J.

1994-08-01

The statistical Thomas-Fermi model is applied to a comprehensive survey of macroscopic nuclear properties. The model uses a Seyler-Blanchard effective nucleon-nucleon interaction, generalized by the addition of one momentum-dependent and one density-dependent term. The adjustable parameters of the interaction were fitted to shell-corrected masses of 1654 nuclei, to the diffuseness of the nuclear surface and to the measured depths of the optical model potential. With these parameters nuclear sizes are well reproduced, and only relatively minor deviations between measured and calculated fission barriers of 36 nuclei are found. The model determines the principal bulk and surface properties of nuclear matter and provides estimates for the more subtle, Droplet Model, properties. The predicted energy vs density relation for neutron matter is in striking correspondence with the 1981 theoretical estimate of Friedman and Pandharipande. Other extreme situations to which the model is applied are a study of Sn isotopes from {sup 82}Sn to {sup 170}Sn, and the rupture into a bubble configuration of a nucleus (constrained to spherical symmetry) which takes place when Z{sup 2}/A exceeds about 100.

A feature-based approach to modeling protein-protein interaction hot spots.

PubMed

Cho, Kyu-il; Kim, Dongsup; Lee, Doheon

2009-05-01

Identifying features that effectively represent the energetic contribution of an individual interface residue to the interactions between proteins remains problematic. Here, we present several new features and show that they are more effective than conventional features. By combining the proposed features with conventional features, we develop a predictive model for interaction hot spots. Initially, 54 multifaceted features, composed of different levels of information including structure, sequence and molecular interaction information, are quantified. Then, to identify the best subset of features for predicting hot spots, feature selection is performed using a decision tree. Based on the selected features, a predictive model for hot spots is created using support vector machine (SVM) and tested on an independent test set. Our model shows better overall predictive accuracy than previous methods such as the alanine scanning methods Robetta and FOLDEF, and the knowledge-based method KFC. Subsequent analysis yields several findings about hot spots. As expected, hot spots have a larger relative surface area burial and are more hydrophobic than other residues. Unexpectedly, however, residue conservation displays a rather complicated tendency depending on the types of protein complexes, indicating that this feature is not good for identifying hot spots. Of the selected features, the weighted atomic packing density, relative surface area burial and weighted hydrophobicity are the top 3, with the weighted atomic packing density proving to be the most effective feature for predicting hot spots. Notably, we find that hot spots are closely related to pi-related interactions, especially pi . . . pi interactions.

Complexity in modeling of residual stresses and strains during polymerization of bone cement: effects of conversion, constraint, heat transfer, and viscoelastic property changes.

PubMed

Gilbert, Jeremy L

2006-12-15

Aseptic loosening of cemented joint prostheses remains a significant concern in orthopedic biomaterials. One possible contributor to cement loosening is the development of porosity, residual stresses, and local fracture of the cement that may arise from the in-situ polymerization of the cement. In-situ polymerization of acrylic bone cement is a complex set of interacting processes that involve polymerization reactions, heat generation and transfer, full or partial mechanical constraint, evolution of conversion- and temperature-dependent viscoelastic material properties, and thermal and conversion-driven changes in the density of the cement. Interactions between heat transfer and polymerization can lead to polymerization fronts moving through the material. Density changes during polymerization can, in the presence of mechanical constraint, lead to the development of locally high residual strain energy and residual stresses. This study models the interactions during bone cement polymerization and determines how residual stresses develop in cement and incorporates temperature and conversion-dependent viscoelastic behavior. The results show that the presence of polymerization fronts in bone cement result in locally high residual strain energies. A novel heredity integral approach is presented to track residual stresses incorporating conversion and temperature dependent material property changes. Finally, the relative contribution of thermal- and conversion-dependent strains to residual stresses is evaluated and it is found that the conversion-based strains are the major contributor to the overall behavior. This framework provides the basis for understanding the complex development of residual stresses and can be used as the basis for developing more complex models of cement behavior.

Annoyance due to noise and air pollution to the residents of heavily frequented streets

NASA Technical Reports Server (NTRS)

Wanner, H. U.; Wehrli, B.; Nemecek, J.; Turrian, V.

1980-01-01

The residents of different streets with varying traffic density and building density were questioned about annoyance due to traffic noise and air pollution. Results show that annoyance felt is dependent not only on the measured noise levels and/or air pollution concentrations, but that there do exist interactions between the residential quarters and annoyance. These interactions should be considered when fixing the limits and standards.

Temperature and population density: interactional effects of environmental factors on phenotypic plasticity, immune defenses, and disease resistance in an insect pest.

PubMed

Silva, Farley W S; Elliot, Simon L

2016-06-01

Temperature and crowding are key environmental factors mediating the transmission and epizooty of infectious disease in ectotherm animals. The host physiology may be altered in a temperature-dependent manner and thus affects the pathogen development and course of diseases within an individual and host population, or the transmission rates (or infectivity) of pathogens shift linearly with the host population density. To our understanding, the knowledge of interactive and synergistic effects of temperature and population density on the host-pathogen system is limited. Here, we tested the interactional effects of these environmental factors on phenotypic plasticity, immune defenses, and disease resistance in the velvetbean caterpillar Anticarsia gemmatalis . Upon egg hatching, caterpillars were reared in thermostat-controlled chambers in a 2 × 4 factorial design: density (1 or 8 caterpillars/pot) and temperature (20, 24, 28, or 32°C). Of the immune defenses assessed, encapsulation response was directly affected by none of the environmental factors; capsule melanization increased with temperature in both lone- and group-reared caterpillars, although the lone-reared ones presented the most evident response, and hemocyte numbers decreased with temperature regardless of the population density. Temperature, but not population density, affected considerably the time from inoculation to death of velvetbean caterpillar. Thus, velvetbean caterpillars succumbed to Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) more quickly at higher temperatures than at lower temperatures. As hypothesized, temperature likely affected caterpillars' movement rates, and thus the contact between conspecifics, which in turn affected the phenotypic expression of group-reared caterpillars. Our results suggest that environmental factors, mainly temperature, strongly affect both the course of disease in velvetbean caterpillar population and its defenses against pathogens. As a soybean pest, velvetbean caterpillar may increase its damage on soybean fields under a scenario of global warming as caterpillars may reach the developmental resistance faster, and thus decrease their susceptibility to biological control by AgMNPV.

Interaction of rate- and size-effect using a dislocation density based strain gradient viscoplasticity model

NASA Astrophysics Data System (ADS)

Nguyen, Trung N.; Siegmund, Thomas; Tomar, Vikas; Kruzic, Jamie J.

2017-12-01

Size effects occur in non-uniform plastically deformed metals confined in a volume on the scale of micrometer or sub-micrometer. Such problems have been well studied using strain gradient rate-independent plasticity theories. Yet, plasticity theories describing the time-dependent behavior of metals in the presence of size effects are presently limited, and there is no consensus about how the size effects vary with strain rates or whether there is an interaction between them. This paper introduces a constitutive model which enables the analysis of complex load scenarios, including loading rate sensitivity, creep, relaxation and interactions thereof under the consideration of plastic strain gradient effects. A strain gradient viscoplasticity constitutive model based on the Kocks-Mecking theory of dislocation evolution, namely the strain gradient Kocks-Mecking (SG-KM) model, is established and allows one to capture both rate and size effects, and their interaction. A formulation of the model in the finite element analysis framework is derived. Numerical examples are presented. In a special virtual creep test with the presence of plastic strain gradients, creep rates are found to diminish with the specimen size, and are also found to depend on the loading rate in an initial ramp loading step. Stress relaxation in a solid medium containing cylindrical microvoids is predicted to increase with decreasing void radius and strain rate in a prior ramp loading step.

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

Dhital, C.; DeBeer-Schmitt, L.; Zhang, Q.

By using magnetization and small-angle neutron scattering (SANS) measurements, we have investigated the magnetic behavior of the Mn 1-xIr xSi system to explore the effect of increased carrier density and spin-orbit interaction on the magnetic properties of MnSi. We determine estimates of the spin wave stiffness and the Dzyalloshinski-Moriya (DM) interaction strength and compare with Mn 1-xCo xSi and Mn 1-xFe xSi. Despite the large differences in atomic mass and size of the substituted elements, Mn 1-xCo xSi and Mn 1-xIr xSi show nearly identical variations in their magnetic properties with substitution. We find a systematic dependence of the transitionmore » temperature, the ordered moment, the helix period, and the DM interaction strength with electron count for Mn 1-xIr xSi, Mn 1-xCo xSi, and Mn 1-xFe xSi, indicating that the magnetic behavior is primarily dependent upon the additional carrier density, rather than on the mass or size of the substituting species. This indicates that the variation in magnetic properties, including the DM interaction strength, is primarily controlled by the electronic structure, as Co and Ir are isovalent. Our work suggests that although the rigid band model of electronic structure, along with Moriya’s model of weak itinerant magnetism, describes this system surprisingly well, phenomenological models for the DM interaction strength are not adequate to describe this system.« less

Effect of boson on-site repulsion on the superfluidity in the boson-fermion-Hubbard model

NASA Astrophysics Data System (ADS)

Sajna, A. S.; Micnas, R.

2018-03-01

We analyze the finite-temperature phase diagram of the boson-fermion-Hubbard model with Feshbach converting interaction, using the coherent-state path-integral method. We show that depending on the position of the bosonic band, this type of interaction, even if weak, can drive the system into the resonant superfluid phase in the strong bosonic interaction limit. It turns out that this phase can exist for an arbitrary number of fermions (i.e., fermionic concentration between 0 and 2), but with the bosonic particle number very close to an integer value. We point out that the standard time-of-flight method in optical lattice experiments can be an adequate technique to confirm the existence of this resonant phase. Moreover, in the nonresonant regime, the enhancement of the critical temperature of the superfluid phase due to Feshbach interaction is also observed. We account for this interesting phenomena for a hole- or particlelike pairing mechanism depending on the system density and mutual location of the fermionic and bosonic bands.

Microscopically based energy density functionals for nuclei using the density matrix expansion: Implementation and pre-optimization

NASA Astrophysics Data System (ADS)

Stoitsov, M.; Kortelainen, M.; Bogner, S. K.; Duguet, T.; Furnstahl, R. J.; Gebremariam, B.; Schunck, N.

2010-11-01

In a recent series of articles, Gebremariam, Bogner, and Duguet derived a microscopically based nuclear energy density functional by applying the density matrix expansion (DME) to the Hartree-Fock energy obtained from chiral effective field theory two- and three-nucleon interactions. Owing to the structure of the chiral interactions, each coupling in the DME functional is given as the sum of a coupling constant arising from zero-range contact interactions and a coupling function of the density arising from the finite-range pion exchanges. Because the contact contributions have essentially the same structure as those entering empirical Skyrme functionals, a microscopically guided Skyrme phenomenology has been suggested in which the contact terms in the DME functional are released for optimization to finite-density observables to capture short-range correlation energy contributions from beyond Hartree-Fock. The present article is the first attempt to assess the ability of the newly suggested DME functional, which has a much richer set of density dependencies than traditional Skyrme functionals, to generate sensible and stable results for nuclear applications. The results of the first proof-of-principle calculations are given, and numerous practical issues related to the implementation of the new functional in existing Skyrme codes are discussed. Using a restricted singular value decomposition optimization procedure, it is found that the new DME functional gives numerically stable results and exhibits a small but systematic reduction of our test χ2 function compared to standard Skyrme functionals, thus justifying its suitability for future global optimizations and large-scale calculations.

Two mechanisms of resonance overlapping in excitation of azimuthal surface waves by rotating relativistic electron beams

NASA Astrophysics Data System (ADS)

Girka, Igor O.; Pavlenko, Ivan V.; Thumm, Manfred

2018-05-01

Azimuthal surface waves are electromagnetic eigenwaves of cylindrical plasma-filled metallic waveguides with a stationary axial magnetic field. These waves with extraordinary polarization can effectively interact with relativistic electron beams rotating along large Larmor orbits in the gap, which separates the plasma column from the waveguide wall. Both widening the layer and increasing the beam particle density are demonstrated to cause resonance overlapping seen from the perspective of the growth rate dependence on the effective wave number.

Radicals mediated magnetism in Ar plasma treated high-density polyethylene

NASA Astrophysics Data System (ADS)

Orendáč, M.; Čižmár, E.; Kažiková, V.; Orendáčová, A.; Řezníčková, A.; Kolská, Z.; Švorčík, V.

2018-05-01

Electron-spin resonance of high-density polyethylene treated by Ar plasma at 300 K was performed in X-band at temperatures from 2.1 K to 290 K. The observed spectra suggest presence of allyl radicals, whereas the central peak may be attributed to polyenyl radicals or dangled bonds. Pronounced narrowing of the resonance line observed above glassy temperature of polyethylene may be ascribed to thermally activated motional effect with the activation energy Ea /kB = 160 K. The absence of strong exchange interactions is suggested by negligible exchange narrowing found at 2.1 K. The suggestion is supported by the analysis of the temperature dependence of the intensity at low temperatures, which is explicable assuming the coexistence of non-interacting radicals and S = 1/2 dimers with a distribution of antiferromagnetic couplings varying from 2 K to nominally 25 K.

Interaction of high voltage surfaces with the space plasma. [solar arrays

NASA Technical Reports Server (NTRS)

Kaufman, H. R.; Robinson, R. S.

1979-01-01

Tests were conducted using plasma densities of approximately 10 to the 5th power - 10 to the 6th power/cu cm. Insulating materials tested were polyimide (Dapton), mica and glass. Surface-area effects were found to be substantially reduced from those previously reported at lower plasma densities. The difference in typical plasma density was felt to be the major cause of this change, although a saturation effect may also be involved. At the 10 to the 5th power/cu cm plasma density range, surface effects on collection current appear limited to roughly 1 cm from the hole. A factor of several reduction of collected current was obtained with both surface scribing and a 2 x 2 cm conducting mesh. It appears possible that the effects of surface treatment might be more significant at lower plasma densities. Effects of repeated tests were also noted, with current collection decreasing with successive tests. Depending on the materials involved, the effect appeared due to either the smoothing of the inside of the insulator hole or the sputtering of insulator on the exposed conductor. A general conclusion was made from a variety of observations, that the generation of vapor is a major factor in the enhancement of collected current.

Anticipatory flexibility: larval population density in moths determines male investment in antennae, wings and testes.

PubMed

Johnson, Tamara L; Symonds, Matthew R E; Elgar, Mark A

2017-11-15

Developmental plasticity provides individuals with a distinct advantage when the reproductive environment changes dramatically. Variation in population density, in particular, can have profound effects on male reproductive success. Females may be easier to locate in dense populations, but there may be a greater risk of sperm competition. Thus, males should invest in traits that enhance fertilization success over traits that enhance mate location. Conversely, males in less dense populations should invest more in structures that will facilitate mate location. In Lepidoptera, this may result in the development of larger antennae to increase the likelihood of detecting female sex pheromones, and larger wings to fly more efficiently. We explored the effects of larval density on adult morphology in the gum-leaf skeletonizer moth, Uraba lugens , by manipulating both the number of larvae and the size of the rearing container. This experimental arrangement allowed us to reveal the cues used by larvae to assess whether absolute number or density influences adult responses. Male investment in testes size depended on the number of individuals, while male investment in wings and antennae depended upon larval density. By contrast, the size of female antennae and wings were influenced by an interaction of larval number and container size. This study demonstrates that male larvae are sensitive to cues that may reveal adult population density, and adjust investment in traits associated with fertilization success and mate detection accordingly. © 2017 The Author(s).

Disease ecology across soil boundaries: effects of below-ground fungi on above-ground host–parasite interactions

PubMed Central

Tao, Leiling; Gowler, Camden D.; Ahmad, Aamina; Hunter, Mark D.; de Roode, Jacobus C.

2015-01-01

Host–parasite interactions are subject to strong trait-mediated indirect effects from other species. However, it remains unexplored whether such indirect effects may occur across soil boundaries and connect spatially isolated organisms. Here, we demonstrate that, by changing plant (milkweed Asclepias sp.) traits, arbuscular mycorrhizal fungi (AMF) significantly affect interactions between a herbivore (the monarch butterfly Danaus plexippus) and its protozoan parasite (Ophryocystis elektroscirrha), which represents an interaction across four biological kingdoms. In our experiment, AMF affected parasite virulence, host resistance and host tolerance to the parasite. These effects were dependent on both the density of AMF and the identity of milkweed species: AMF indirectly increased disease in monarchs reared on some species, while alleviating disease in monarchs reared on other species. The species-specificity was driven largely by the effects of AMF on both plant primary (phosphorus) and secondary (cardenolides; toxins in milkweeds) traits. Our study demonstrates that trait-mediated indirect effects in disease ecology are extensive, such that below-ground interactions between AMF and plant roots can alter host–parasite interactions above ground. In general, soil biota may play an underappreciated role in the ecology of many terrestrial host–parasite systems. PMID:26468247

Disease ecology across soil boundaries: effects of below-ground fungi on above-ground host-parasite interactions.

PubMed

Tao, Leiling; Gowler, Camden D; Ahmad, Aamina; Hunter, Mark D; de Roode, Jacobus C

2015-10-22

Host-parasite interactions are subject to strong trait-mediated indirect effects from other species. However, it remains unexplored whether such indirect effects may occur across soil boundaries and connect spatially isolated organisms. Here, we demonstrate that, by changing plant (milkweed Asclepias sp.) traits, arbuscular mycorrhizal fungi (AMF) significantly affect interactions between a herbivore (the monarch butterfly Danaus plexippus) and its protozoan parasite (Ophryocystis elektroscirrha), which represents an interaction across four biological kingdoms. In our experiment, AMF affected parasite virulence, host resistance and host tolerance to the parasite. These effects were dependent on both the density of AMF and the identity of milkweed species: AMF indirectly increased disease in monarchs reared on some species, while alleviating disease in monarchs reared on other species. The species-specificity was driven largely by the effects of AMF on both plant primary (phosphorus) and secondary (cardenolides; toxins in milkweeds) traits. Our study demonstrates that trait-mediated indirect effects in disease ecology are extensive, such that below-ground interactions between AMF and plant roots can alter host-parasite interactions above ground. In general, soil biota may play an underappreciated role in the ecology of many terrestrial host-parasite systems. © 2015 The Author(s).

Size-density scaling in protists and the links between consumer-resource interaction parameters.

PubMed

DeLong, John P; Vasseur, David A

2012-11-01

Recent work indicates that the interaction between body-size-dependent demographic processes can generate macroecological patterns such as the scaling of population density with body size. In this study, we evaluate this possibility for grazing protists and also test whether demographic parameters in these models are correlated after controlling for body size. We compiled data on the body-size dependence of consumer-resource interactions and population density for heterotrophic protists grazing algae in laboratory studies. We then used nested dynamic models to predict both the height and slope of the scaling relationship between population density and body size for these protists. We also controlled for consumer size and assessed links between model parameters. Finally, we used the models and the parameter estimates to assess the individual- and population-level dependence of resource use on body-size and prey-size selection. The predicted size-density scaling for all models matched closely to the observed scaling, and the simplest model was sufficient to predict the pattern. Variation around the mean size-density scaling relationship may be generated by variation in prey productivity and area of capture, but residuals are relatively insensitive to variation in prey size selection. After controlling for body size, many consumer-resource interaction parameters were correlated, and a positive correlation between residual prey size selection and conversion efficiency neutralizes the apparent fitness advantage of taking large prey. Our results indicate that widespread community-level patterns can be explained with simple population models that apply consistently across a range of sizes. They also indicate that the parameter space governing the dynamics and the steady states in these systems is structured such that some parts of the parameter space are unlikely to represent real systems. Finally, predator-prey size ratios represent a kind of conundrum, because they are widely observed but apparently have little influence on population size and fitness, at least at this level of organization. © 2012 The Authors. Journal of Animal Ecology © 2012 British Ecological Society.

Minimal nuclear energy density functional

NASA Astrophysics Data System (ADS)

Bulgac, Aurel; Forbes, Michael McNeil; Jin, Shi; Perez, Rodrigo Navarro; Schunck, Nicolas

2018-04-01

We present a minimal nuclear energy density functional (NEDF) called "SeaLL1" that has the smallest number of possible phenomenological parameters to date. SeaLL1 is defined by seven significant phenomenological parameters, each related to a specific nuclear property. It describes the nuclear masses of even-even nuclei with a mean energy error of 0.97 MeV and a standard deviation of 1.46 MeV , two-neutron and two-proton separation energies with rms errors of 0.69 MeV and 0.59 MeV respectively, and the charge radii of 345 even-even nuclei with a mean error ɛr=0.022 fm and a standard deviation σr=0.025 fm . SeaLL1 incorporates constraints on the equation of state (EoS) of pure neutron matter from quantum Monte Carlo calculations with chiral effective field theory two-body (NN ) interactions at the next-to-next-to-next-to leading order (N3LO) level and three-body (NNN ) interactions at the next-to-next-to leading order (N2LO) level. Two of the seven parameters are related to the saturation density and the energy per particle of the homogeneous symmetric nuclear matter, one is related to the nuclear surface tension, two are related to the symmetry energy and its density dependence, one is related to the strength of the spin-orbit interaction, and one is the coupling constant of the pairing interaction. We identify additional phenomenological parameters that have little effect on ground-state properties but can be used to fine-tune features such as the Thomas-Reiche-Kuhn sum rule, the excitation energy of the giant dipole and Gamow-Teller resonances, the static dipole electric polarizability, and the neutron skin thickness.

Minimal nuclear energy density functional

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

Bulgac, Aurel; Forbes, Michael McNeil; Jin, Shi

Inmore » this paper, we present a minimal nuclear energy density functional (NEDF) called “SeaLL1” that has the smallest number of possible phenomenological parameters to date. SeaLL1 is defined by seven significant phenomenological parameters, each related to a specific nuclear property. It describes the nuclear masses of even-even nuclei with a mean energy error of 0.97 MeV and a standard deviation of 1.46 MeV , two-neutron and two-proton separation energies with rms errors of 0.69 MeV and 0.59 MeV respectively, and the charge radii of 345 even-even nuclei with a mean error ε r = 0.022 fm and a standard deviation σ r = 0.025 fm . SeaLL1 incorporates constraints on the equation of state (EoS) of pure neutron matter from quantum Monte Carlo calculations with chiral effective field theory two-body ( NN ) interactions at the next-to-next-to-next-to leading order (N3LO) level and three-body ( NNN ) interactions at the next-to-next-to leading order (N2LO) level. Two of the seven parameters are related to the saturation density and the energy per particle of the homogeneous symmetric nuclear matter, one is related to the nuclear surface tension, two are related to the symmetry energy and its density dependence, one is related to the strength of the spin-orbit interaction, and one is the coupling constant of the pairing interaction. Finally, we identify additional phenomenological parameters that have little effect on ground-state properties but can be used to fine-tune features such as the Thomas-Reiche-Kuhn sum rule, the excitation energy of the giant dipole and Gamow-Teller resonances, the static dipole electric polarizability, and the neutron skin thickness.« less

Minimal nuclear energy density functional

DOE PAGES

Bulgac, Aurel; Forbes, Michael McNeil; Jin, Shi; ...

2018-04-17

Inmore » this paper, we present a minimal nuclear energy density functional (NEDF) called “SeaLL1” that has the smallest number of possible phenomenological parameters to date. SeaLL1 is defined by seven significant phenomenological parameters, each related to a specific nuclear property. It describes the nuclear masses of even-even nuclei with a mean energy error of 0.97 MeV and a standard deviation of 1.46 MeV , two-neutron and two-proton separation energies with rms errors of 0.69 MeV and 0.59 MeV respectively, and the charge radii of 345 even-even nuclei with a mean error ε r = 0.022 fm and a standard deviation σ r = 0.025 fm . SeaLL1 incorporates constraints on the equation of state (EoS) of pure neutron matter from quantum Monte Carlo calculations with chiral effective field theory two-body ( NN ) interactions at the next-to-next-to-next-to leading order (N3LO) level and three-body ( NNN ) interactions at the next-to-next-to leading order (N2LO) level. Two of the seven parameters are related to the saturation density and the energy per particle of the homogeneous symmetric nuclear matter, one is related to the nuclear surface tension, two are related to the symmetry energy and its density dependence, one is related to the strength of the spin-orbit interaction, and one is the coupling constant of the pairing interaction. Finally, we identify additional phenomenological parameters that have little effect on ground-state properties but can be used to fine-tune features such as the Thomas-Reiche-Kuhn sum rule, the excitation energy of the giant dipole and Gamow-Teller resonances, the static dipole electric polarizability, and the neutron skin thickness.« less

Multispecies reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Aghamohammadi, A.; Fatollahi, A. H.; Khorrami, M.; Shariati, A.

2000-10-01

Multispecies reaction-diffusion systems, for which the time evolution equations of correlation functions become a closed set, are considered. A formal solution for the average densities is found. Some special interactions and the exact time dependence of the average densities in these cases are also studied. For the general case, the large-time behavior of the average densities has also been obtained.

Quantum non-Abelian hydrodynamics: Anyonic or spin-orbital entangled liquids, nonunitarity of scattering matrix and charge fractionalization

NASA Astrophysics Data System (ADS)

Pareek, Tribhuvan Prasad

2015-09-01

In this article, we develop an exact (nonadiabatic, nonperturbative) density matrix scattering theory for a two component quantum liquid which interacts or scatters off from a generic spin-dependent quantum potential. The generic spin dependent quantum potential [Eq. (1)] is a matrix potential, hence, adiabaticity criterion is ill-defined. Therefore the full matrix potential should be treated nonadiabatically. We succeed in doing so using the notion of vectorial matrices which allows us to obtain an exact analytical expression for the scattered density matrix (SDM), ϱsc [Eq. (30)]. We find that the number or charge density in scattered fluid, Tr(ϱsc), expressions in Eqs. (32) depends on nontrivial quantum interference coefficients, Qα β 0ijk, which arises due to quantum interference between spin-independent and spin-dependent scattering amplitudes and among spin-dependent scattering amplitudes. Further it is shown that Tr(ϱsc) can be expressed in a compact form [Eq. (39)] where the effect of quantum interference coefficients can be included using a vector Qαβ, which allows us to define a vector order parameterQ. Since the number density is obtained using an exact scattered density matrix, therefore, we do not need to prove that Q is non-zero. However, for sake of completeness, we make detailed mathematical analysis for the conditions under which the vector order parameterQ would be zero or nonzero. We find that in presence of spin-dependent interaction the vector order parameterQ is necessarily nonzero and is related to the commutator and anti-commutator of scattering matrix S with its dagger S† [Eq. (78)]. It is further shown that Q≠0, implies four physically equivalent conditions,i.e., spin-orbital entanglement is nonzero, non-Abelian scattering phase, i.e., matrices, scattering matrix is nonunitary and the broken time reversal symmetry for SDM. This also implies that quasi particle excitation are anyonic in nature, hence, charge fractionalization is a natural consequence. This aspect has also been discussed from the perspective of number or charge density conservation, which implies i.e., Tr(ϱ} sc) = Tr(ϱin). On the other hand Q = 0 turns out to be a mathematically forced unphysical solution in presence of spin-dependent potential or scattering which is equivalent to Abelian hydrodynamics, unitary scattering matrix, absence of spin-space entanglement and preserved time reversal symmetry. We have formulated the theory using mesoscopic language, specifically, we have considered two terminal systems connected to spin-dependent scattering region, which is equivalent to having two potential wells separated by a generic spin-dependent potential barrier. The formulation using mesoscopic language is practically useful because it leads directly to the measured quantities such as conductance and spin-polarization density in the leads, however, the presented formulation is not limited to the mesoscopic system only, its generality has been stressed at various places in this article.

Defects and anharmonicity induced electron spectra of YBa2Cu3O7-δ superconductors

NASA Astrophysics Data System (ADS)

Singh, Anu; Indu, B. D.

2018-05-01

The effects of defects and anharmonicities on the electron density of states (EDOS) have been studied in high-temperature superconductors (HTS) adopting the many body quantum dynamical theory of electron Green's functions via a generalized Hamiltonian that includes the effects of electron-phonon interactions, anharmonicities and point impurities. The automatic emergence of pairons and temperature dependence of EDOS are appear as special feature of the theory. The results thus obtained and their numerical analysis for YBa2Cu3O7-δ superconductors clearly demonstrate that the presence of defects, anharmonicities and electron-phonon interactions modifies the behavior of EDOS over a wide range of temperature.

Orbitally limited pair-density-wave phase of multilayer superconductors

NASA Astrophysics Data System (ADS)

Möckli, David; Yanase, Youichi; Sigrist, Manfred

2018-04-01

We investigate the magnetic field dependence of an ideal superconducting vortex lattice in the parity-mixed pair-density-wave phase of multilayer superconductors within a circular cell Ginzburg-Landau approach. In multilayer systems, due to local inversion symmetry breaking, a Rashba spin-orbit coupling is induced at the outer layers. This combined with a perpendicular paramagnetic (Pauli) limiting magnetic field stabilizes a staggered layer dependent pair-density-wave phase in the superconducting singlet channel. The high-field pair-density-wave phase is separated from the low-field BCS phase by a first-order phase transition. The motivating guiding question in this paper is: What is the minimal necessary Maki parameter αM for the appearance of the pair-density-wave phase of a superconducting trilayer system? To address this problem we generalize the circular cell method for the regular flux-line lattice of a type-II superconductor to include paramagnetic depairing effects. Then, we apply the model to the trilayer system, where each of the layers are characterized by Ginzburg-Landau parameter κ0 and a Maki parameter αM. We find that when the spin-orbit Rashba interaction compares to the superconducting condensation energy, the orbitally limited pair-density-wave phase stabilizes for Maki parameters αM>10 .

Cell density-dependent differential proliferation of neural stem cells on omnidirectional nanopore-arrayed surface.

PubMed

Cha, Kyoung Je; Kong, Sun-Young; Lee, Ji Soo; Kim, Hyung Woo; Shin, Jae-Yeon; La, Moonwoo; Han, Byung Woo; Kim, Dong Sung; Kim, Hyun-Jung

2017-10-12

Recently, the importance of surface nanotopography in the determination of stem cell fate and behavior has been revealed. In the current study, we generated polystyrene cell-culture dishes with an omnidirectional nanopore arrayed surface (ONAS) (diameter: 200 nm, depth: 500 nm, center-to-center distance: 500 nm) and investigated the effects of nanotopography on rat neural stem cells (NSCs). NSCs cultured on ONAS proliferated better than those on the flat surface when cell density was low and showed less spontaneous differentiation during proliferation in the presence of mitogens. Interestingly, NSCs cultured on ONAS at clonal density demonstrated a propensity to generate neurospheres, whereas those on the flat surface migrated out, proliferated as individuals, and spread out to attach to the surface. However, the differential patterns of proliferation were cell density-dependent since the distinct phenomena were lost when cell density was increased. ONAS modulated cytoskeletal reorganization and inhibited formation of focal adhesion, which is generally observed in NSCs grown on flat surfaces. ONAS appeared to reinforce NSC-NSC interaction, restricted individual cell migration and prohibited NSC attachment to the nanopore surface. These data demonstrate that ONAS maintains NSCs as undifferentiated while retaining multipotency and is a better topography for culturing low density NSCs.

Superfluidity in Strongly Interacting Fermi Systems with Applications to Neutron Stars

NASA Astrophysics Data System (ADS)

Khodel, Vladimir

The rotational dynamics and cooling history of neutron stars is influenced by the superfluid properties of nucleonic matter. In this thesis a novel separation technique is applied to the analysis of the gap equation for neutron matter. It is shown that the problem can be recast into two tasks: solving a simple system of linear integral equations for the shape functions of various components of the gap function and solving a system of non-linear algebraic equations for their scale factors. Important simplifications result from the fact that the ratio of the gap amplitude to the Fermi energy provides a small parameter in this problem. The relationship between the analytic structure of the shape functions and the density interval for the existence of superfluid gap is discussed. It is shown that in 1S0 channel the position of the first zero of the shape function gives an estimate of the upper critical density. The relation between the resonant behavior of the two-neutron interaction in this channel and the density dependence of the gap is established. The behavior of the gap in the limits of low and high densities is analyzed. Various approaches to calculation of the scale factors are considered: model cases, angular averaging, and perturbation theory. An optimization-based approach is proposed. The shape functions and scale factors for Argonne υ14 and υ18 potentials are determined in singlet and triplet channels. Dependence of the solution on the value of effective mass and medium polarization is studied.

The Origins of Scintillator Non-Proportionality

NASA Astrophysics Data System (ADS)

Moses, W. W.; Bizarri, G. A.; Williams, R. T.; Payne, S. A.; Vasil'ev, A. N.; Singh, J.; Li, Q.; Grim, J. Q.; Choong, W.-S.

2012-10-01

Recent years have seen significant advances in both theoretically understanding and mathematically modeling the underlying causes of scintillator non-proportionality. The core cause is that the interaction of radiation with matter invariably leads to a non-uniform ionization density in the scintillator, coupled with the fact that the light yield depends on the ionization density. The mechanisms that lead to the luminescence dependence on ionization density are incompletely understood, but several important features have been identified, notably Auger-like processes (where two carriers of excitation interact with each other, causing one to de-excite non-radiatively), the inability of excitation carriers to recombine (caused either by trapping or physical separation), and the carrier mobility. This paper reviews the present understanding of the fundamental origins of scintillator non-proportionality, specifically the various theories that have been used to explain non-proportionality.

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

PubMed

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

2013-01-01

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

Analysis of dependent scattering mechanism in hard-sphere Yukawa random media

NASA Astrophysics Data System (ADS)

Wang, B. X.; Zhao, C. Y.

2018-06-01

The structural correlations in the microscopic structures of random media can induce the dependent scattering mechanism and thus influence the optical scattering properties. Based on our recent theory on the dependent scattering mechanism in random media composed of discrete dipolar scatterers [B. X. Wang and C. Y. Zhao, Phys. Rev. A 97, 023836 (2018)], in this paper, we study the hard-sphere Yukawa random media, in order to further elucidate the role of structural correlations in the dependent scattering mechanism and hence optical scattering properties. Here, we consider charged colloidal suspensions, whose effective pair interaction between colloids is described by a screened Coulomb (Yukawa) potential. By means of adding salt ions, the pair interaction between the charged particles can be flexibly tailored and therefore the structural correlations are modified. It is shown that this strategy can affect the optical properties significantly. For colloidal TiO2 suspensions, the modification of electric and magnetic dipole excitations induced by the structural correlations can substantially influence the optical scattering properties, in addition to the far-field interference effect described by the structure factor. However, this modification is only slightly altered by different salt concentrations and is mainly because of the packing-density-dependent screening effect. On the other hand, for low refractive index colloidal polystyrene suspensions, the dependent scattering mechanism mainly involves the far-field interference effect, and the effective exciting field amplitude for the electric dipole almost remains unchanged under different structural correlations. The present study has profound implications for understanding the role of structural correlations in the dependent scattering mechanism.

New optimization scheme to obtain interaction potentials for oxide glasses

NASA Astrophysics Data System (ADS)

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

2018-05-01

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

Calibration of the fine-structure constant of graphene by time-dependent density-functional theory

NASA Astrophysics Data System (ADS)

Sindona, A.; Pisarra, M.; Vacacela Gomez, C.; Riccardi, P.; Falcone, G.; Bellucci, S.

2017-11-01

One of the amazing properties of graphene is the ultrarelativistic behavior of its loosely bound electrons, mimicking massless fermions that move with a constant velocity, inversely proportional to a fine-structure constant αg of the order of unity. The effective interaction between these quasiparticles is, however, better controlled by the coupling parameter αg*=αg/ɛ , which accounts for the dynamic screening due to the complex permittivity ɛ of the many-valence electron system. This concept was introduced in a couple of previous studies [Reed et al., Science 330, 805 (2010) and Gan et al., Phys. Rev. B 93, 195150 (2016)], where inelastic x-ray scattering measurements on crystal graphite were converted into an experimentally derived form of αg* for graphene, over an energy-momentum region on the eV Å -1 scale. Here, an accurate theoretical framework is provided for αg*, using time-dependent density-functional theory in the random-phase approximation, with a cutoff in the interaction between excited electrons in graphene, which translates to an effective interlayer interaction in graphite. The predictions of the approach are in excellent agreement with the above-mentioned measurements, suggesting a calibration method to substantially improve the experimental derivation of αg*, which tends to a static limiting value of ˜0.14 . Thus, the ab initio calibration procedure outlined demonstrates the accuracy of perturbation expansion treatments for the two-dimensional gas of massless Dirac fermions in graphene, in parallel with quantum electrodynamics.

Interaction between fractional Josephson vortices in multi-gap superconductor tunnel junctions

NASA Astrophysics Data System (ADS)

Kim, Ju H.

In a long Josephson junction (LJJ) with two-band superconductors, fractionalization of Josephson vortices (fluxons) can occur in the broken time reversal symmetry state when spatial phase textures (i-solitons) are excited. Excitation of i-solitons in each superconductor layer of the junction, arising due to the presence of two condensates and the interband Josephson effect, leads to spatial variation of the critical current density between the superconductor layers. Similar to the situation in a YBa2 Cu3O7 - x superconductor film grain boundary, this spatial dependence of the crtitical current density can self-generate magnetic flux in the insulator layer, resulting in fractional fluxons with large and small fraction of flux quantum. Similar to fluxons in one-band superconductor LJJ, these fractional fluxons are found to interact with each other. The interaction between large and small fractional fluxons determines the size of a fluxon which includes two (one large and one small) fractional fluxons. We discuss the nature of interaction between fractional fluxons and suggest that i-soliton excitations in multi-gap superconductor LJJs may be probed by using magnetic flux measurements.

Effect of Temper Condition on Stress Relaxation Behavior of an Aluminum Copper Lithium Alloy

NASA Astrophysics Data System (ADS)

Mishra, Sumeet; Beura, Vikrant Kumar; Singh, Amit; Yadava, Manasij; Nayan, Niraj

2018-07-01

Deformation behavior of an Al-Cu-Li alloy in different temper conditions (solutionized and T8) is investigated using stress relaxation tests. Fundamental parameters such as the apparent and physical activation volume, strain rate sensitivity, effective stress, and exhaustion rate of mobile dislocation density are determined from single and multiple relaxation tests. It was found that dislocation-dislocation interaction controls the kinetics of plastic deformation in the solutionized sample, whereas dislocation-precipitate interaction is the overriding factor in the presence of T1 precipitates. The apparent activation volume was found to be significantly lower in the presence of T1 precipitates compared with solutionized samples. Strain rate sensitivity and effective stress were found to be higher in the presence of T1 precipitates. In addition, multiple relaxation tests showed that irrespective of microstructural features (solutes, semi-coherent precipitates), the mobile dislocation density reduces during the relaxation period. Further evidence regarding reduction in mobile dislocation density is obtained from uniaxial tensile tests carried out after stress relaxation tests, where both solutionized and T8 samples show an increase in strength. Additional discussion on relaxation strain is included to provide a complete overview regarding the time-dependent deformation behavior of the Al-Cu-Li alloy in different temper conditions.

Effect of Temper Condition on Stress Relaxation Behavior of an Aluminum Copper Lithium Alloy

NASA Astrophysics Data System (ADS)

Mishra, Sumeet; Beura, Vikrant Kumar; Singh, Amit; Yadava, Manasij; Nayan, Niraj

2018-04-01

Deformation behavior of an Al-Cu-Li alloy in different temper conditions (solutionized and T8) is investigated using stress relaxation tests. Fundamental parameters such as the apparent and physical activation volume, strain rate sensitivity, effective stress, and exhaustion rate of mobile dislocation density are determined from single and multiple relaxation tests. It was found that dislocation-dislocation interaction controls the kinetics of plastic deformation in the solutionized sample, whereas dislocation-precipitate interaction is the overriding factor in the presence of T1 precipitates. The apparent activation volume was found to be significantly lower in the presence of T1 precipitates compared with solutionized samples. Strain rate sensitivity and effective stress were found to be higher in the presence of T1 precipitates. In addition, multiple relaxation tests showed that irrespective of microstructural features (solutes, semi-coherent precipitates), the mobile dislocation density reduces during the relaxation period. Further evidence regarding reduction in mobile dislocation density is obtained from uniaxial tensile tests carried out after stress relaxation tests, where both solutionized and T8 samples show an increase in strength. Additional discussion on relaxation strain is included to provide a complete overview regarding the time-dependent deformation behavior of the Al-Cu-Li alloy in different temper conditions.

Hartree-Fock studies of hypernuclear properties

NASA Astrophysics Data System (ADS)

Lanskoy, D. E.

1998-08-01

The Skyrme-Hartree-Fock approach is approved as a powerful tool to reproduce general properties of Λ hypernuclear spectra [1-4] and to relate hypernuclear observables to effective interaction features. In this contribution, we consider briefly some less common hypernuclear systems, which appear to be quite sensitive to details of the relevant interactions. Particularly, we address possible manifestations of the polarization of a hypernuclear core (i.e. core distortion due to hyperon addition), which is driven in terms of the Skyrme force mainly by counterbalance between the two-body ΛN force and the three-body ΛNN (or density-dependent ΛN) one.

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

PubMed Central

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

2008-01-01

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

Optical properties of body-centered tetragonal C4: Insights from many-body perturbation and time-dependent density functional theories

NASA Astrophysics Data System (ADS)

Tarighi Ahmadpour, Mahdi; Rostamnejadi, Ali; Hashemifar, S. Javad

2018-04-01

We study the electronic structure and optical properties of a body-centered tetragonal phase of carbon (bct-C4) within the framework of time-dependent density functional theory and Bethe-Salpeter equation. The results indicate that the optical properties of bct-C4 are strongly affected by the electron-hole interaction. It is demonstrated that the long-range corrected exchange-correlation kernels could fairly reproduce the Bethe-Salpeter equation results. The effective carrier number reveals that at energies above 30 eV, the excitonic effects are not dominant any more and that the optical transitions originate mainly from electronic excitations. The emerged peaks in the calculated electron energy loss spectra are discussed in terms of plasmon excitations and interband transitions. The results of the research indicate that bct-C4 is an indirect wide-band-gap semiconductor, which is transparent in the visible region and opaque in the ultraviolet spectral range.

Dimensional Effects on the Charge Density Waves in Ultrathin Films of TiSe 2

DOE PAGES

Chen, P.; Chan, Y. -H.; Wong, M. -H.; ...

2016-09-20

Charge density wave (CDW) formation in solids is a critical phenomenon involving the collective reorganization of the electrons and atoms in the system into a wave structure, and it is expected to be sensitive to the geometric constraint of the system at the nanoscale. Here, we study the CDW transition in TiSe 2, a quasi-two-dimensional layered material, to determine the effects of quantum confinement and changing dimensions in films ranging from a single layer to multilayers. Of key interest is the characteristic length scale for the transformation from a two-dimensional case to the three-dimensional limit. Angle-resolved photoemission (ARPES) measurements ofmore » films with thicknesses up to six layers reveal substantial variations in the energy structure of discrete quantum well states; however, the temperature-dependent band-gap renormalization converges at just three layers. The results indicate a layer-dependent mixture of two transition temperatures and a very-short-range CDW interaction within a three-dimensional framework.« less

Organic Farming: Biodiversity Impacts Can Depend on Dispersal Characteristics and Landscape Context

PubMed Central

Feber, Ruth E.; Johnson, Paul J.; Bell, James R.; Chamberlain, Dan E.; Firbank, Leslie G.; Fuller, Robert J.; Manley, Will; Mathews, Fiona; Norton, Lisa R.; Townsend, Martin; Macdonald, David W.

2015-01-01

Organic farming, a low intensity system, may offer benefits for a range of taxa, but what affects the extent of those benefits is imperfectly understood. We explored the effects of organic farming and landscape on the activity density and species density of spiders and carabid beetles, using a large sample of paired organic and conventional farms in the UK. Spider activity density and species density were influenced by both farming system and surrounding landscape. Hunting spiders, which tend to have lower dispersal capabilities, had higher activity density, and more species were captured, on organic compared to conventional farms. There was also evidence for an interaction, as the farming system effect was particularly marked in the cropped area before harvest and was more pronounced in complex landscapes (those with little arable land). There was no evidence for any effect of farming system or landscape on web-building spiders (which include the linyphiids, many of which have high dispersal capabilities). For carabid beetles, the farming system effects were inconsistent. Before harvest, higher activity densities were observed in the crops on organic farms compared with conventional farms. After harvest, no difference was detected in the cropped area, but more carabids were captured on conventional compared to organic boundaries. Carabids were more species-dense in complex landscapes, and farming system did not affect this. There was little evidence that non-cropped habitat differences explained the farming system effects for either spiders or carabid beetles. For spiders, the farming system effects in the cropped area were probably largely attributable to differences in crop management; reduced inputs of pesticides (herbicides and insecticides) and fertilisers are possible influences, and there was some evidence for an effect of non-crop plant species richness on hunting spider activity density. The benefits of organic farming may be greatest for taxa with lower dispersal abilities generally. The evidence for interactions among landscape and farming system in their effects on spiders highlights the importance of developing strategies for managing farmland at the landscape-scale for most effective conservation of biodiversity. PMID:26309040

Organic Farming: Biodiversity Impacts Can Depend on Dispersal Characteristics and Landscape Context.

PubMed

Feber, Ruth E; Johnson, Paul J; Bell, James R; Chamberlain, Dan E; Firbank, Leslie G; Fuller, Robert J; Manley, Will; Mathews, Fiona; Norton, Lisa R; Townsend, Martin; Macdonald, David W

2015-01-01

Organic farming, a low intensity system, may offer benefits for a range of taxa, but what affects the extent of those benefits is imperfectly understood. We explored the effects of organic farming and landscape on the activity density and species density of spiders and carabid beetles, using a large sample of paired organic and conventional farms in the UK. Spider activity density and species density were influenced by both farming system and surrounding landscape. Hunting spiders, which tend to have lower dispersal capabilities, had higher activity density, and more species were captured, on organic compared to conventional farms. There was also evidence for an interaction, as the farming system effect was particularly marked in the cropped area before harvest and was more pronounced in complex landscapes (those with little arable land). There was no evidence for any effect of farming system or landscape on web-building spiders (which include the linyphiids, many of which have high dispersal capabilities). For carabid beetles, the farming system effects were inconsistent. Before harvest, higher activity densities were observed in the crops on organic farms compared with conventional farms. After harvest, no difference was detected in the cropped area, but more carabids were captured on conventional compared to organic boundaries. Carabids were more species-dense in complex landscapes, and farming system did not affect this. There was little evidence that non-cropped habitat differences explained the farming system effects for either spiders or carabid beetles. For spiders, the farming system effects in the cropped area were probably largely attributable to differences in crop management; reduced inputs of pesticides (herbicides and insecticides) and fertilisers are possible influences, and there was some evidence for an effect of non-crop plant species richness on hunting spider activity density. The benefits of organic farming may be greatest for taxa with lower dispersal abilities generally. The evidence for interactions among landscape and farming system in their effects on spiders highlights the importance of developing strategies for managing farmland at the landscape-scale for most effective conservation of biodiversity.

Three-Nucleon Forces and Triplet Pairing in Neutron Matter

NASA Astrophysics Data System (ADS)

Papakonstantinou, P.; Clark, J. W.

2017-12-01

The existence of superfluidity of the neutron component in the core of a neutron star, associated specifically with triplet P-wave pairing, is currently an open question that is central to interpretation of the observed cooling curves and other neutron-star observables. Ab initio theoretical calculations aimed at resolving this issue face unique challenges in the relevant high-density domain, which reaches beyond the saturation density of symmetrical nuclear matter. These issues include uncertainties in the three-nucleon (3N) interaction and in the effects of strong short-range correlations—and more generally of in-medium modification of nucleonic self-energies and interactions. A survey of existing solutions of the gap equations in the triplet channel demonstrates that the net impact on the gap magnitude of 3N forces, coupled channels, and mass renormalization shows extreme variation dependent on specific theoretical inputs, in some cases even pointing to the absence of a triplet gap, thus motivating a detailed analysis of competing effects within a well-controlled model. In the present study, we track the effects of the 3N force and in-medium modifications in the representative case of the ^3P_2 channel, based on the Argonne v_{18} two-nucleon (2N) interaction supplemented by 3N interactions of the Urbana IX family. Sensitivity of the results to the input interaction is clearly demonstrated. We point out consistency issues with respect to the simultaneous treatment of 3N forces and in-medium effects, which warrant further investigation. We consider this pilot study as the first step toward a systematic and comprehensive exploration of coupled-channel ^3P F_2 pairing using a broad range of 2N and 3N interactions from the current generation of refined semi-phenomenological models and models derived from chiral effective field theory.

Effect of van der Waals interactions on the structural and binding properties of GaSe

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

Sarkisov, Sergey Y., E-mail: sarkisov@mail.tsu.ru; Kosobutsky, Alexey V., E-mail: kosobutsky@kemsu.ru; Kemerovo State University, Krasnaya 6, 650043 Kemerovo

The influence of van der Waals interactions on the lattice parameters, band structure, elastic moduli and binding energy of layered GaSe compound has been studied using projector-augmented wave method within density functional theory. We employed the conventional local/semilocal exchange-correlation functionals and recently developed van der Waals functionals which are able to describe dispersion forces. It is found that application of van der Waals density functionals allows to substantially increase the accuracy of calculations of the lattice constants a and c and interlayer distance in GaSe at ambient conditions and under hydrostatic pressure. The pressure dependences of the a-parameter, Ga–Ga, Ga–Semore » bond lengths and Ga–Ga–Se bond angle are characterized by a relatively low curvature, while c(p) has a distinct downward bowing due to nonlinear shrinking of the interlayer spacing. From the calculated binding energy curves we deduce the interlayer binding energy of GaSe, which is found to be in the range 0.172–0.197 eV/layer (14.2–16.2 meV/Å{sup 2}). - Highlights: • Effects of van der Waals interactions are analyzed using advanced density functionals. • Calculations with vdW-corrected functionals closely agree with experiment. • Interlayer binding energy of GaSe is estimated to be 14.2–16.2 meV/Å{sup 2}.« less

Pressure effect on the superconducting and the normal state of β -B i2Pd

NASA Astrophysics Data System (ADS)

Pristáš, G.; Orendáč, Mat.; Gabáni, S.; Kačmarčík, J.; Gažo, E.; Pribulová, Z.; Correa-Orellana, A.; Herrera, E.; Suderow, H.; Samuely, P.

2018-04-01

The pressure effect up to 24.0 kbar on superconducting and normal-state properties of β -B i2Pd single crystal (Tc≈4.98 K at ambient pressure) has been investigated by measurements of the electrical resistivity. In addition, we have performed the heat capacity measurements in the temperature range 0.7-300 K at ambient pressure. The recent calculations of electronic density of states, electron-phonon interaction spectral function, and phonon density of states of β -B i2Pd [Zheng and Margine, Phys. Rev. B 95, 014512 (2017), 10.1103/PhysRevB.95.014512], are used to fit the resistivity and the heat capacity data. In the superconducting state we have focused on the influence of pressure on the superconducting transition temperature Tc and upper critical field Hc 2 and a negative effect with d Tc/d p =-0.025 K /kbar and d Hc 2/d p =-8 mT /kbar is found. A simplified Bloch-Grüneisen model was used to analyze the pressure effect on the temperature dependence of the normal-state resistivity. The obtained results point to a decrease of the electron-phonon coupling parameter λ and to a shift of phonon frequencies to higher values with pressure. Moreover, the temperature dependence of the normal-state resistivity follows a T2 dependence above Tc up to about 25 K. Together with the enhanced value of Sommerfeld coefficient γ =13.23 mJ mo l-1K-2 these results point to a certain role of the electron-electron interaction in the superconducting pairing mechanism in β -B i2Pd .

Modeling of dislocation channel width evolution in irradiated metals

DOE PAGES

Doyle, Peter J.; Benensky, Kelsa M.; Zinkle, Steven J.

2017-11-08

Defect-free dislocation channel formation has been reported to promote plastic instability during tensile testing via localized plastic flow, leading to a distinct loss of ductility and strain hardening in many low-temperature irradiated materials. In order to study the underlying mechanisms governing dislocation channel width and formation, the channel formation process is modeled via a simple stochastic dislocation-jog process dependent upon grain size, defect cluster density, and defect size. Dislocations traverse a field of defect clusters and jog stochastically upon defect interaction, forming channels of low defect-density. And based upon prior molecular dynamics (MD) simulations and in-situ experimental transmission electron microscopymore » (TEM) observations, each dislocation encounter with a dislocation loop or stacking fault tetrahedron (SFT) is assumed to cause complete absorption of the defect cluster, prompting the dislocation to jog up or down by a distance equal to half the defect cluster diameter. Channels are predicted to form rapidly and are comparable to reported TEM measurements for many materials. Predicted channel widths are found to be most strongly dependent on mean defect size and correlated well with a power law dependence on defect diameter and density, and distance from the dislocation source. Due to the dependence of modeled channel width on defect diameter and density, maximum channel width is predicted to slowly increase as accumulated dose increases. The relatively weak predicted dependence of channel formation width with distance, in accordance with a diffusion analogy, implies that after only a few microns from the source, most channels observed via TEM analyses may not appear to vary with distance because of limitations in the field-of-view to a few microns. Furthermore, examinations of the effect of the so-called “source-broadening” mechanism of channel formation showed that its effect is simply to add a minimum thickness to the channel without affecting channel dependence on the given parameters.« less

Modeling of dislocation channel width evolution in irradiated metals

NASA Astrophysics Data System (ADS)

Doyle, Peter J.; Benensky, Kelsa M.; Zinkle, Steven J.

2018-02-01

Defect-free dislocation channel formation has been reported to promote plastic instability during tensile testing via localized plastic flow, leading to a distinct loss of ductility and strain hardening in many low-temperature irradiated materials. In order to study the underlying mechanisms governing dislocation channel width and formation, the channel formation process is modeled via a simple stochastic dislocation-jog process dependent upon grain size, defect cluster density, and defect size. Dislocations traverse a field of defect clusters and jog stochastically upon defect interaction, forming channels of low defect-density. Based upon prior molecular dynamics (MD) simulations and in-situ experimental transmission electron microscopy (TEM) observations, each dislocation encounter with a dislocation loop or stacking fault tetrahedron (SFT) is assumed to cause complete absorption of the defect cluster, prompting the dislocation to jog up or down by a distance equal to half the defect cluster diameter. Channels are predicted to form rapidly and are comparable to reported TEM measurements for many materials. Predicted channel widths are found to be most strongly dependent on mean defect size and correlated well with a power law dependence on defect diameter and density, and distance from the dislocation source. Due to the dependence of modeled channel width on defect diameter and density, maximum channel width is predicted to slowly increase as accumulated dose increases. The relatively weak predicted dependence of channel formation width with distance, in accordance with a diffusion analogy, implies that after only a few microns from the source, most channels observed via TEM analyses may not appear to vary with distance because of limitations in the field-of-view to a few microns. Further, examinations of the effect of the so-called "source-broadening" mechanism of channel formation showed that its effect is simply to add a minimum thickness to the channel without affecting channel dependence on the given parameters.

Modeling of dislocation channel width evolution in irradiated metals

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

Doyle, Peter J.; Benensky, Kelsa M.; Zinkle, Steven J.

Defect-free dislocation channel formation has been reported to promote plastic instability during tensile testing via localized plastic flow, leading to a distinct loss of ductility and strain hardening in many low-temperature irradiated materials. In order to study the underlying mechanisms governing dislocation channel width and formation, the channel formation process is modeled via a simple stochastic dislocation-jog process dependent upon grain size, defect cluster density, and defect size. Dislocations traverse a field of defect clusters and jog stochastically upon defect interaction, forming channels of low defect-density. And based upon prior molecular dynamics (MD) simulations and in-situ experimental transmission electron microscopymore » (TEM) observations, each dislocation encounter with a dislocation loop or stacking fault tetrahedron (SFT) is assumed to cause complete absorption of the defect cluster, prompting the dislocation to jog up or down by a distance equal to half the defect cluster diameter. Channels are predicted to form rapidly and are comparable to reported TEM measurements for many materials. Predicted channel widths are found to be most strongly dependent on mean defect size and correlated well with a power law dependence on defect diameter and density, and distance from the dislocation source. Due to the dependence of modeled channel width on defect diameter and density, maximum channel width is predicted to slowly increase as accumulated dose increases. The relatively weak predicted dependence of channel formation width with distance, in accordance with a diffusion analogy, implies that after only a few microns from the source, most channels observed via TEM analyses may not appear to vary with distance because of limitations in the field-of-view to a few microns. Furthermore, examinations of the effect of the so-called “source-broadening” mechanism of channel formation showed that its effect is simply to add a minimum thickness to the channel without affecting channel dependence on the given parameters.« less

Transitioning NWChem to the Next Generation of Manycore Machines

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

Bylaska, Eric J.; Apra, E; Kowalski, Karol

The NorthWest chemistry (NWChem) modeling software is a popular molecular chemistry simulation software that was designed from the start to work on massively parallel processing supercomputers [1-3]. It contains an umbrella of modules that today includes self-consistent eld (SCF), second order Møller-Plesset perturbation theory (MP2), coupled cluster (CC), multiconguration self-consistent eld (MCSCF), selected conguration interaction (CI), tensor contraction engine (TCE) many body methods, density functional theory (DFT), time-dependent density functional theory (TDDFT), real-time time-dependent density functional theory, pseudopotential plane-wave density functional theory (PSPW), band structure (BAND), ab initio molecular dynamics (AIMD), Car-Parrinello molecular dynamics (MD), classical MD, hybrid quantum mechanicsmore » molecular mechanics (QM/MM), hybrid ab initio molecular dynamics molecular mechanics (AIMD/MM), gauge independent atomic orbital nuclear magnetic resonance (GIAO NMR), conductor like screening solvation model (COSMO), conductor-like screening solvation model based on density (COSMO-SMD), and reference interaction site model (RISM) solvation models, free energy simulations, reaction path optimization, parallel in time, among other capabilities [4]. Moreover, new capabilities continue to be added with each new release.« less

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

NASA Astrophysics Data System (ADS)

Farzanehpour, Mehdi; Tokatly, Ilya; Nano-Bio Spectroscopy Group; ETSF Scientific Development Centre Team

2015-03-01

We present a rigorous formulation of the time-dependent density functional theory for interacting lattice electrons strongly coupled to cavity photons. We start with an example of one particle on a Hubbard dimer coupled to a single photonic mode, which is equivalent to the single mode spin-boson model or the quantum Rabi model. For this system we prove that the electron-photon wave function is a unique functional of the electronic density and the expectation value of the photonic coordinate, provided the initial state and the density satisfy a set of well defined conditions. Then we generalize the formalism to many interacting electrons on a lattice coupled to multiple photonic modes and prove the general mapping theorem. We also show that for a system evolving from the ground state of a lattice Hamiltonian any density with a continuous second time derivative is locally v-representable. Spanish Ministry of Economy and Competitiveness (Grant No. FIS2013-46159-C3-1-P), Grupos Consolidados UPV/EHU del Gobierno Vasco (Grant No. IT578-13), COST Actions CM1204 (XLIC) and MP1306 (EUSpec).

A Game of Russian Roulette for a Generalist Dinoflagellate Parasitoid: Host Susceptibility Is the Key to Success

PubMed Central

Alacid, Elisabet; Park, Myung G.; Turon, Marta; Petrou, Katherina; Garcés, Esther

2016-01-01

Marine microbial interactions involving eukaryotes and their parasites play an important role in shaping the structure of phytoplankton communities. These interactions may alter population densities of the main host, which in turn may have consequences for the other concurrent species. The effect generalist parasitoids exert on a community is strongly dependent on the degree of host specificity. Parvilucifera sinerae is a generalist parasitoid able to infect a wide range of dinoflagellates, including toxic-bloom-forming species. A density-dependent chemical cue has been identified as the trigger for the activation of the infective stage. Together these traits make Parvilucifera-dinoflagellate hosts a good model to investigate the degree of specificity of a generalist parasitoid, and the potential effects that it could have at the community level. Here, we present for the first time, the strategy by which a generalist dinoflagellate parasitoid seeks out its host and determine whether it exhibits host preferences, highlighting key factors in determining infection. Our results demonstrate that in its infective stage, P. sinerae is able to sense potential hosts, but does not actively select among them. Instead, the parasitoids contact the host at random, governed by the encounter probability rate and once encountered, the chance to penetrate inside the host cell and develop the infection strongly depends on the degree of host susceptibility. As such, their strategy for persistence is more of a game of Russian roulette, where the chance of survival is dependent on the susceptibility of the host. Our study identifies P. sinerae as a potential key player in community ecology, where in mixed dinoflagellate communities consisting of hosts that are highly susceptible to infection, parasitoid preferences may mediate coexistence between host species, reducing the dominance of the superior competitor. Alternatively, it may increase competition, leading to species exclusion. If, however, highly susceptible hosts are absent from the community, the parasitoid population could suffer a dilution effect maintaining a lower parasitoid density. Therefore, both host community structure and host susceptibility will determine infectivity in the field. PMID:27252688

Nucleation and hysteresis of vapor-liquid phase transitions in confined spaces: effects of fluid-wall interaction.

PubMed

Men, Yumei; Yan, Qingzhao; Jiang, Guangfeng; Zhang, Xianren; Wang, Wenchuan

2009-05-01

In this work, we propose a method to stabilize a nucleus in the framework of lattice density-functional theory (LDFT) by imposing a suitable constraint. Using this method, the shape of critical nucleus and height of the nucleation barrier can be determined without using a predefined nucleus as input. As an application of this method, we study the nucleation behavior of vapor-liquid transition in nanosquare pores with infinite length and relate the observed hysteresis loop on an adsorption isotherm to the nucleation mechanism. According to the dependence of hysteresis and the nucleation mechanism on the fluid-wall interaction, w , in this work, we have classified w into three regions ( w>0.9 , 0.1< or =w< or =0.9 , and w<0.1 ), which are denoted as strongly, moderately, and weakly attractive fluid-wall interaction, respectively. The dependence of hysteresis on the fluid-wall interaction is interpreted by the different nucleation mechanisms. Our constrained LDFT calculations also show that the different transition paths may induce different nucleation behaviors. The transition path dependence should be considered if morphological transition of nuclei exists during a nucleation process.

Parasite fitness traits under environmental variation: disentangling the roles of a chytrid's immediate host and external environment.

PubMed

Van den Wyngaert, Silke; Vanholsbeeck, Olivier; Spaak, Piet; Ibelings, Bas W

2014-10-01

Parasite environments are heterogeneous at different levels. The first level of variability is the host itself. The second level represents the external environment for the hosts, to which parasites may be exposed during part of their life cycle. Both levels are expected to affect parasite fitness traits. We disentangle the main and interaction effects of variation in the immediate host environment, here the diatom Asterionella formosa (variables host cell volume and host condition through herbicide pre-exposure) and variation in the external environment (variables host density and acute herbicide exposure) on three fitness traits (infection success, development time and reproductive output) of a chytrid parasite. Herbicide exposure only decreased infection success in a low host density environment. This result reinforces the hypothesis that chytrid zoospores use photosynthesis-dependent chemical cues to locate its host. At high host densities, chemotaxis becomes less relevant due to increasing chance contact rates between host and parasite, thereby following the mass-action principle in epidemiology. Theoretical support for this finding is provided by an agent-based simulation model. The immediate host environment (cell volume) substantially affected parasite reproductive output and also interacted with the external herbicide exposed environment. On the contrary, changes in the immediate host environment through herbicide pre-exposure did not increase infection success, though it had subtle effects on zoospore development time and reproductive output. This study shows that both immediate host and external environment as well as their interaction have significant effects on parasite fitness. Disentangling these effects improves our understanding of the processes underlying parasite spread and disease dynamics.

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

NASA Astrophysics Data System (ADS)

Shchekin, Alexander K.; Lebedeva, Tatiana S.

2017-03-01

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

Effects of surface nanostructuring and impurity doping on ultrafast carrier dynamics of silicon photovoltaic cells: a pump-probe study

NASA Astrophysics Data System (ADS)

Chen, Tianyu; Nam, Yoon-Ho; Wang, Xinke; Han, Peng; Sun, Wenfeng; Feng, Shengfei; Ye, Jiasheng; Song, Jae-Won; Lee, Jung-Ho; Zhang, Chao; Zhang, Yan

2018-01-01

We present femtosecond optical pump-terahertz probe studies on the ultrafast dynamical processes of photo-generated charge carriers in silicon photovoltaic cells with various nanostructured surfaces and doping densities. The pump-probe measurements provide direct insight on the lifetime of photo-generated carriers, frequency-dependent complex dielectric response along with photoconductivity of silicon photovoltaic cells excited by optical pump pulses. A lifetime of photo-generated carriers of tens of nanosecond is identified from the time-dependent pump-induced attenuation of the terahertz transmission. In addition, we find a large value of the imaginary part of the dielectric function and of the real part of the photoconductivity in silicon photovoltaic cells with micron length nanowires. We attribute these findings to the result of defect-enhanced electron-photon interactions. Moreover, doping densities of phosphorous impurities in silicon photovoltaic cells are also quantified using the Drude-Smith model with our measured frequency-dependent complex photoconductivities.

Allelopathy and resource competition: the effects of Phragmites australis invasion in plant communities.

PubMed

Uddin, Md Nazim; Robinson, Randall William

2017-12-01

Phragmites australis, a ubiquitous wetland plant, has been considered one of the most invasive species in the world. Allelopathy appears to be one of the invasion mechanisms, however, the effects could be masked by resource competition among target plants. The difficulty of distinguishing allelopathy from resource competition among plants has hindered investigations of the role of phytotoxic allelochemicals in plant communities. This has been addressed via experiments conducted in both the greenhouse and laboratory by growing associated plants, Melaleuca ericifolia, Rumex conglomeratus, and model plant, Lactuca sativa at varying densities with the allelopathic plant, P. australis, its litter and leachate of P. australis litter. This study investigated the potential interacting influences of allelopathy and resource competition on plant growth-density relationships. In greenhouse, the root exudates mediated effects showed the strongest growth inhibition of M. ericifolia at high density whereas litter mediated results revealed increased growth at medium density treatments compared to low and high density. Again, laboratory experiments related to seed germination and seedling growth of L. sativa and R. conglomeratus exhibited phytotoxicity decreased showing positive growth as plant density increased and vice versa. Overall, the differential effects were observed among experiments but maximum individual plant biomass and some other positive effects on plant traits such as root and shoot length, chlorophyll content occurred at an intermediate density. This was attributed to the sharing of the available phytotoxin among plants at high densities which is compatible to density-dependent phytotoxicity model. The results demonstrated that plant-plant interference is the combined effect of allelopathy and resource competition with many other factors but this experimental design, target-neighbor mixed-culture in combination of plant grown at varying densities with varying level of phytotoxins, mono-culture, can successfully separate allelopathic effects from competition.

Molecular simulation insights on the in vacuo adsorption of amino acids on graphene oxide surfaces with varying surface oxygen densities

NASA Astrophysics Data System (ADS)

Rahmani, Farzin; Nouranian, Sasan; Mahdavi, Mina; Al-Ostaz, Ahmed

2016-11-01

In this fundamental study, a series of molecular dynamics simulations were performed in vacuo to investigate the energetics and select geometries of 20 standard amino acids (AAs) on pristine graphene (PG) and graphene oxide (GO) surfaces as a function of graphene surface oxygen density. These interactions are of key interest to graphene/biomolecular systems. Our results indicate that aromatic AAs exhibit the strongest total interactions with the PG surfaces due to π-π stacking. Tryptophan (Trp) has the highest aromaticity due to its indole side chain and, hence, has the strongest interaction among all AAs (-16.66 kcal/mol). Aliphatic, polar, and charged AAs show various levels of affinity to the PG sheets depending on the strength of their side chain hydrophobic interactions. For example, arginine (Arg) with its guanidinium side chain exhibits the strongest interaction with the PG sheets (-13.81 kcal/mol) following aromatic AAs. Also, glycine (Gly; a polar AA) has the weakest interaction with the PG sheets (-7.29 kcal/mol). When oxygen-containing functional groups are added to the graphene sheets, the π-π stacking in aromatic AAs becomes disrupted and perfect parallelism of the aromatic rings is lost. Moreover, hydrogen bonding and/or electrostatic interactions become more pronounced. Charged AAs exhibit the strongest interactions with the GO surfaces. In general, the AA-GO interactions increase with increasing surface oxygen density, and the effect is more pronounced at higher O/C ratios. This study provides a quantitative measure of AA-graphene interactions for the design and tuning of biomolecular systems suitable for biosensing, drug delivery, and gene delivery applications.

Quantum Fluctuations in Quasi-One-Dimensional Dipolar Bose-Einstein Condensates

NASA Astrophysics Data System (ADS)

Edler, D.; Mishra, C.; Wächtler, F.; Nath, R.; Sinha, S.; Santos, L.

2017-08-01

Recent experiments have revealed that beyond-mean-field corrections are much more relevant in weakly interacting dipolar condensates than in their nondipolar counterparts. We show that in quasi-one-dimensional geometries quantum corrections in dipolar and nondipolar condensates are strikingly different due to the peculiar momentum dependence of the dipolar interactions. The energy correction of the condensate presents not only a modified density dependence, but it may even change from attractive to repulsive at a critical density due to the surprising role played by the transversal directions. The anomalous quantum correction translates into a strongly modified physics for quantum-stabilized droplets and dipolar solitons. Moreover, and for similar reasons, quantum corrections of three-body correlations, and hence of three-body losses, are strongly modified by the dipolar interactions. This intriguing physics can be readily probed in current experiments with magnetic atoms.

Quantum Fluctuations in Quasi-One-Dimensional Dipolar Bose-Einstein Condensates.

PubMed

Edler, D; Mishra, C; Wächtler, F; Nath, R; Sinha, S; Santos, L

2017-08-04

Recent experiments have revealed that beyond-mean-field corrections are much more relevant in weakly interacting dipolar condensates than in their nondipolar counterparts. We show that in quasi-one-dimensional geometries quantum corrections in dipolar and nondipolar condensates are strikingly different due to the peculiar momentum dependence of the dipolar interactions. The energy correction of the condensate presents not only a modified density dependence, but it may even change from attractive to repulsive at a critical density due to the surprising role played by the transversal directions. The anomalous quantum correction translates into a strongly modified physics for quantum-stabilized droplets and dipolar solitons. Moreover, and for similar reasons, quantum corrections of three-body correlations, and hence of three-body losses, are strongly modified by the dipolar interactions. This intriguing physics can be readily probed in current experiments with magnetic atoms.

Molecular Dynamics of Hot Dense Plasmas: New Horizons

NASA Astrophysics Data System (ADS)

Graziani, Frank

2011-10-01

We describe the status of a new time-dependent simulation capability for hot dense plasmas. The backbone of this multi-institutional computational and experimental effort--the Cimarron Project--is the massively parallel molecular dynamics (MD) code ``ddcMD''. The project's focus is material conditions such as exist in inertial confinement fusion experiments, and in many stellar interiors: high temperatures, high densities, significant electromagnetic fields, mixtures of high- and low- Zelements, and non-Maxwellian particle distributions. Of particular importance is our ability to incorporate into this classical MD code key atomic, radiative, and nuclear processes, so that their interacting effects under non-ideal plasma conditions can be investigated. This talk summarizes progress in computational methodology, discusses strengths and weaknesses of quantum statistical potentials as effective interactions for MD, explains the model used for quantum events possibly occurring in a collision and highlights some significant results obtained to date. We describe the status of a new time-dependent simulation capability for hot dense plasmas. The backbone of this multi-institutional computational and experimental effort--the Cimarron Project--is the massively parallel molecular dynamics (MD) code ``ddcMD''. The project's focus is material conditions such as exist in inertial confinement fusion experiments, and in many stellar interiors: high temperatures, high densities, significant electromagnetic fields, mixtures of high- and low- Zelements, and non-Maxwellian particle distributions. Of particular importance is our ability to incorporate into this classical MD code key atomic, radiative, and nuclear processes, so that their interacting effects under non-ideal plasma conditions can be investigated. This talk summarizes progress in computational methodology, discusses strengths and weaknesses of quantum statistical potentials as effective interactions for MD, explains the model used for quantum events possibly occurring in a collision and highlights some significant results obtained to date. This work is performed under the auspices of the U. S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Effects of ecological interactions and environmental conditions on community dynamics in an estuarine ecosystem

NASA Astrophysics Data System (ADS)

Liu, H.; Minello, T.; Sutton, G.

2016-02-01

Coastal marine ecosystems are both productive and vulnerable to human and natural stressors. Examining the relative importance of fishing, environmental variability, and habitat alteration on ecosystem dynamics is challenging. Intensive harvest and habitat loss have resulted in widespread concerns related to declines in fisheries production, but causal mechanisms are rarely clear. In this study, we modeled trophic dynamics in Galveston Bay, Texas, using fishery-independent catch data for blue crab, shrimp, red drum, Atlantic croaker and spotted seatrout along with habitat information collected by the Texas Parks and Wildlife Department during 1984 - 2014. We developed a multispecies state-space model to examine ecological interactions and partition the relative effects of trophic interactions and environmental conditions on the community dynamics. Preliminary results showed the importance of salinity, density-dependence, and trophic interactions. We are continuing to explore these results from a perspective of fish community compensatory responses to exploitation, reflecting both direct and indirect effects of harvesting under the influence of climate variability.

Algorithmic implementation of particle-particle ladder diagram approximation to study strongly-correlated metals and semiconductors

NASA Astrophysics Data System (ADS)

Prayogi, A.; Majidi, M. A.

2017-07-01

In condensed-matter physics, strongly-correlated systems refer to materials that exhibit variety of fascinating properties and ordered phases, depending on temperature, doping, and other factors. Such unique properties most notably arise due to strong electron-electron interactions, and in some cases due to interactions involving other quasiparticles as well. Electronic correlation effects are non-trivial that one may need a sufficiently accurate approximation technique with quite heavy computation, such as Quantum Monte-Carlo, in order to capture particular material properties arising from such effects. Meanwhile, less accurate techniques may come with lower numerical cost, but the ability to capture particular properties may highly depend on the choice of approximation. Among the many-body techniques derivable from Feynman diagrams, we aim to formulate algorithmic implementation of the Ladder Diagram approximation to capture the effects of electron-electron interactions. We wish to investigate how these correlation effects influence the temperature-dependent properties of strongly-correlated metals and semiconductors. As we are interested to study the temperature-dependent properties of the system, the Ladder diagram method needs to be applied in Matsubara frequency domain to obtain the self-consistent self-energy. However, at the end we would also need to compute the dynamical properties like density of states (DOS) and optical conductivity that are defined in the real frequency domain. For this purpose, we need to perform the analytic continuation procedure. At the end of this study, we will test the technique by observing the occurrence of metal-insulator transition in strongly-correlated metals, and renormalization of the band gap in strongly-correlated semiconductors.

Effects of the U boson on the inner edge of neutron star crusts

NASA Astrophysics Data System (ADS)

Zheng, Hao; Chen, Lie-Wen

2012-02-01

We explore effects of the light vector U boson, which is weakly coupled to nucleons, on the transition density ρt and pressure Pt at the inner edge separating the liquid core from the solid crust of neutron stars. Three methods, i.e., the thermodynamical approach, the curvature matrix approach, and the Vlasov equation approach, are used to determine the transition density ρt with the Skyrme effective nucleon-nucleon interactions. We find that the ρt and Pt depend on not only the ratio of coupling strength to mass squared of the U boson g2/μ2 but also its mass μ due to the finite-range interaction from the U-boson exchange. In particular, our results indicate that the ρt and Pt are sensitive to both g2/μ2 and μ if the U-boson mass μ is larger than about 2 MeV. Furthermore, we show that both g2/μ2 and μ can have significant influence on the mass-radius relation and the crustal fraction of total moment of inertia of neutron stars. In addition, we study the exchange term contribution of the U boson based on the density matrix expansion method, and demonstrate that the exchange term effects on the nuclear matter equation of state as well as the ρt and Pt are generally negligible.

Consequences of cannibalism and competition for food in a smallmouth bass population: An individual-based modeling study

USGS Publications Warehouse

Dong, Q.; DeAngelis, D.L.

1998-01-01

We used an individual-based modeling approach to study the consequences of cannibalism and competition for food in a freshwater fish population. We simulated the daily foraging, growth, and survival of the age-0 fish and older juvenile individuals of a sample population to reconstruct patterns of density dependence in the age-0 fish during the growth season. Cannibalism occurs as a part of the foraging process. For age-0 fish, older juvenile fish are both potential cannibals and competitors of food. We found that competition and cannibalism produced intraclass and interclass density dependence. Our modeling results suggested the following. (1) With low density of juvenile fish and weak interclass interactions, the age-0 fish recruitment shows a Beverton-Holt type of density dependence. (2) With high density of juvenile fish and strong interclass interactions, the age-0 fish recruitment shows a Ricker type of density dependence, and overcompensation occurs. (3) Interclass competition of food is responsible for much of the overcompensation. (4) Cannibalism intensifies the changes in the recruitment that are brought about by competition. Cannibalism can (a) generally reduce the recruitment, (b) particularly reduce the maximum level of recruitment, (c) cause overcompensation to occur at lower densities, and (d) produce a stronger overcompensation. (5) Growth is also a function of density. Cannibalism generally improves average growth of cannibals. (6) Variation in the lengths of age-0 fish increases with density and with a decreased average growth. These results imply that cannibalism and competition for food could strongly affect recruitment dynamics. Our model also showed that the rate of cannibalism either could be fairly even through the whole season or could vary dramatically. The individual-based modeling approach can help ecologists understand the mechanistic connection between daily behavioral and physiological processes operating at the level of individual organisms and seasonal patterns of population structure and dynamics. ?? Copyright by the American Fisheries Society 1998.

Handling Density Conversion in TPS.

PubMed

Isobe, Tomonori; Mori, Yutaro; Takei, Hideyuki; Sato, Eisuke; Tadano, Kiichi; Kobayashi, Daisuke; Tomita, Tetsuya; Sakae, Takeji

2016-01-01

Conversion from CT value to density is essential to a radiation treatment planning system. Generally CT value is converted to the electron density in photon therapy. In the energy range of therapeutic photon, interactions between photons and materials are dominated with Compton scattering which the cross-section depends on the electron density. The dose distribution is obtained by calculating TERMA and kernel using electron density where TERMA is the energy transferred from primary photons and kernel is a volume considering spread electrons. Recently, a new method was introduced which uses the physical density. This method is expected to be faster and more accurate than that using the electron density. As for particle therapy, dose can be calculated with CT-to-stopping power conversion since the stopping power depends on the electron density. CT-to-stopping power conversion table is also called as CT-to-water-equivalent range and is an essential concept for the particle therapy.

Unified description of the slip phenomena in sheared polymer films: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Priezjev, Nikolai

2010-03-01

The dynamic behavior of the slip length in shear flow of polymer melts past atomically smooth surfaces is investigated using MD simulations. The polymer melt was modeled as a collection of FENE-LJ bead-spring chains. We consider shear flow conditions at low pressures and weak wall-fluid interaction energy so that fluid velocity profiles are linear throughout the channel at all shear rates examined. In agreement with earlier studies we confirm that for shear- thinning fluids the slip length passes through a local minimum at low shear rates and then increases rapidly at higher shear rates. We found that the rate dependence of the slip length depends on the lattice orientation at high shear rates. The MD results show that the ratio of slip length to viscosity follows a master curve when plotted as a function of a single variable that depends on the structure factor, contact density and temperature of the first fluid layer near the solid wall. The universal dependence of the slip length holds for a number of parameters of the interface: fluid density and structure (chain length), wall-fluid interaction energy, wall density, lattice orientation, thermal or solid walls.

Electrostatic and hydrodynamics effects in a sedimented magnetorheological suspension.

PubMed

Domínguez-García, P; Pastor, J M; Melle, Sonia; Rubio, Miguel A

2009-08-01

We present experimental results on the equilibrium microstructure of a sedimented magnetorheological suspension, namely, an aqueous suspension of micron-sized superparamagnetic particles. We develop a study of the electrical interactions on the suspension by processing video-microscopy images of the sedimented particles. We calculate the pair distribution function, g(r), which yields the electrostatic pair potential u(r), showing an anomalous attractive interaction for distances on the order of twice the particle diameter, with characteristic parameters whose values show a dependence with the two-dimensional concentration of particles. The repulsive body of the potential is adjusted to a DLVO expression in order to calculate the Debye screening length and the effective surface charge density. Influence of confinement and variations on the Boltzmann sedimentation profile because of the electrostatic interactions appear to be essential for the interpretation of experimental results.

Density-dependent seedling mortality varies with light availability and species abundance in wet and dry Hawaiian forests

Treesearch

Faith Inman-Narahari; Rebecca Ostertag; Stephen P. Hubbell; Christian P. Giardina; Susan Cordell; Lawren Sack; Andrew MacDougall

2016-01-01

Conspecific density may contribute to patterns of species assembly through negative density dependence (NDD) as predicted by the Janzen-Connell hypothesis, or through facilitation (positive density dependence; PDD). Conspecific density effects are expected to be more negative in darker and wetter environments due to higher pathogen abundance and...

A feature-based approach to modeling protein–protein interaction hot spots

PubMed Central

Cho, Kyu-il; Kim, Dongsup; Lee, Doheon

2009-01-01

Identifying features that effectively represent the energetic contribution of an individual interface residue to the interactions between proteins remains problematic. Here, we present several new features and show that they are more effective than conventional features. By combining the proposed features with conventional features, we develop a predictive model for interaction hot spots. Initially, 54 multifaceted features, composed of different levels of information including structure, sequence and molecular interaction information, are quantified. Then, to identify the best subset of features for predicting hot spots, feature selection is performed using a decision tree. Based on the selected features, a predictive model for hot spots is created using support vector machine (SVM) and tested on an independent test set. Our model shows better overall predictive accuracy than previous methods such as the alanine scanning methods Robetta and FOLDEF, and the knowledge-based method KFC. Subsequent analysis yields several findings about hot spots. As expected, hot spots have a larger relative surface area burial and are more hydrophobic than other residues. Unexpectedly, however, residue conservation displays a rather complicated tendency depending on the types of protein complexes, indicating that this feature is not good for identifying hot spots. Of the selected features, the weighted atomic packing density, relative surface area burial and weighted hydrophobicity are the top 3, with the weighted atomic packing density proving to be the most effective feature for predicting hot spots. Notably, we find that hot spots are closely related to π–related interactions, especially π · · · π interactions. PMID:19273533

A fitness trade-off between seasons causes multigenerational cycles in phenotype and population size

PubMed Central

Betini, Gustavo S; McAdam, Andrew G; Griswold, Cortland K; Norris, D Ryan

2017-01-01

Although seasonality is widespread and can cause fluctuations in the intensity and direction of natural selection, we have little information about the consequences of seasonal fitness trade-offs for population dynamics. Here we exposed populations of Drosophila melanogaster to repeated seasonal changes in resources across 58 generations and used experimental and mathematical approaches to investigate how viability selection on body size in the non-breeding season could affect demography. We show that opposing seasonal episodes of natural selection on body size interacted with both direct and delayed density dependence to cause populations to undergo predictable multigenerational density cycles. Our results provide evidence that seasonality can set the conditions for life-history trade-offs and density dependence, which can, in turn, interact to cause multigenerational population cycles. DOI: http://dx.doi.org/10.7554/eLife.18770.001 PMID:28164780

Detection of a Novel Mechanism of Acousto-Optic Modulation of Incoherent Light

PubMed Central

Jarrett, Christopher W.; Caskey, Charles F.; Gore, John C.

2014-01-01

A novel form of acoustic modulation of light from an incoherent source has been detected in water as well as in turbid media. We demonstrate that patterns of modulated light intensity appear to propagate as the optical shadow of the density variations caused by ultrasound within an illuminated ultrasonic focal zone. This pattern differs from previous reports of acousto-optical interactions that produce diffraction effects that rely on phase shifts and changes in light directions caused by the acoustic modulation. Moreover, previous studies of acousto-optic interactions have mainly reported the effects of sound on coherent light sources via photon tagging, and/or the production of diffraction phenomena from phase effects that give rise to discrete sidebands. We aimed to assess whether the effects of ultrasound modulation of the intensity of light from an incoherent light source could be detected directly, and how the acoustically modulated (AOM) light signal depended on experimental parameters. Our observations suggest that ultrasound at moderate intensities can induce sufficiently large density variations within a uniform medium to cause measurable modulation of the intensity of an incoherent light source by absorption. Light passing through a region of high intensity ultrasound then produces a pattern that is the projection of the density variations within the region of their interaction. The patterns exhibit distinct maxima and minima that are observed at locations much different from those predicted by Raman-Nath, Bragg, or other diffraction theory. The observed patterns scaled appropriately with the geometrical magnification and sound wavelength. We conclude that these observed patterns are simple projections of the ultrasound induced density changes which cause spatial and temporal variations of the optical absorption within the illuminated sound field. These effects potentially provide a novel method for visualizing sound fields and may assist the interpretation of other hybrid imaging methods. PMID:25105880

Skin friction and heat transfer correlations for high-speed low-density flow past a flat plate

NASA Technical Reports Server (NTRS)

Woronowicz, Michael S.; Baganoff, Donald

1991-01-01

The independent and dependent variables associated with drag and heat transfer to a flat plate at zero incidence in high-speed, rarefied flow are analyzed anew to reflect the importance of kinetic effects occurring near the plate surface on energy and momentum transfer, rather than following arguments normally used to describe continuum, higher density flowfields. A new parameter, the wall Knudsen number Knx,w, based on an estimate of the mean free path length of molecules having just interacted with the surface of the plate, is introduced and used to correlate published drag and heat transfer data. The new parameter is shown to provide better correlation than either the viscous interaction parameter X or the widely-used slip parameter Voo for drag and heat transfer data over a wide range of Mach numbers, Reynolds numbers, and plate-to-freestream stagnation temperature ratios.

Adsorption properties of the molecule resveratrol on CNT(8,0-10) nanotube: Geometry optimization, molecular structure, spectroscopic (NMR, UV/Vis, excited state), FMO, MEP and HOMO-LUMO investigations

NASA Astrophysics Data System (ADS)

Sheikhi, Masoome; Shahab, Siyamak; Khaleghian, Mehrnoosh; Hajikolaee, Fatemeh Haji; Balakhanava, Iryna; Alnajjar, Radwan

2018-05-01

In the present work the adsorption properties of the molecule Resveratrol (RSV) (trans-3,5,4‧-Trihydroxystilbene) on CNT(8,0-10) nanotube was investigated by Density Functional Theory (DFT) in the gaseous phase for the first time. The non-bonded interaction effects of compounds RSV and CNT(8,0-10) nanotube on the electronic properties, chemical shift tensors and natural charge were determined and discussed. The electronic spectra of the RSV and the complex CNT(8,0-10)/RSV in the gaseous phase were calculated by Time Dependent Density Functional Theory (TD-DFT) for investigation of the maximum wavelength value of the RSV before and after the non-bonded interaction with the CNT(8,0-10) nanotube and molecular orbitals involved in the formation of absorption spectrum of the complex RSV at maximum wavelength.

Kondo scattering in δ-doped LaTiO3/SrTiO3 interfaces: Renormalization by spin-orbit interactions

NASA Astrophysics Data System (ADS)

Das, Shubhankar; Rastogi, A.; Wu, Lijun; Zheng, Jin-Cheng; Hossain, Z.; Zhu, Yimei; Budhani, R. C.

2014-08-01

We present a study of δ doping at the LaTiO3/SrTiO3 interface with isostructural antiferromagnetic perovskite LaCrO3 that dramatically alters the properties of the two-dimensional electron gas at the interface. The effects include a reduction in sheet-carrier density, prominence of the low-temperature resistivity minimum, enhancement of weak antilocalization below 10 K, and observation of a strong anisotropic magnetoresistance (MR). The positive and negative MR for out-of-plane and in-plane fields, respectively, and the field and temperature dependencies of MR suggest Kondo scattering by localized Ti3+ moments renormalized by spin-orbit interaction at T < 10 K, with the increased δ-layer thickness. Electron-energy-loss spectroscopy and density functional calculations provide convincing evidence of blocking of electron transfer from LTO to STO by the δ layer.

On the applicability of density dependent effective interactions in cluster-forming systems

NASA Astrophysics Data System (ADS)

Montes-Saralegui, Marta; Kahl, Gerhard; Nikoubashman, Arash

2017-02-01

We systematically studied the validity and transferability of the force-matching algorithm for computing effective pair potentials in a system of dendritic polymers, i.e., a particular class of ultrasoft colloids. We focused on amphiphilic dendrimers, macromolecules which can aggregate into clusters of overlapping particles to minimize the contact area with the surrounding implicit solvent. Simulations were performed for both the monomeric and coarse-grained models in the liquid phase at densities ranging from infinite dilution up to values close to the freezing point. The effective pair potentials for the coarse-grained simulations were computed from the monomeric simulations both in the zero-density limit (Φeff0) and at each investigated finite density (Φeff). Conducting the coarse-grained simulations with Φeff0 at higher densities is not appropriate as they failed at reproducing the structural properties of the monomeric simulations. In contrast, we found excellent agreement between the spatial dendrimer distributions obtained from the coarse-grained simulations with Φeff and the microscopically detailed simulations at low densities, where the macromolecules were distributed homogeneously in the system. However, the reliability of the coarse-grained simulations deteriorated significantly as the density was increased further and the cluster occupation became more polydisperse. Under these conditions, the effective pair potential of the coarse-grained model can no longer be computed by averaging over the whole system, but the local density needs to be taken into account instead.

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

PubMed Central

Flesch, Aaron D.; Hutto, Richard L.; van Leeuwen, Willem J. D.; Hartfield, Kyle; Jacobs, Sky

2015-01-01

Spatial variation in resources is a fundamental driver of habitat quality but the realized value of resources at any point in space may depend on the effects of conspecifics and stochastic factors, such as weather, which vary through time. We evaluated the relative and combined effects of habitat resources, weather, and conspecifics on habitat quality for ferruginous pygmy-owls (Glaucidium brasilianum) in the Sonoran Desert of northwest Mexico by monitoring reproductive output and conspecific abundance over 10 years in and around 107 territory patches. Variation in reproductive output was much greater across space than time, and although habitat resources explained a much greater proportion of that variation (0.70) than weather (0.17) or conspecifics (0.13), evidence for interactions among each of these components of the environment was strong. Relative to habitat that was persistently low in quality, high-quality habitat buffered the negative effects of conspecifics and amplified the benefits of favorable weather, but did not buffer the disadvantages of harsh weather. Moreover, the positive effects of favorable weather at low conspecific densities were offset by intraspecific competition at high densities. Although realized habitat quality declined with increasing conspecific density suggesting interference mechanisms associated with an Ideal Free Distribution, broad spatial heterogeneity in habitat quality persisted. Factors linked to food resources had positive effects on reproductive output but only where nest cavities were sufficiently abundant to mitigate the negative effects of heterospecific enemies. Annual precipitation and brooding-season temperature had strong multiplicative effects on reproductive output, which declined at increasing rates as drought and temperature increased, reflecting conditions predicted to become more frequent with climate change. Because the collective environment influences habitat quality in complex ways, integrated approaches 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.

PubMed

Flesch, Aaron D; Hutto, Richard L; van Leeuwen, Willem J D; Hartfield, Kyle; Jacobs, Sky

2015-01-01

Spatial variation in resources is a fundamental driver of habitat quality but the realized value of resources at any point in space may depend on the effects of conspecifics and stochastic factors, such as weather, which vary through time. We evaluated the relative and combined effects of habitat resources, weather, and conspecifics on habitat quality for ferruginous pygmy-owls (Glaucidium brasilianum) in the Sonoran Desert of northwest Mexico by monitoring reproductive output and conspecific abundance over 10 years in and around 107 territory patches. Variation in reproductive output was much greater across space than time, and although habitat resources explained a much greater proportion of that variation (0.70) than weather (0.17) or conspecifics (0.13), evidence for interactions among each of these components of the environment was strong. Relative to habitat that was persistently low in quality, high-quality habitat buffered the negative effects of conspecifics and amplified the benefits of favorable weather, but did not buffer the disadvantages of harsh weather. Moreover, the positive effects of favorable weather at low conspecific densities were offset by intraspecific competition at high densities. Although realized habitat quality declined with increasing conspecific density suggesting interference mechanisms associated with an Ideal Free Distribution, broad spatial heterogeneity in habitat quality persisted. Factors linked to food resources had positive effects on reproductive output but only where nest cavities were sufficiently abundant to mitigate the negative effects of heterospecific enemies. Annual precipitation and brooding-season temperature had strong multiplicative effects on reproductive output, which declined at increasing rates as drought and temperature increased, reflecting conditions predicted to become more frequent with climate change. Because the collective environment influences habitat quality in complex ways, integrated approaches that consider habitat resources, stochastic factors, and conspecifics are necessary to accurately assess habitat quality.

Thickness dependence of the interfacial Dzyaloshinskii–Moriya interaction in inversion symmetry broken systems

PubMed Central

Cho, Jaehun; Kim, Nam-Hui; Lee, Sukmock; Kim, June-Seo; Lavrijsen, Reinoud; Solignac, Aurelie; Yin, Yuxiang; Han, Dong-Soo; van Hoof, Niels J. J.; Swagten, Henk J. M.; Koopmans, Bert; You, Chun-Yeol

2015-01-01

In magnetic multilayer systems, a large spin-orbit coupling at the interface between heavy metals and ferromagnets can lead to intriguing phenomena such as the perpendicular magnetic anisotropy, the spin Hall effect, the Rashba effect, and especially the interfacial Dzyaloshinskii–Moriya (IDM) interaction. This interfacial nature of the IDM interaction has been recently revisited because of its scientific and technological potential. Here we demonstrate an experimental technique to straightforwardly observe the IDM interaction, namely Brillouin light scattering. The non-reciprocal spin wave dispersions, systematically measured by Brillouin light scattering, allow not only the determination of the IDM energy densities beyond the regime of perpendicular magnetization but also the revelation of the inverse proportionality with the thickness of the magnetic layer, which is a clear signature of the interfacial nature. Altogether, our experimental and theoretical approaches involving double time Green's function methods open up possibilities for exploring magnetic hybrid structures for engineering the IDM interaction. PMID:26154986

Probing the cross-effect of strains in non-linear elasticity of nearly regular polymer networks by pure shear deformation.

PubMed

Katashima, Takuya; Urayama, Kenji; Chung, Ung-il; Sakai, Takamasa

2015-05-07

The pure shear deformation of the Tetra-polyethylene glycol gels reveals the presence of an explicit cross-effect of strains in the strain energy density function even for the polymer networks with nearly regular structure including no appreciable amount of structural defect such as trapped entanglement. This result is in contrast to the expectation of the classical Gaussian network model (Neo Hookean model), i.e., the vanishing of the cross effect in regular networks with no trapped entanglement. The results show that (1) the cross effect of strains is not dependent on the network-strand length; (2) the cross effect is not affected by the presence of non-network strands; (3) the cross effect is proportional to the network polymer concentration including both elastically effective and ineffective strands; (4) no cross effect is expected exclusively in zero limit of network concentration in real polymer networks. These features indicate that the real polymer networks with regular network structures have an explicit cross-effect of strains, which originates from some interaction between network strands (other than entanglement effect) such as nematic interaction, topological interaction, and excluded volume interaction.

Impact of jamming on collective cell migration

NASA Astrophysics Data System (ADS)

Nnetu, Kenechukwu David; Knorr, Melanie; Pawlizak, Steve; Fuhs, Thomas; Zink, Mareike; KäS, Josef A.

2012-02-01

Multi-cellular migration plays an important role in physiological processes such as embryogenesis, cancer metastasis and tissue repair. During migration, single cells undergo cycles of extension, adhesion and retraction resulting in morphological changes. In a confluent monolayer, there are inter-cellular interactions and crowding, however, the impact of these interactions on the dynamics and elasticity of the monolayer at the multi-cellular and single cell level is not well understood. Here we study the dynamics of a confluent epithelial monolayer by simultaneously measuring cell motion at the multi-cellular and single cell level for various cell densities and tensile elasticity. At the multi-cellular level, the system exhibited spatial kinetic transitions from isotropic to anisotropic migration on long times and the velocity of the monolayer decreased with increasing cell density. Moreover, the dynamics was spatially and temporally heterogeneous. Interestingly, the dynamics was also heterogeneous in wound-healing assays and the correlation length was fitted by compressed exponential. On the single cell scale, we observed transient caging effects with increasing cage rearrangement times as the system age due to an increase in density. Also, the density dependent elastic modulus of the monolayer scaled as a weak power law. Together, these findings suggest that caging effects at the single cell level initiates a slow and heterogeneous dynamics at the multi-cellular level which is similar to the glassy dynamics of deformable colloidal systems.

Revealing electronic open quantum systems with subsystem TDDFT

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

Krishtal, Alisa, E-mail: alisa.krishtal@rutgers.edu; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu

2016-03-28

Open quantum systems (OQSs) are perhaps the most realistic systems one can approach through simulations. In recent years, describing OQSs with Density Functional Theory (DFT) has been a prominent avenue of research with most approaches based on a density matrix partitioning in conjunction with an ad-hoc description of system-bath interactions. We propose a different theoretical approach to OQSs based on partitioning of the electron density. Employing the machinery of subsystem DFT (and its time-dependent extension), we provide a novel way of isolating and analyzing the various terms contributing to the coupling between the system and the surrounding bath. To illustratemore » the theory, we provide numerical simulations on a toy system (a molecular dimer) and on a condensed phase system (solvated excimer). The simulations show that non-Markovian dynamics in the electronic system-bath interactions are important in chemical applications. For instance, we show that the superexchange mechanism of transport in donor-bridge-acceptor systems is a non-Markovian interaction between the donor-acceptor (OQS) with the bridge (bath) which is fully characterized by real-time subsystem time-dependent DFT.« less

Revealing electronic open quantum systems with subsystem TDDFT.

PubMed

Krishtal, Alisa; Pavanello, Michele

2016-03-28

Open quantum systems (OQSs) are perhaps the most realistic systems one can approach through simulations. In recent years, describing OQSs with Density Functional Theory (DFT) has been a prominent avenue of research with most approaches based on a density matrix partitioning in conjunction with an ad-hoc description of system-bath interactions. We propose a different theoretical approach to OQSs based on partitioning of the electron density. Employing the machinery of subsystem DFT (and its time-dependent extension), we provide a novel way of isolating and analyzing the various terms contributing to the coupling between the system and the surrounding bath. To illustrate the theory, we provide numerical simulations on a toy system (a molecular dimer) and on a condensed phase system (solvated excimer). The simulations show that non-Markovian dynamics in the electronic system-bath interactions are important in chemical applications. For instance, we show that the superexchange mechanism of transport in donor-bridge-acceptor systems is a non-Markovian interaction between the donor-acceptor (OQS) with the bridge (bath) which is fully characterized by real-time subsystem time-dependent DFT.

Revealing electronic open quantum systems with subsystem TDDFT

NASA Astrophysics Data System (ADS)

Krishtal, Alisa; Pavanello, Michele

2016-03-01

Open quantum systems (OQSs) are perhaps the most realistic systems one can approach through simulations. In recent years, describing OQSs with Density Functional Theory (DFT) has been a prominent avenue of research with most approaches based on a density matrix partitioning in conjunction with an ad-hoc description of system-bath interactions. We propose a different theoretical approach to OQSs based on partitioning of the electron density. Employing the machinery of subsystem DFT (and its time-dependent extension), we provide a novel way of isolating and analyzing the various terms contributing to the coupling between the system and the surrounding bath. To illustrate the theory, we provide numerical simulations on a toy system (a molecular dimer) and on a condensed phase system (solvated excimer). The simulations show that non-Markovian dynamics in the electronic system-bath interactions are important in chemical applications. For instance, we show that the superexchange mechanism of transport in donor-bridge-acceptor systems is a non-Markovian interaction between the donor-acceptor (OQS) with the bridge (bath) which is fully characterized by real-time subsystem time-dependent DFT.

Harmonic plasma waves excitation and structure evolution of intense ion beams in background plasmas

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

Hu, Zhang-Hu, E-mail: zhanghu@dlut.edu.cn; Wang, You-Nian

2016-08-15

The long-term dynamic evolutions of intense ion beams in plasmas have been investigated with two-dimensional electromagnetic particle simulations, taking into account the effect of the two-stream instability between beam ions and plasma electrons. Depending on the initial beam radial density profile and velocity distribution, ring structures may be formed in the beam edge regions. At the later stage of beam-plasma interactions, the ion beams are strongly modulated by the two-stream instability and multiple density spikes are formed in the longitudinal direction. The formation of these density spikes is shown to result from the excitation of harmonic plasma waves when themore » instability gets saturated. Comparisons between the beam cases with initial flat-top and Gaussian radial density profiles are made, and a higher instability growth rate is observed for the flat-top profile case.« less

Effect of repulsive and attractive three-body forces on nucleus-nucleus elastic scattering

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

Furumoto, T.; Sakuragi, Y.; Yamamoto, Y.

2009-10-15

The effect of the three-body force (TBF) is studied in nucleus-nucleus elastic scattering on the basis of Brueckner theory for nucleon-nucleon (NN) effective interaction (complex G matrix) in the nuclear matter. A new G matrix called CEG07 proposed recently by the present authors includes the TBF effect and reproduces a realistic saturation curve in the nuclear matter, and it is shown to well reproduce proton-nucleus elastic scattering. The microscopic optical potential for the nucleus-nucleus system is obtained by folding the G matrix with nucleon density distributions in colliding nuclei. We first analyze in detail the {sup 16}O+{sup 16}O elastic scatteringmore » at E/A=70 MeV. The observed cross sections are nicely reproduced up to the most backward scattering angles only when the TBF effect is included. The use of the frozen-density approximation (FDA) is essentially important to properly estimate the effect of the TBF in nucleus-nucleus scattering. Other prescriptions for defining the local density have also been tested, but only the FDA prescription gives a proper description of the experimental cross sections as well as the effect of the TBF. The effects of the three-body attraction and the {omega}-rearrangement term are also analyzed. The CEG07 interaction is compared with CDM3Y6, which is a reliable and successful effective density-dependent NN interaction used in the double-folding model. The CEG07 G matrix is also tested in the elastic scattering of {sup 16}O by the {sup 12}C, {sup 28}Si, and {sup 40}Ca targets at E/A=93.9 MeV, and in the elastic scattering of {sup 12}C by the {sup 12}C target at E/A=135 MeV with great success. The decisive effect of the TBF is clearly seen also in those systems. Finally, we have tested CEG07a, CEG07b, and CEG07c for the {sup 16}O+{sup 16}O system at various energies.« less

Single-particle potential of the Λ hyperon in nuclear matter with chiral effective field theory NLO interactions including effects of Y N N three-baryon interactions

NASA Astrophysics Data System (ADS)

Kohno, M.

2018-03-01

Adopting hyperon-nucleon and hyperon-nucleon-nucleon interactions parametrized in chiral effective field theory, single-particle potentials of the Λ and Σ hyperons are evaluated in symmetric nuclear matter and in pure neutron matter within the framework of lowest-order Bruckner theory. The chiral NLO interaction bears strong Λ N -Σ N coupling. Although the Λ potential is repulsive if the coupling is switched off, the Λ N -Σ N correlation brings about the attraction consistent with empirical data. The Σ potential is repulsive, which is also consistent with empirical information. The interesting result is that the Λ potential becomes shallower beyond normal density. This provides the possibility of solving the hyperon puzzle without introducing ad hoc assumptions. The effects of the Λ N N -Λ N N and Λ N N -Σ N N three-baryon forces are considered. These three-baryon forces are first reduced to normal-ordered effective two-baryon interactions in nuclear matter and then incorporated in the G -matrix equation. The repulsion from the Λ N N -Λ N N interaction is of the order of 5 MeV at normal density and becomes larger with increasing density. The effects of the Λ N N -Σ N N coupling compensate the repulsion at normal density. The net effect of the three-baryon interactions on the Λ single-particle potential is repulsive at higher densities.

On the stability of the electronic system in transition metal dichalcogenides.

PubMed

Faraggi, M N; Zubizarreta, X; Arnau, A; Silkin, V M

2016-05-11

Based on first-principles calculations, we prove that the origin of charge-density wave formation in metallic layered transition metal dichalcogenides (TMDC) is not due to an electronic effect, like the Fermi surface (FS) nesting, as it had been proposed. In particular, we consider NbSe2, NbS2, TaSe2, and TaS2 as representative examples of 2H-TMDC polytypes. Our main result consists that explicit inclusion of the matrix elements in first-principles calculations of the electron susceptibility [Formula: see text] removes, due to strong momentum dependence of the matrix elements, almost all the information about the FS topologies in the resulting [Formula: see text]. This finding strongly supports an interpretation in which the momentum dependence of the electron-phonon interaction is the only reason why the phenomenon of charge-density waves appears in this class of materials.

Sensory Organ Like Response of Zigzag Edge Graphene Nanoribbons

NASA Astrophysics Data System (ADS)

Shenoy, Vijay; Bhowmick, Somnath

2011-03-01

Using a continuum Dirac theory, we study the density and spin response of zigzag edge terminated graphene ribbons subjected to edge potentials and Zeeman fields. Our analytical calculations of the density and spin responses of the closed system (fixed particle number) to the static edge fields, show a highly nonlinear Weber-Fechner type behavior where the response depends logarithmically on the edge potential. The dependence of the response on the size of the system (e.g.~width of a nanoribbon) is also uncovered. Zigzag edge graphene nanoribbons, therefore, provide a realization of response of organs such as the eye and ear that obey Weber-Fechner law. We validate our analytical results with tight binding calculations. These results are crucial in understanding important effects of electron-electron interactions in graphene nanoribbons such as edge magnetism etc., and also suggest possibilities for device applications of graphene nanoribbons. Work supported by DST, India through MONAMI and Ramanujan grants.

Binding energies and modelling of nuclei in semiclassical simulations

NASA Astrophysics Data System (ADS)

Pérez-García, M. Ángeles; Tsushima, K.; Valcarce, A.

2008-03-01

We study the binding energies of spin isospin saturated nuclei with nucleon number 8⩽A⩽100 in semiclassical Monte Carlo many-body simulations. The model Hamiltonian consists of (i) nucleon kinetic energy, (ii) a nucleon nucleon interaction potential, and (iii) an effective Pauli potential which depends on density. The basic ingredients of the nucleon nucleon potential are a short-range repulsion, and a medium-range attraction. Our results demonstrate that one can always expect to obtain the empirical binding energies for a set of nuclei by introducing a proper density dependent Pauli potential in terms of a single variable, the nucleon number, A. The present work shows that in the suggested procedure there is a delicate counterbalance of kinetic and potential energetic contributions allowing a good reproduction of the experimental nuclear binding energies. This type of calculations may be of interest in further reproduction of other properties of nuclei such as radii and also exotic nuclei.

Ductile failure initiation and evolution in porous polycrystalline aggregates due to interfacial effects

NASA Astrophysics Data System (ADS)

Ashmawi, Waeil Muhammad Al-Anwar

New analytical and computational formulations have been developed for the investigation of micro structurally induced ductile failure mechanisms in porous polycrystalline aggregates with low and high (CSL) angle grain-boundaries (GBs). A multiple-slip rate-dependent crystalline constitutive formulation that is coupled to the evolution of mobile and immobile dislocation densities, a new internal porosity formulation for void nucleation and growth, and specialized computational schemes have been developed to obtain a detailed understanding of the multi-scale interrelated physical mechanisms that result in ductile failure in polycrystalline materials. Comprehensive transmission and pile-up mechanisms have also been introduced to investigate dislocation-density impedance and slip-rate incompatibility at the GBs. The interrelated effects of GB orientation, mobile and immobile dislocation densities, strain hardening, geometrical softening, localized plastic strains, and dislocation-density transmission and blockage on void growth, interaction, and coalescence have been studied. Criteria have been developed to identify and monitor the initiation and development of potential dislocation-density activity sites adjacent to GB regions. These interactions play an important role in the formation of GB pile-up and transmission regions. The effects of GB structure and orientation on ductile failure have been accounted for by the development of GB interfacial kinematic conditions that account for a multitude of dislocation-density interactions with GBs, such as full and partial transmission, impedance, blockage, and absorption. Pile-ups and transmission regions are identified and monitored as the deformation and failure evolve. These kinematic conditions are linked to the initiation and evolution of failure modes by the development of a new internal porosity evolution formulation that accounts for void nucleation and growth. The internal porosity relation is coupled with the proposed dislocation-density based crystalline constitutive formulation, the interfacial GB dislocation-density interaction models, and the specialized computational schemes to obtain detailed predictions of the behavior of aggregates with explicit voids that have different orientations and combinations of sizes, shapes, and spacings. Results from the present study indicate that material failure is a competition between different interrelated effects, such as stress triaxiality, accumulated plastic shear strain, temperature, dislocation density concentration, and grain and GB crystallographic orientations. For all void arrangements, as the void size is increased, specimen necking is diffuse and failure is concentrated in the ligament regions. Furthermore, there are more dislocation-density activity sites for potential transmission and pile-ups at the GBs. Failure is concentrated along the void peripheries and within intervoid ligaments. It has been shown that the evolution of the mobile dislocation density saturation curves, and their saturation rate are directly related to the aggregate response. Nucleation and growth for all void distributions have occurred in regions of maximum dislocation density and along preferred crystallographic orientations. Spatial distributions of porosity, accumulated plastic strains, and pressure have been obtained to further elucidate how these parameters evolve and affect void to void interaction in critical ligament and localized regions as a function of intervoid spacing and nominal strains. These failure predictions can be also used to identify intergranular and transgranular failure propagation. The present study underscores the importance of using dislocation-density based multiple-slip crystalline constitutive formulations and GB interfacial mechanisms that are consistent with experimental observations and results to accurately characterize the microstructural evolution of deformation and failure modes on a length scale that is commensurate with the material competition between the inherent strengthening and softening mechanisms of crystalline systems.

Role of translational entropy in spatially inhomogeneous, coarse-grained models

NASA Astrophysics Data System (ADS)

Langenberg, Marcel; Jackson, Nicholas E.; de Pablo, Juan J.; Müller, Marcus

2018-03-01

Coarse-grained models of polymer and biomolecular systems have enabled the computational study of cooperative phenomena, e.g., self-assembly, by lumping multiple atomistic degrees of freedom along the backbone of a polymer, lipid, or DNA molecule into one effective coarse-grained interaction center. Such a coarse-graining strategy leaves the number of molecules unaltered. In order to treat the surrounding solvent or counterions on the same coarse-grained level of description, one can also stochastically group several of those small molecules into an effective, coarse-grained solvent bead or "fluid element." Such a procedure reduces the number of molecules, and we discuss how to compensate the concomitant loss of translational entropy by density-dependent interactions in spatially inhomogeneous systems.

Density-dependence in the establishment of juvenile Allium ursinum individuals in a monodominant stand of conspecific adults

NASA Astrophysics Data System (ADS)

Morschhauser, Tamás; Rudolf, Kinga; Botta-Dukát, Zoltán; Oborny, Beáta

2009-09-01

We studied the establishment of new genets in a wild garlic population ( Allium ursinum L.) in the herb layer of an oak-hornbeam forest. We tested whether establishment could be successful in relatively small gaps (25 cm) surrounded by adult individuals. Furthermore, we asked whether more empty space in the neighborhood would increase the success. Newly germinated individuals were selected, and observed throughout the growth season. The success of establishment was characterized by the biomass of the bulb at the end of the season. The surrounding vegetation cover was recorded in a 25 cm resolution. We found that the success of establishment had a peak at intermediate neighborhood density. At higher densities, a significant, linear decline was found, indicating competition with the neighbors. At lower values, this trend did not continue, but a plateau was observed, indicating the effect of inverse density-dependence (an Allee effect). The results suggest that a rather broad radius (>25 cm) should be considered when predicting the establishment of new genets in A. ursinum, and beside competition, facilitative interactions should also be taken into consideration. This may explain the tendency of the species for maintaining high, often monodominant cover in the herb layer. Due to the observed efficiency of gap-filling and lateral spreading by sexual reproduction, we predict considerable genetic diversity even in high-cover A. ursinum patches.

Phase Diagram and Electronic Structure of Praseodymium and Plutonium

DOE PAGES

Lanatà, Nicola; Yao, Yongxin; Wang, Cai-Zhuang; ...

2015-01-29

We develop a new implementation of the Gutzwiller approximation in combination with the local density approximation, which enables us to study complex 4f and 5f systems beyond the reach of previous approaches. We calculate from first principles the zero-temperature phase diagram and electronic structure of Pr and Pu, finding good agreement with the experiments. Our study of Pr indicates that its pressure-induced volume-collapse transition would not occur without change of lattice structure—contrarily to Ce. Our study of Pu shows that the most important effect originating the differentiation between the equilibrium densities of its allotropes is the competition between the Peierlsmore » effect and the Madelung interaction and not the dependence of the electron correlations on the lattice structure.« less

The impact of anisotropy and interaction range on the self-assembly of Janus ellipsoids

NASA Astrophysics Data System (ADS)

Ruth, D. P.; Gunton, J. D.; Rickman, J. M.; Li, Wei

2014-12-01

We assess the roles of anisotropy and interaction range on the self-assembly of Janus colloidal particles. In particular, Monte Carlo simulation is employed to investigate the propensity for the formation of aggregates in a spheroidal model of a colloid having a relatively short-ranged interaction that is consistent with experimentally realizable systems. By monitoring the equilibrium distribution of aggregates as a function of temperature and density, we identify a "micelle" transition temperature and discuss its dependence on particle shape. We find that, unlike systems with longer ranged interactions, this system does not form micelles below a transition temperature at low density. Rather, larger clusters comprising 20-40 particles characterize the transition. We then examine the dependence of the second virial coefficient on particle shape and well width to determine how these important system parameters affect aggregation. Finally, we discuss possible strategies suggested by this work to promote self-assembly for the encapsulation of particles.

Geometry dependence of electron donating or accepting abilities of amine groups in 4,4‧-disulfanediylbis(methylene)dithiazol-2-amine: Pyramidal versus planar

NASA Astrophysics Data System (ADS)

Karabıyık, Hasan; Kırılmış, Cumhur; Karabıyık, Hande

2017-08-01

The molecular and crystal structure of the title compound in which two thiazole-2-amine rings are linked to each other by disulfide bridge (sbnd Csbnd Ssbnd Ssbnd Csbnd) were studied by single-crystal X-ray diffraction, FT-IR, NMR spectroscopy, quantum chemical calculations and topological analyses on the electron density. A novel synthesis route for the compounds having symmetrical disulfide bridge is reported. The most important result regarding the compound is about electron donating or accepting properties of the terminal amine groups. Planar amine group acts as an electron-donating group, while pyramidal amine behaves as electron-accepting group. This inference was confirmed by scrutiny of crystallographic geometry and quantum chemical studies. To ascertain underlying reasons for this fact, intermolecular interactions (Nsbnd H⋯N type H-bonds and Csbnd H···π interactions) were studied. These interactions involving aromatic thiazole rings are verified by topological electron density and Hirshfeld surface analyses. Intermolecular interactions do not have an effect on the differentiation in electron donating or accepting ability of amine groups, because both amine groups are involved in Nsbnd H⋯N type H-bonds. In methodological sense, it has been understood that Ehrenfest forces acting on electron density are useful theoretical probe to analyze intra-molecular charge transfer processes.

The effect of plant sterols on serum triglyceride concentrations is dependent on baseline concentrations: a pooled analysis of 12 randomised controlled trials.

PubMed

Demonty, Isabelle; Ras, Rouyanne T; van der Knaap, Henk C M; Meijer, Linsie; Zock, Peter L; Geleijnse, Johanna M; Trautwein, Elke A

2013-02-01

Plant sterols (PS) are well known for their low-density lipoprotein cholesterol-lowering effect. Until recently, they were believed to have little or no impact on blood triglycerides (TG). However, studies taken individually were possibly lacking statistical power to detect modest TG decreases. This study was performed to quantify the TG-lowering effect of PS by pooling individual subject data from 12 randomised controlled trials that investigated the effects of PS on blood lipids. The main outcome variable was the control-adjusted PS effect on relative (%) and absolute (mmol/L) changes in TG. The relative and absolute changes in high-density lipoprotein cholesterol (HDL-C) were also assessed. Differences in changes of serum lipid concentrations between PS and control treatments were estimated by an ANCOVA using a random effect model which included PS intake (active or control), study and predefined subject characteristics. The twelve randomised controlled trials included in total 935 hypercholesterolaemic subjects not preselected based on their baseline TG concentrations. In most studies, the PS dose ranged between 1.6 and 2.5 g/day. PS intake significantly lowered serum TG by 6.0% (95% CI: -10.7, -1.2) or 0.12 mmol/L (95% CI: -0.20, -0.04). No significant interaction was observed between PS intake and baseline TG concentrations on relative changes, but, on absolute changes, interaction was significant with larger TG decreases observed with higher TG concentrations at baseline. No effects were observed on HDL-C concentrations. These results show that PS exert a modest TG-lowering effect which is dependent on baseline concentrations.

Detection of density dependence requires density manipulations and calculation of lambda.

PubMed

Fowler, N L; Overath, R Deborah; Pease, Craig M

2006-03-01

To investigate density-dependent population regulation in the perennial bunchgrass Bouteloua rigidiseta, we experimentally manipulated density by removing adults or adding seeds to replicate quadrats in a natural population for three annual intervals. We monitored the adjacent control quadrats for 14 annual intervals. We constructed a population projection matrix for each quadrat in each interval, calculated lambda, and did a life table response experiment (LTRE) analysis. We tested the effects of density upon lambda by comparing experimental and control quadrats, and by an analysis of the 15-year observational data set. As measured by effects on lambda and on N(t+1/Nt in the experimental treatments, negative density dependence was strong: the population was being effectively regulated. The relative contributions of different matrix elements to treatment effect on lambda differed among years and treatments; overall the pattern was one of small contributions by many different life cycle stages. In contrast, density dependence could not be detected using only the observational (control quadrats) data, even though this data set covered a much longer time span. Nor did experimental effects on separate matrix elements reach statistical significance. These results suggest that ecologists may fail to detect density dependence when it is present if they have only descriptive, not experimental, data, do not have data for the entire life cycle, or analyze life cycle components separately.

Ensemble density variational methods with self- and ghost-interaction-corrected functionals

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

Pastorczak, Ewa; Pernal, Katarzyna, E-mail: pernalk@gmail.com

2014-05-14

Ensemble density functional theory (DFT) offers a way of predicting excited-states energies of atomic and molecular systems without referring to a density response function. Despite a significant theoretical work, practical applications of the proposed approximations have been scarce and they do not allow for a fair judgement of the potential usefulness of ensemble DFT with available functionals. In the paper, we investigate two forms of ensemble density functionals formulated within ensemble DFT framework: the Gross, Oliveira, and Kohn (GOK) functional proposed by Gross et al. [Phys. Rev. A 37, 2809 (1988)] alongside the orbital-dependent eDFT form of the functional introducedmore » by Nagy [J. Phys. B 34, 2363 (2001)] (the acronym eDFT proposed in analogy to eHF – ensemble Hartree-Fock method). Local and semi-local ground-state density functionals are employed in both approaches. Approximate ensemble density functionals contain not only spurious self-interaction but also the so-called ghost-interaction which has no counterpart in the ground-state DFT. We propose how to correct the GOK functional for both kinds of interactions in approximations that go beyond the exact-exchange functional. Numerical applications lead to a conclusion that functionals free of the ghost-interaction by construction, i.e., eDFT, yield much more reliable results than approximate self- and ghost-interaction-corrected GOK functional. Additionally, local density functional corrected for self-interaction employed in the eDFT framework yields excitations energies of the accuracy comparable to that of the uncorrected semi-local eDFT functional.« less

A New Computational Tool for Understanding Light-Matter Interactions

DTIC Science & Technology

2016-02-11

SECURITY CLASSIFICATION OF: Plasmonic resonance of a metallic nanostructure results from coherent motion of its conduction electrons driven by...Box 12211 Research Triangle Park, NC 27709-2211 Plasmonics , light-matter interaction, time-dependent density functional theory, modeling and...reviewed journals: Final Report: A New Computational Tool For Understanding Light-Matter Interactions Report Title Plasmonic resonance of a metallic

Hall effect at a tunable metal-insulator transition

NASA Astrophysics Data System (ADS)

Teizer, W.; Hellman, F.; Dynes, R. C.

2003-03-01

Using a rotating magnetic field, the Hall effect in three-dimensional amorphous GdxSi1-x has been measured in the critical regime of the metal-insulator transition for a constant total magnetic field. The Hall coefficient R0 is negative, indicating electronlike conductivity, with a magnitude that increases with decreasing conductivity. R0 diverges at the metal-insulator transition, and displays critical behavior with exponent -1 [R0˜(H-HC)-1]. This dependence is interpreted as a linear decrease in the density of mobile carriers n˜R-10˜H-HC, indicative of the dominant influence of interaction effects.

Influence of predator density on nonindependent effects of multiple predator species.

PubMed

Griffen, Blaine D; Williamson, Tucker

2008-02-01

Interactions between multiple predator species are frequent in natural communities and can have important implications for shared prey survival. Predator density may be an important component of these interactions between predator species, as the frequency of interactions between species is largely determined by species density. Here we experimentally examine the importance of predator density for interactions between predator species and subsequent impacts on prey. We show that aggressive interactions between the predatory shore crabs Carcinus maenas and Hemigrapsus sanguineus increased with predator density, yet did not increase as fast as negative interactions between conspecifics. At low density, interactions between conspecific and heterospecific predators had similar inhibitory impacts on predator function, whereas conspecific interference was greater than interference from heterospecifics at high predator density. Thus the impact of conspecific interference at high predator density was sufficient in itself that interactions with a second predator species had no additional impact on per capita predation. Spatial and temporal variability in predator density is a ubiquitous characteristic of natural systems that should be considered in studies of multiple predator species.

Interactive effects of fire and large herbivores on web-building spiders.

PubMed

Foster, C N; Barton, P S; Wood, J T; Lindenmayer, D B

2015-09-01

Altered disturbance regimes are a major driver of biodiversity loss worldwide. Maintaining or re-creating natural disturbance regimes is therefore the focus of many conservation programmes. A key challenge, however, is to understand how co-occurring disturbances interact to affect biodiversity. We experimentally tested for the interactive effects of prescribed fire and large macropod herbivores on the web-building spider assemblage of a eucalypt forest understorey and investigated the role of vegetation in mediating these effects using path analysis. Fire had strong negative effects on the density of web-building spiders, which were partly mediated by effects on vegetation structure, while negative effects of large herbivores on web density were not related to changes in vegetation. Fire amplified the effects of large herbivores on spiders, both via vegetation-mediated pathways and by increasing herbivore activity. The importance of vegetation-mediated pathways and fire-herbivore interactions differed for web density and richness and also differed between web types. Our results demonstrate that for some groups of web-building spiders, the effects of co-occurring disturbance drivers may be mostly additive, whereas for other groups, interactions between drivers can amplify disturbance effects. In our study system, the use of prescribed fire in the presence of high densities of herbivores could lead to reduced densities and altered composition of web-building spiders, with potential cascading effects through the arthropod food web. Our study highlights the importance of considering both the independent and interactive effects of disturbances, as well as the mechanisms driving their effects, in the management of disturbance regimes.

Are there any narrow K--nuclear states?

NASA Astrophysics Data System (ADS)

Hrtánková, Jaroslava; Mareš, Jiří

2017-07-01

We performed self-consistent calculations of K--nuclear quasi-bound states using a single-nucleon K- optical potential derived from chiral meson-baryon coupled-channel interaction models, supplemented by a phenomenological K- multinucleon potential introduced recently to achieve good fits to kaonic atom data [1]. Our calculations show that the effect of K- multinucleon interactions on K- widths in nuclei is decisive. The resulting widths are considerably larger than corresponding binding energies. Moreover, when the density dependence of the K--multinucleon interactions derived in the fits of kaonic atoms is extended to the nuclear interior, the only two models acceptable after imposing as additional constraint the single-nucleon fraction of K- absorption at rest do not yield any kaonic nuclear bound state in majority of considered nuclei.

Resource Effects on Solitary Bee Reproduction in a Managed Crop Pollination System.

PubMed

Pitts-Singer, Theresa L

2015-08-01

Population density may affect solitary bee maternal resource allocation. The number of Megachile rotundata (F.), alfalfa leafcutting bee, females released for seed production of Medicago sativa L., alfalfa, may limit flower availability for nest provisioning. In turn, pollinator abundance also may affect crop yield. The M. sativa pollination system presents an opportunity to test for effects of density dependence and maternal manipulation on M. rotundata reproduction. A multiyear study was performed on M. sativa fields upon which M. rotundata densities were altered to induce low, medium, and high density situations. Numbers of adult bees and open flowers were recorded weekly; bee reproduction variables were collected once. Fields varied in plant performance for each site and year, and the intended bee densities were not realized. Therefore, the variable density index (DI) was derived to describe the number of female bees per area of flowers over the study period. As DI increased, percentages of pollinated flowers, established females, and healthy brood significantly increased, and the number of pollinated flowers per female and of dead or diseased brood significantly decreased. Sex ratio was significantly more female biased as DI increased. Overwintered offspring weights were similar regardless of DI, but significantly differed by year for both sexes, and for males also by field and year × field interaction. Overall, resource limitation was not found in this field study. Other density-dependent factors may have induced a bee dispersal response soon after bees were released in the fields that circumvented the need for, or impact of, maternal manipulation. Published by Oxford University Press on behalf of Entomological Society of America 2015. This work is written by a US Government employee and is in the public domain in the US.

Muon reactivation in muon-catalyzed D-T fusion

NASA Astrophysics Data System (ADS)

Rafelski, H. E.; Müller, B.; Rafelski, J.; Trautmann, D.; Viollier, R. D.

We comprehensively reanalyze and search for the density dependence of the effective muon alpha sticking fraction ωsff observed experimentally in muon catalyzed deuterium-tritium fusion. In our work particular emphasis has been put on the density dependent dense hydrogen stopping power. The main technical details and improvements in this work are: The (αμ) + 2s and 2p states are treated independently and are assigned individual reaction rates. The essential muonic excitation rates have been recalculated taking into account finite nuclear mass effects. The stopping power for a charged projectile in liquid heavy hydrogen is modified to account for dynamic screening effects and a density dependent effective ionization potential. It is shown that the medium dependent stopping power for the (αμ) + ion is the crucial factor controlling the density dependence of the effective sticking fraction. It is also pointed out that the muonic helium K α X-ray yield and the sticking fraction at high density can not be simultaneously brought into agreement with the experimental results without invoking novel mechanisms suppressing Stark mixing in the (Heμ) L-shell.

Urban characteristics attributable to density-driven tie formation

NASA Astrophysics Data System (ADS)

Pan, Wei; Ghoshal, Gourab; Krumme, Coco; Cebrian, Manuel; Pentland, Alex

2013-06-01

Motivated by empirical evidence on the interplay between geography, population density and societal interaction, we propose a generative process for the evolution of social structure in cities. Our analytical and simulation results predict both super-linear scaling of social-tie density and information contagion as a function of the population. Here we demonstrate that our model provides a robust and accurate fit for the dependency of city characteristics with city-size, ranging from individual-level dyadic interactions (number of acquaintances, volume of communication) to population level variables (contagious disease rates, patenting activity, economic productivity and crime) without the need to appeal to heterogeneity, modularity, specialization or hierarchy.

Information loss in effective field theory: Entanglement and thermal entropies

NASA Astrophysics Data System (ADS)

Boyanovsky, Daniel

2018-03-01

Integrating out high energy degrees of freedom to yield a low energy effective field theory leads to a loss of information with a concomitant increase in entropy. We obtain the effective field theory of a light scalar field interacting with heavy fields after tracing out the heavy degrees of freedom from the time evolved density matrix. The initial density matrix describes the light field in its ground state and the heavy fields in equilibrium at a common temperature T . For T =0 , we obtain the reduced density matrix in a perturbative expansion; it reveals an emergent mixed state as a consequence of the entanglement between light and heavy fields. We obtain the effective action that determines the time evolution of the reduced density matrix for the light field in a nonperturbative Dyson resummation of one-loop correlations of the heavy fields. The Von-Neumann entanglement entropy associated with the reduced density matrix is obtained for the nonresonant and resonant cases in the asymptotic long time limit. In the nonresonant case the reduced density matrix displays an incipient thermalization albeit with a wave-vector, time and coupling dependent effective temperature as a consequence of memory of initial conditions. The entanglement entropy is time independent and is the thermal entropy for this effective, nonequilibrium temperature. In the resonant case the light field fully thermalizes with the heavy fields, the reduced density matrix loses memory of the initial conditions and the entanglement entropy becomes the thermal entropy of the light field. We discuss the relation between the entanglement entropy ultraviolet divergences and renormalization.

Silicon chemistry in interstellar clouds

NASA Technical Reports Server (NTRS)

Langer, William D.; Glassgold, A. E.

1989-01-01

Interstellar SiO was discovered shortly after CO but it has been detected mainly in high density and high temperature regions associated with outflow sources. A new model of interstellar silicon chemistry that explains the lack of SiO detections in cold clouds is presented which contains an exponential temperature dependence for the SiO abundance. A key aspect of the model is the sensitivity of SiO production by neutral silicon reactions to density and temperature, which arises from the dependence of the rate coefficients on the population of the excited fine structure levels of the silicon atom. This effect was originally pointed out in the context of neutral reactions of carbon and oxygen by Graff, who noted that the leading term in neutral atom-molecule interactions involves the quadrupole moment of the atom. Similar to the case of carbon, the requirement that Si has a quadrupole moment requires population of the J = 1 level, which lies 111K above the J = 0 ground state and has a critical density n(cr) equal to or greater than 10(6)/cu cm. The SiO abundance then has a temperature dependence proportional to exp(-111/T) and a quadratic density dependence for n less than n(cr). As part of the explanation of the lack of SiO detections at low temperatures and densities, this model also emphasizes the small efficiencies of the production routes and the correspondingly long times needed to reach equilibrium. Measurements of the abundance of SiO, in conjunction with theory, can provide information on the physical properties of interstellar clouds such as the abundances of oxygen bearing molecules and the depletion of interstellar silicon.

Magnetotransport of High Mobility Holes in Monolayer and Bilayer WSe2

NASA Astrophysics Data System (ADS)

Tutuc, Emanuel

Transition metal dichalcogenides have attracted significant interest because of their two-dimensional crystal structure, large band-gap, and strong spin-orbit interaction which leads to spin-valley locking. Recent advances in sample fabrication have allowed the experimental study of low temperature magneto-transport of high mobility holes in WSe2. We review here the main results of these studies which reveal clear quantum Hall states in mono- and bilayer WSe2. The data allows the extraction of an effective hole mass of m* = 0.45me (me is the bare electron mass) in both mono and bilayer WSe2. A systematic study of the carrier distribution in bilayer WSe2 determined from a Fourier analysis of the Shubnikov-de Haas oscillations indicates that the two layers are weakly coupled. The individual layer density dependence on gate bias shows negative compressibility, a signature of strong electron-electron interaction in these materials associated with the large effective mass. We discuss the interplay between cyclotron and Zeeman splitting using the dependence of the quantum Hall state sequence on carrier density, and the angle between the magnetic field and the WSe2 plane. Work done in collaboration with B. Fallahazad, H. C. P. Movva, K. Kim, S. K. Banerjee, T. Taniguchi, and K. Watanabe. This work supported by the Nanoelectronics Research Initiative SWAN center, Intel Corp., and National Science Foundation.

Female elk contacts are neither frequency nor density dependent

USGS Publications Warehouse

Cross, Paul C.; Creech, Tyler G.; Ebinger, Michael R.; Manlove, Kezia R.; Irvine, Kathryn M.; Henningsen, John C.; Rogerson, Jared D.; Scurlock, Brandon M.; Creely, Scott

2013-01-01

Identifying drivers of contact rates among individuals is critical to understanding disease dynamics and implementing targeted control measures. We studied the interaction patterns of 149 female elk (Cervus canadensis) distributed across five different regions of western Wyoming over three years, defining a contact as an approach within one body length (∼2 m). Using hierarchical models that account for correlations within individuals, pairs, and groups, we found that pairwise contact rates within a group declined by a factor of three as group sizes increased 33-fold. Per capita contact rates, however, increased with group size according to a power function, such that female elk contact rates fell in between the predictions of density- or frequency-dependent disease models. We found similar patterns for the duration of contacts. Our results suggest that larger elk groups are likely to play a disproportionate role in the disease dynamics of directly transmitted infections in elk. Supplemental feeding of elk had a limited impact on pairwise interaction rates and durations, but per capita rates were more than two times higher on feeding grounds. Our statistical approach decomposes the variation in contact rate into individual, dyadic, and environmental effects, and provides insight into factors that may be targeted by disease control programs. In particular, female elk contact patterns were driven more by environmental factors such as group size than by either individual or dyad effects.

From direct detection to relic abundance: the case of proton-philic spin-dependent inelastic Dark Matter

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

Scopel, Stefano; Yu, Hyeonhye, E-mail: scopel@sogang.ac.kr, E-mail: skyh2yu@gmail.com

We discuss strategies to make inferences on the thermal relic abundance of a Weakly Interacting Massive Particle (WIMP) when the same effective dimension-six operator that explains an experimental excess in direct detection is assumed to drive decoupling at freeze-out, and apply them to the explicit scenario of WIMP inelastic up-scattering with spin-dependent couplings to protons (proton-philic Spin-dependent Inelastic Dark Matter, pSIDM), a phenomenological set-up containing two Dark Matter (DM) particles χ{sub 1} and χ{sub 2} with masses m {sub χ}= m {sub χ{sub 1}} and m {sub χ{sub 2}}= m {sub χ}+δ that we have shown in a previous papermore » to explain the DAMA effect in compliance with the constraints from other detectors. We also update experimental constraints on pSIDM, extend the analysis to the most general spin-dependent momentum-dependent interactions allowed by non-relativistic Effective Field Theory (EFT), and consider for the WIMP velocity distribution in our Galaxy f ( v ) both a halo-independent approach and a standard Maxwellian. Under these conditions we find that the DAMA effect can be explained in terms of the particle χ{sub 1} in compliance with all the other constraints for all the analyzed EFT couplings and also for a Maxwellian f ( v ). As far as the relic abundance is concerned, we show that the problem of calculating it by using direct detection data to fix the model parameters is affected by a strong sensitivity on f ( v ) and by the degeneracy between the WIMP local density ρ{sub χ} and the WIMP-nucleon scattering cross section, since ρ{sub χ} must be rescaled with respect to the observed DM density in the neighborhood of the Sun when the calculated relic density Ω is smaller than the observed one Ω{sub 0}. As a consequence, a DM direct detection experiment is not directly sensitive to the physical cut-off scale of the EFT, but on some dimensional combination that does not depend on the actual value of Ω. However, such degeneracy can be used to develop a consistency test on the possibility that the WIMP is a thermal relic in the first place. When we apply it to the pSIDM scenario we find that only a WIMP with the standard spin-dependent interaction O=χ-bar {sub 1γ}{sup μ}γ{sup 5χ{sub 2}} q-bar γ{sub μ}γ{sup 5} q + h.c. with quarks can be a thermal relic for, approximately, 10 GeV\\;≲ m {sub χ}≲ 16 GeV, 17 keV\\;≲ δ≲ 28 keV, and a large uncertainty on Ω, 6× 10{sup −7}Ω{sub 0≲} Ω ≲ Ω{sub 0}. In order for the scenario to work the WIMP galactic velocity distribution must depart from a Maxwellian. Moreover, all the χ{sub 2} states must have already decayed today, and this requires some additional mechanism besides that provided by the O operator.« less

Factorial experimental design for the culture of human embryonic stem cells as aggregates in stirred suspension bioreactors reveals the potential for interaction effects between bioprocess parameters.

PubMed

Hunt, Megan M; Meng, Guoliang; Rancourt, Derrick E; Gates, Ian D; Kallos, Michael S

2014-01-01

Traditional optimization of culture parameters for the large-scale culture of human embryonic stem cells (ESCs) as aggregates is carried out in a stepwise manner whereby the effect of varying each culture parameter is investigated individually. However, as evidenced by the wide range of published protocols and culture performance indicators (growth rates, pluripotency marker expression, etc.), there is a lack of systematic investigation into the true effect of varying culture parameters especially with respect to potential interactions between culture variables. Here we describe the design and execution of a two-parameter, three-level (3(2)) factorial experiment resulting in nine conditions that were run in duplicate 125-mL stirred suspension bioreactors. The two parameters investigated here were inoculation density and agitation rate, which are easily controlled, but currently, poorly characterized. Cell readouts analyzed included fold expansion, maximum density, and exponential growth rate. Our results reveal that the choice of best case culture parameters was dependent on which cell property was chosen as the primary output variable. Subsequent statistical analyses via two-way analysis of variance indicated significant interaction effects between inoculation density and agitation rate specifically in the case of exponential growth rates. Results indicate that stepwise optimization has the potential to miss out on the true optimal case. In addition, choosing an optimum condition for a culture output of interest from the factorial design yielded similar results when repeated with the same cell line indicating reproducibility. We finally validated that human ESCs remain pluripotent in suspension culture as aggregates under our optimal conditions and maintain their differentiation capabilities as well as a stable karyotype and strong expression levels of specific human ESC markers over several passages in suspension bioreactors.

Spatial variation and density-dependent dispersal in competitive coexistence.

PubMed Central

Amarasekare, Priyanga

2004-01-01

It is well known that dispersal from localities favourable to a species' growth and reproduction (sources) can prevent competitive exclusion in unfavourable localities (sinks). What is perhaps less well known is that too much emigration can undermine the viability of sources and cause regional competitive exclusion. Here, I investigate two biological mechanisms that reduce the cost of dispersal to source communities. The first involves increasing the spatial variation in the strength of competition such that sources can withstand high rates of emigration; the second involves reducing emigration from sources via density-dependent dispersal. I compare how different forms of spatial variation and modes of dispersal influence source viability, and hence source-sink coexistence, under dominance and pre-emptive competition. A key finding is that, while spatial variation substantially reduces dispersal costs under both types of competition, density-dependent dispersal does so only under dominance competition. For instance, when spatial variation in the strength of competition is high, coexistence is possible (regardless of the type of competition) even when sources experience high emigration rates; when spatial variation is low, coexistence is restricted even under low emigration rates. Under dominance competition, density-dependent dispersal has a strong effect on coexistence. For instance, when the emigration rate increases with density at an accelerating rate (Type III density-dependent dispersal), coexistence is possible even when spatial variation is quite low; when the emigration rate increases with density at a decelerating rate (Type II density-dependent dispersal), coexistence is restricted even when spatial variation is quite high. Under pre-emptive competition, density-dependent dispersal has only a marginal effect on coexistence. Thus, the diversity-reducing effects of high dispersal rates persist under pre-emptive competition even when dispersal is density dependent, but can be significantly mitigated under dominance competition if density-dependent dispersal is Type III rather than Type II. These results lead to testable predictions about source-sink coexistence under different regimes of competition, spatial variation and dispersal. They identify situations in which density-independent dispersal provides a reasonable approximation to species' dispersal patterns, and those under which consideration of density-dependent dispersal is crucial to predicting long-term coexistence. PMID:15306322

Recent α decay half-lives and analytic expression predictions including superheavy nuclei

NASA Astrophysics Data System (ADS)

Royer, G.; Zhang, H. F.

2008-03-01

New recent experimental α decay half-lives have been compared with the results obtained from previously proposed formulas depending only on the mass and charge numbers of the α emitter and the Qα value. For the heaviest nuclei they are also compared with calculations using the Density-Dependent M3Y (DDM3Y) effective interaction and the Viola-Seaborg-Sobiczewski (VSS) formulas. The correct agreement allows us to make predictions for the α decay half-lives of other still unknown superheavy nuclei from these analytic formulas using the extrapolated Qα of G. Audi, A. H. Wapstra, and C. Thibault [Nucl. Phys. A729, 337 (2003)].

Emergence of ratio-dependent and predator-dependent functional responses for pollination mutualism and seed parasitism

USGS Publications Warehouse

DeAngelis, Donald L.; Holland, J. Nathaniel

2006-01-01

Prey (N) dependence [g(N)], predator (P) dependence [g(P) or g(N,P)], and ratio dependence [f(P/N)] are often seen as contrasting forms of the predator's functional response describing predator consumption rates on prey resources in predator–prey and parasitoid–host interactions. Analogously, prey-, predator-, and ratio-dependent functional responses are apparently alternative functional responses for other types of consumer–resource interactions. These include, for example, the fraction of flowers pollinated or seeds parasitized in pollination (pre-dispersal) seed-parasitism mutualisms, such as those between fig wasps and fig trees or yucca moths and yucca plants. Here we examine the appropriate functional responses for how the fraction of flowers pollinated and seeds parasitized vary with the density of pollinators (predator dependence) or the ratio of pollinator and flower densities (ratio dependence). We show that both types of functional responses can emerge from minor, but biologically important variations on a single model. An individual-based model was first used to describe plant–pollinator interactions. Conditional upon on whether the number of flowers visited by the pollinator was limited by factors other than search time (e.g., by the number of eggs it had to lay, if it was also a seed parasite), and on whether the pollinator could directly find flowers on a plant, or had to search, the simulation results lead to either a predator-dependent or a ratio-dependent functional response. An analytic model was then used to show mathematically how these two cases can arise.

Molecular dynamics simulation of water in and around carbon nanotubes: A coarse-grained description

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

Pantawane, Sanwardhini; Choudhury, Niharendu, E-mail: nihcho@barc.gov.in

2016-05-23

In the present study, we intend to investigate behaviour of water in and around hydrophobic open ended carbon nanotubes (CNTs) using a coarse-grained, core-softened model potential for water. The model potential considered here for water has recently been shown to successfully reproduce dynamic, thermodynamic and structural anomalies of water. The epitome of the study is to understand the incarceration of this coarse-grained water in a single-file carbon nanotube. In order to examine the effect of fluid-water van der Waals interaction on the structure of fluid in and around the nanotube, we have simulated three different CNT-water systems with varying degreemore » of solute-water dispersion interaction. The analyses of the radial one-particle density profiles reveal varying degree of permeation and wetting of the CNT interior depending on the degree of fluid-solute attractive van der Waals interaction. A peak in the radial density profile slightly off the nanotube axis signifies a zigzag chain of water molecule around the CNT axis. The average numbers of water molecules inside the CNT have been shown to increase with the increase in fluid-water attractive dispersion interaction.« less

The impact of baryonic discs on the shapes and profiles of self-interacting dark matter halos

NASA Astrophysics Data System (ADS)

Sameie, Omid; Creasey, Peter; Yu, Hai-Bo; Sales, Laura V.; Vogelsberger, Mark; Zavala, Jesús

2018-06-01

We employ isolated N-body simulations to study the response of self-interacting dark matter (SIDM) halos in the presence of the baryonic potentials. Dark matter self-interactions lead to kinematic thermalization in the inner halo, resulting in a tight correlation between the dark matter and baryon distributions. A deep baryonic potential shortens the phase of SIDM core expansion and triggers core contraction. This effect can be further enhanced by a large self-scattering cross section. We find the final SIDM density profile is sensitive to the baryonic concentration and the strength of dark matter self-interactions. Assuming a spherical initial halo, we also study evolution of the SIDM halo shape together with the density profile. The halo shape at later epochs deviates from spherical symmetry due to the influence of the non-spherical disc potential, and its significance depends on the baryonic contribution to the total gravitational potential, relative to the dark matter one. In addition, we construct a multi-component model for the Milky Way, including an SIDM halo, a stellar disc and a bulge, and show it is consistent with observations from stellar kinematics and streams.

Evidence for density dependence in foraging and migratory behavior of a subtropical nearshore seabird

USGS Publications Warehouse

Lamb, Juliet S.; Satgé, Yvan G.; Jodice, Patrick G. R.

2017-01-01

Density-dependent competition for food resources influences both foraging ecology and reproduction in a variety of animals. The relationship between colony size, local prey depletion, and reproductive output in colonial central-place foragers has been extensively studied in seabirds; however, most studies have focused on effects of intraspecific competition during the breeding season, while little is known about whether density-dependent resource depletion influences individual migratory behavior outside the breeding season. Using breeding colony size as a surrogate for intraspecific resource competition, we tested for effects of colony size on breeding home range, nestling health, and migratory patterns of a nearshore colonial seabird, the brown pelican (Pelecanus occidentalis), originating from seven breeding colonies of varying sizes in the subtropical northern Gulf of Mexico. We found evidence for density-dependent effects on foraging behavior during the breeding season, as individual foraging areas increased linearly with the number of breeding pairs per colony. Contrary to our predictions, however, nestlings from more numerous colonies with larger foraging ranges did not experience either decreased condition or increased stress. During nonbreeding, individuals from larger colonies were more likely to migrate, and traveled longer distances, than individuals from smaller colonies, indicating that the influence of density-dependent effects on distribution persists into the nonbreeding period. We also found significant effects of individual physical condition, particularly body size, on migratory behavior, which in combination with colony size suggesting that dominant individuals remain closer to breeding sites during winter. We conclude that density-dependent competition may be an important driver of both the extent of foraging ranges and the degree of migration exhibited by brown pelicans. However, the effects of density-dependent competition on breeding success and population regulation remain uncertain in this system.

Manipulation of particles by weak forces

NASA Technical Reports Server (NTRS)

Adler, M. S.; Savkar, S. D.; Summerhayes, H. R.

1972-01-01

Quantitative relations between various force fields and their effects on the motion of particles of various sizes and physical characteristics were studied. The forces considered were those derived from light, heat, microwaves, electric interactions, magnetic interactions, particulate interactions, and sound. A physical understanding is given of the forces considered as well as formulae which express how the size of the force depends on the physical and electrical properties of the particle. The drift velocity in a viscous fluid is evaluated as a function of initial acceleration and the effects of thermal random motion are considered. A means of selectively sorting or moving particles by choosing a force system and/or environment such that the particle of interest reacts uniquely was developed. The forces considered and a demonstration of how the initial acceleration, drift velocity, and ultimate particle density distribution is affected by particle, input, and environmental parameters are tabulated.

Nonlinear effects of climate and density in the dynamics of a fluctuating population of reindeer.

PubMed

Tyler, Nicholas J C; Forchhammer, Mads C; Øritsland, Nils Are

2008-06-01

Nonlinear and irregular population dynamics may arise as a result of phase dependence and coexistence of multiple attractors. Here we explore effects of climate and density in the dynamics of a highly fluctuating population of wild reindeer (Rangifer tarandus platyrhynchus) on Svalbard observed over a period of 29 years. Time series analyses revealed that density dependence and the effects of local climate (measured as the degree of ablation [melting] of snow during winter) on numbers were both highly nonlinear: direct negative density dependence was found when the population was growing (Rt > 0) and during phases of the North Atlantic Oscillation (NAO) characterized by winters with generally high (1979-1995) and low (1996-2007) indices, respectively. A growth-phase-dependent model explained the dynamics of the population best and revealed the influence of density-independent processes on numbers that a linear autoregressive model missed altogether. In particular, the abundance of reindeer was enhanced by ablation during phases of growth (Rt > 0), an observation that contrasts with the view that periods of mild weather in winter are normally deleterious for reindeer owing to icing of the snowpack. Analyses of vital rates corroborated the nonlinearity described in the population time series and showed that both starvation mortality in winter and fecundity were nonlinearly related to fluctuations in density and the level of ablation. The erratic pattern of growth of the population of reindeer in Adventdalen seems, therefore, to result from a combination of the effects of nonlinear density dependence, strong density-dependent mortality, and variable density independence related to ablation in winter.

Study of Electron Gas on a Neutron-Rich Nuclear Pasta

NASA Astrophysics Data System (ADS)

Ramirez-Homs, Enrique

This study used a classical molecular dynamics model to observe the role of electron gas on the formation of nuclear structures at subsaturation densities (rho < 0.015 fm-3) and low temperatures (T < 1MeV ). The simulations were performed by varying the Coulomb interaction strength on systems of isospin symmetric and asymmetric matter with periodic boundary conditions. The effect was quantified on the fragment size multiplicity, the inter-particle distance, the isospin content of the clusters, the nucleon mobility and cluster persistence, and on the nuclear structure shapes. The existence of the nuclear pasta structures was observed even with the absence of the Coulomb interaction but with a modication of the shapes formed. It was found that the presence of the electron gas tends to distribute matter more evenly, forms less compact objects, decreases the isospin content of clusters, modies the nucleon mobility, reduces the persistence and the fragment size multiplicity, but does not alter the inter-particle distance in clusters. The degree of these effects also varied on the nuclear structures and depended on their isospin content, temperature, and density.

Thermalization time scales for WIMP capture by the Sun in effective theories

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

Widmark, A., E-mail: axel.widmark@fysik.su.se

I study the process of dark matter capture by the Sun, under the assumption of a Weakly Interacting Massive Particle (WIMP), in the framework of non-relativistic effective field theory. Hypothetically, WIMPs from the galactic halo can scatter against atomic nuclei in the solar interior, settle to thermal equilibrium with the solar core and annihilate to produce an observable flux of neutrinos. In particular, I examine the thermalization process using Monte-Carlo integration of WIMP trajectories. I consider WIMPs in a mass range of 10–1000 GeV and WIMP-nucleon interaction operators with different dependence on spin and transferred momentum. I find that themore » density profiles of captured WIMPs are in accordance with a thermal profile described by the Sun's gravitational potential and core temperature. Depending on the operator that governs the interaction, the majority of the thermalization time is spent in either the solar interior or exterior. If normalizing the WIMP-nuclei interaction strength to a specific capture rate, I find that the thermalization time differs at most by 3 orders of magnitude between operators. In most cases of interest, the thermalization time is many orders of magnitude shorter than the age of the solar system.« less

AC conductivity of a quantum Hall line junction

NASA Astrophysics Data System (ADS)

Agarwal, Amit; Sen, Diptiman

2009-09-01

We present a microscopic model for calculating the AC conductivity of a finite length line junction made up of two counter- or co-propagating single mode quantum Hall edges with possibly different filling fractions. The effect of density-density interactions and a local tunneling conductance (σ) between the two edges is considered. Assuming that σ is independent of the frequency ω, we derive expressions for the AC conductivity as a function of ω, the length of the line junction and other parameters of the system. We reproduce the results of Sen and Agarwal (2008 Phys. Rev. B 78 085430) in the DC limit (\\omega \\to 0 ), and generalize those results for an interacting system. As a function of ω, the AC conductivity shows significant oscillations if σ is small; the oscillations become less prominent as σ increases. A renormalization group analysis shows that the system may be in a metallic or an insulating phase depending on the strength of the interactions. We discuss the experimental implications of this for the behavior of the AC conductivity at low temperatures.

Theory of nitrogen doping of carbon nanoribbons: Edge effects

DOE PAGES

Jiang, Jie; Turnbull, Joseph; Lu, Wenchang; ...

2012-01-01

Nitrogen doping of a carbon nanoribbon is profoundly affected by its one-dimensional character, symmetry, and interaction with edge states. Using state-of-the-art ab initio calculations, including hybrid exact-exchange density functional theory, we find that, for N-doped zigzag ribbons, the electronic properties are strongly dependent upon sublattice effects due to the non-equivalence of the two sublattices. For armchair ribbons, N-doping effects are different depending upon the ribbon family: for families 2 and 0, the N-induced levels are in the conduction band, while for family 1 the N levels are in the gap. In zigzag nanoribbons, nitrogen close to the edge is amore » deep center, while in armchair nanoribbons its behavior is close to an effective-mass-like donor with the ionization energy dependent on the value of the band gap. In chiral nanoribbons, we find strong dependence of the impurity level and formation energy upon the edge position of the dopant, while such site-specificity is not manifested in the magnitude of the magnetization.« less

Quantum Monte Carlo Studies of Interaction-Induced Localization in Quantum Dots and Wires

NASA Astrophysics Data System (ADS)

Devrim Güçlü, A.

2009-03-01

We investigate interaction-induced localization of electrons in both quantum dots and inhomogeneous quantum wires using variational and diffusion quantum Monte Carlo methods. Quantum dots and wires are highly tunable systems that enable the study of the physics of strongly correlated electrons. With decreasing electronic density, interactions become stronger and electrons are expected to localize at their classical positions, as in Wigner crystallization in an infinite 2D system. (1) Dots: We show that the addition energy shows a clear progression from features associated with shell structure to those caused by commensurability of a Wigner crystal. This cross-over is, then, a signature of localization; it occurs near rs˜20. For higher values of rs, the configuration symmetry of the quantum dot becomes fully consistent with the classical ground state. (2) Wires: We study an inhomogeneous quasi-one-dimensional system -- a wire with two regions, one at low density and the other high. We find that strong localization occurs in the low density quantum point contact region as the gate potential is increased. The nature of the transition from high to low density depends on the density gradient -- if it is steep, a barrier develops between the two regions, causing Coulomb blockade effects. We find no evidence for ferromagnetic spin polarization for the range of parameters studied. The picture emerging here is in good agreement with the experimental measurements of tunneling between two wires. Collaborators: C. J. Umrigar (Cornell), Hong Jiang (Fritz Haber Institut), Amit Ghosal (IISER Calcutta), and H. U. Baranger (Duke).

Self-interaction effects on charge-transfer collisions

DOE PAGES

Quashie, Edwin E.; Saha, Bidhan C.; Andrade, Xavier; ...

2017-04-27

In this article, we investigate the role of the self-interaction error in the simulation of collisions using time-dependent density functional theory (TDDFT) and Ehrenfest dynamics. In addition, we compare many different approximations of the exchange and correlation potential, using as a test system the collision of H + + CH 4 at 30 eV. We find that semilocal approximations, like the Perdew-Burke- Ernzerhof (PBE), and even hybrid functionals, such as the Becke, 3-parameter, Lee-Yang-Parr (B3LYP), produce qualitatively incorrect predictions for the scattering of the proton. This discrepancy appears because the self-interaction error allows the electrons to jump too easily tomore » the proton, leading to radically different forces with respect to the non-self-interacting case. Lastly, from our results, we conclude that using a functional that is self-interaction free is essential to properly describing charge-transfer collisions between ions and molecules in TDDFT.« less

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

PubMed Central

Zubillaga, María; Skewes, Oscar; Soto, Nicolás; Rabinovich, Jorge E.; Colchero, Fernando

2014-01-01

Understanding the mechanisms that drive population dynamics is fundamental for management of wild populations. The guanaco (Lama guanicoe) is one of two wild camelid species in South America. We evaluated the effects of density dependence and weather variables on population regulation based on a time series of 36 years of population sampling of guanacos in Tierra del Fuego, Chile. The population density varied between 2.7 and 30.7 guanaco/km2, with an apparent monotonic growth during the first 25 years; however, in the last 10 years the population has shown large fluctuations, suggesting that it might have reached its carrying capacity. We used a Bayesian state-space framework and model selection to determine the effect of density and environmental variables on guanaco population dynamics. Our results show that the population is under density dependent regulation and that it is currently fluctuating around an average carrying capacity of 45,000 guanacos. We also found a significant positive effect of previous winter temperature while sheep density has a strong negative effect on the guanaco population growth. We conclude that there are significant density dependent processes and that climate as well as competition with domestic species have important effects determining the population size of guanacos, with important implications for management and conservation. PMID:25514510

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

PubMed

Zubillaga, María; Skewes, Oscar; Soto, Nicolás; Rabinovich, Jorge E; Colchero, Fernando

2014-01-01

Understanding the mechanisms that drive population dynamics is fundamental for management of wild populations. The guanaco (Lama guanicoe) is one of two wild camelid species in South America. We evaluated the effects of density dependence and weather variables on population regulation based on a time series of 36 years of population sampling of guanacos in Tierra del Fuego, Chile. The population density varied between 2.7 and 30.7 guanaco/km2, with an apparent monotonic growth during the first 25 years; however, in the last 10 years the population has shown large fluctuations, suggesting that it might have reached its carrying capacity. We used a Bayesian state-space framework and model selection to determine the effect of density and environmental variables on guanaco population dynamics. Our results show that the population is under density dependent regulation and that it is currently fluctuating around an average carrying capacity of 45,000 guanacos. We also found a significant positive effect of previous winter temperature while sheep density has a strong negative effect on the guanaco population growth. We conclude that there are significant density dependent processes and that climate as well as competition with domestic species have important effects determining the population size of guanacos, with important implications for management and conservation.

Paws without claws? Ecological effects of large carnivores in anthropogenic landscapes

PubMed Central

Sahlén, E.; Elmhagen, B.; Chamaillé-Jammes, S.; Sand, H.; Lone, K.; Cromsigt, J. P. G. M.

2016-01-01

Large carnivores are frequently presented as saviours of biodiversity and ecosystem functioning through their creation of trophic cascades, an idea largely based on studies coming primarily out of relatively natural landscapes. However, in large parts of the world, particularly in Europe, large carnivores live in and are returning to strongly human-modified ecosystems. At present, we lack a coherent framework to predict the effects of large carnivores in these anthropogenic landscapes. We review how human actions influence the ecological roles of large carnivores by affecting their density or behaviour or those of mesopredators or prey species. We argue that the potential for density-mediated trophic cascades in anthropogenic landscapes is limited to unproductive areas where even low carnivore numbers may impact prey densities or to the limited parts of the landscape where carnivores are allowed to reach ecologically functional densities. The potential for behaviourally mediated trophic cascades may be larger and more widespread, because even low carnivore densities affect prey behaviour. We conclude that predator–prey interactions in anthropogenic landscapes will be highly context-dependent and human actions will often attenuate the ecological effects of large carnivores. We highlight the knowledge gaps and outline a new research avenue to study the role of carnivores in anthropogenic landscapes. PMID:27798302

Cultivar-dependent root colonization, antifungal metabolite accumulation and gene expression in the wheat-Pseudomonas interaction

USDA-ARS?s Scientific Manuscript database

We explored the role of host genotype in three aspects of the wheat-Pseudomonas biocontrol interaction: rhizosphere population density, accumulation of rhizosphere 2,4-diacetylphloroglucinol (DAPG), and Pseudomonas-mediated changes in root gene expression. Wheat cultivars varied in ability to suppo...

On the molecular origins of biomass recalcitrance: the interaction network and solvation structures of cellulose microfibrils.

PubMed

Gross, Adam S; Chu, Jhih-Wei

2010-10-28

Biomass recalcitrance is a fundamental bottleneck to producing fuels from renewable sources. To understand its molecular origin, we characterize the interaction network and solvation structures of cellulose microfibrils via all-atom molecular dynamics simulations. The network is divided into three components: intrachain, interchain, and intersheet interactions. Analysis of their spatial dependence and interaction energetics indicate that intersheet interactions are the most robust and strongest component and do not display a noticeable dependence on solvent exposure. Conversely, the strength of surface-exposed intrachain and interchain hydrogen bonds is significantly reduced. Comparing the interaction networks of I(β) and I(α) cellulose also shows that the number of intersheet interactions is a clear descriptor that distinguishes the two allomorphs and is consistent with the observation that I(β) is the more stable form. These results highlight the dominant role of the often-overlooked intersheet interactions in giving rise to biomass recalcitrance. We also analyze the solvation structures around the surfaces of microfibrils and show that the structural and chemical features at cellulose surfaces constrict water molecules into specific density profiles and pair correlation functions. Calculations of water density and compressibility in the hydration shell show noticeable but not drastic differences. Therefore, specific solvation structures are more prominent signatures of different surfaces.

Phase separation of a Lennard-Jones fluid interacting with a long, condensed polymer chain: implications for the nuclear body formation near chromosomes.

PubMed

Oh, Inrok; Choi, Saehyun; Jung, YounJoon; Kim, Jun Soo

2015-08-28

Phase separation in a biological cell nucleus occurs in a heterogeneous environment filled with a high density of chromatins and thus it is inevitably influenced by interactions with chromatins. As a model system of nuclear body formation in a cell nucleus filled with chromatins, we simulate the phase separation of a low-density Lennard-Jones (LJ) fluid interacting with a long, condensed polymer chain. The influence of the density variation of LJ particles above and below the phase boundary and the role of attractive interactions between LJ particles and polymer segments are investigated at a fixed value of strong self-interaction between LJ particles. For a density of LJ particles above the phase boundary, phase separation occurs and a dense domain of LJ particles forms irrespective of interactions with the condensed polymer chain whereas its localization relative to the polymer chain is determined by the LJ-polymer attraction strength. Especially, in the case of moderately weak attractions, the domain forms separately from the polymer chain and subsequently associates with the polymer chain. When the density is below the phase boundary, however, the formation of a dense domain is possible only when the LJ-polymer attraction is strong enough, for which the domain grows in direct contact with the interacting polymer chain. In this work, different growth behaviors of LJ particles result from the differences in the density of LJ particles and in the LJ-polymer interaction, and this work suggests that the distinct formation of activity-dependent and activity-independent nuclear bodies (NBs) in a cell nucleus may originate from the differences in the concentrations of body-specific NB components and in their interaction with chromatins.

Contribution to the beam plasma material interactions during material processing with TEA CO2 laser radiation

NASA Astrophysics Data System (ADS)

Jaschek, Rainer; Konrad, Peter E.; Mayerhofer, Roland; Bergmann, Hans W.; Bickel, Peter G.; Kowalewicz, Roland; Kuttenberger, Alfred; Christiansen, Jens

1995-03-01

The TEA-CO2-laser (transversely excited atmospheric pressure) is a tool for the pulsed processing of materials with peak power densities up to 1010 W/cm2 and a FWHM of 70 ns. The interaction between the laser beam, the surface of the work piece and the surrounding atmosphere as well as gas pressure and the formation of an induced plasma influences the response of the target. It was found that depending on the power density and the atmosphere the response can take two forms. (1) No target modification due to optical break through of the atmosphere and therefore shielding of the target (air pressure above 10 mbar, depending on the material). (2) Processing of materials (air pressure below 10 mbar, depending on the material) with melting of metallic surfaces (power density above 0.5 109 W/cm2), hole formation (power density of 5 109 W/cm2) and shock hardening (power density of 3.5 1010 W/cm2). All those phenomena are usually linked with the occurrence of laser supported combustion waves and laser supported detonation waves, respectively for which the mechanism is still not completely understood. The present paper shows how short time photography and spatial and temporal resolved spectroscopy can be used to better understand the various processes that occur during laser beam interaction. The spectra of titanium and aluminum are observed and correlated with the modification of the target. If the power density is high enough and the gas pressure above a material and gas composition specific threshold, the plasma radiation shows only spectral lines of the background atmosphere. If the gas pressure is below this threshold, a modification of the target surface (melting, evaporation and solid state transformation) with TEA-CO2- laser pulses is possible and the material specific spectra is observed. In some cases spatial and temporal resolved spectroscopy of a plasma allows the calculation of electron temperatures by comparison of two spectral lines.

Oscillatory interaction between O impurities and Al adatoms on Al(111) and its effect on nucleation and growth.

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

Hansen, Henri; Linke, Udo; Feibelman, Peter Julian

2003-07-01

We present a combined experimental and theoretical study of submonolayer growth in the presence of predeposited immobile impurities. Scanning tunneling microscopy measurements of Al/Al(1 1 1) epitaxy in the presence of oxygen adsorbates show that immobile O impurities influence all aspects of the early stages of homoepitaxial growth on Al(1 1 1). Possible scenarios for modified growth are investigated using kinetic Monte Carlo simulations. Dependences of island density on temperature, impurity concentration and strength and type of adatom-impurity interaction are compared. The comparison shows that the morphology of the growing Al film cannot result from only one interaction type: attractivemore » or repulsive. An oscillatory interaction, suggested by ab initio calculations, is proposed to explain the behavior of the system.« less

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

USGS Publications Warehouse

Leirs, H.; Stenseth, N.C.; Nichols, J.D.; Hines, J.E.; Verhagen, R.; Verheyen, W.

1997-01-01

Ecology has long been troubled by the controversy over how populations are regulated. Some ecologists focus on the role of environmental effects, whereas others argue that density-dependent feedback mechanisms are central. The relative importance of both processes is still hotly debated, but clear examples of both processes acting in the same population are rare. Keyfactor analysis (regression of population changes on possible causal factors) and time-series analysis are often used to investigate the presence of density dependence, but such approaches may be biased and provide no information on actual demographic rates. Here we report on both density-dependent and density-independent effects in a murid rodent pest species, the multimammate rat Mastomys natalensis (Smith, 1834), using statistical capture-recapture models. Both effects occur simultaneously, but we also demonstrate that they do not affect all demographic rates in the same way. We have incorporated the obtained estimates of demographic rates in a population dynamics model and show that the observed dynamics are affected by stabilizing nonlinear density-dependent components coupled with strong deterministic and stochastic seasonal components.

Hypoxic areas, density-dependence and food limitation drive the body condition of a heavily exploited marine fish predator

PubMed Central

Käll, Filip; Hansson, Martin; Baranova, Tatjana; Karlsson, Olle; Lundström, Karl; Neuenfeldt, Stefan; Hjelm, Joakim

2016-01-01

Investigating the factors regulating fish condition is crucial in ecology and the management of exploited fish populations. The body condition of cod (Gadus morhua) in the Baltic Sea has dramatically decreased during the past two decades, with large implications for the fishery relying on this resource. Here, we statistically investigated the potential drivers of the Baltic cod condition during the past 40 years using newly compiled fishery-independent biological data and hydrological observations. We evidenced a combination of different factors operating before and after the ecological regime shift that occurred in the Baltic Sea in the early 1990s. The changes in cod condition related to feeding opportunities, driven either by density-dependence or food limitation, along the whole period investigated and to the fivefold increase in the extent of hypoxic areas in the most recent 20 years. Hypoxic areas can act on cod condition through different mechanisms related directly to species physiology, or indirectly to behaviour and trophic interactions. Our analyses found statistical evidence for an effect of the hypoxia-induced habitat compression on cod condition possibly operating via crowding and density-dependent processes. These results furnish novel insights into the population dynamics of Baltic Sea cod that can aid the management of this currently threatened population. PMID:27853557

Computational studies of molecular charge transfer complexes of heterocyclic 4-methylepyridine-2-azomethine-p-benzene derivatives with picric acid and m-dinitrobenzene.

PubMed

Al-Harbi, L M; El-Mossalamy, E H; Obaid, A Y; Al-Jedaani, A H

2014-01-01

Charge transfer complexes of substituted aryl Schiff bases as donors with picric acid and m-dinitrobenzene as acceptors were investigated by using computational analysis calculated by Configuration Interaction Singles Hartree-Fock (CIS-HF) at standard 6-31G∗ basis set and Time-Dependent Density-Functional Theory (TD-DFT) levels of theory at standard 6-31G∗∗ basis set, infrared spectra, visible and nuclear magnetic resonance spectra are investigated. The optimized geometries and vibrational frequencies were evaluated. The energy and oscillator strength were calculated by Configuration Interaction Singles Hartree-Fock method (CIS-HF) and the Time-Dependent Density-Functional Theory (TD-DFT) results. Electronic properties, such as HOMO and LUMO energies and band gaps of CTCs set, were studied by the Time-Dependent density functional theory with Becke-Lee-Young-Parr (B3LYP) composite exchange correlation functional and by Configuration Interaction Singles Hartree-Fock method (CIS-HF). The ionization potential Ip and electron affinity EA were calculated by PM3, HF and DFT methods. The columbic force was calculated theoretically by using (CIS-HF and TD-DFT) methods. This study confirms that the theoretical calculation of vibrational frequencies for (aryl Schiff bases--(m-dinitrobenzene and picric acid)) complexes are quite useful for the vibrational assignment and for predicting new vibrational frequencies. Copyright © 2013 Elsevier B.V. All rights reserved.

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

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-07-01

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.

A sequence-dependent rigid-base model of DNA

NASA Astrophysics Data System (ADS)

Gonzalez, O.; Petkevičiutė, D.; Maddocks, J. H.

2013-02-01

A novel hierarchy of coarse-grain, sequence-dependent, rigid-base models of B-form DNA in solution is introduced. The hierarchy depends on both the assumed range of energetic couplings, and the extent of sequence dependence of the model parameters. A significant feature of the models is that they exhibit the phenomenon of frustration: each base cannot simultaneously minimize the energy of all of its interactions. As a consequence, an arbitrary DNA oligomer has an intrinsic or pre-existing stress, with the level of this frustration dependent on the particular sequence of the oligomer. Attention is focussed on the particular model in the hierarchy that has nearest-neighbor interactions and dimer sequence dependence of the model parameters. For a Gaussian version of this model, a complete coarse-grain parameter set is estimated. The parameterized model allows, for an oligomer of arbitrary length and sequence, a simple and explicit construction of an approximation to the configuration-space equilibrium probability density function for the oligomer in solution. The training set leading to the coarse-grain parameter set is itself extracted from a recent and extensive database of a large number of independent, atomic-resolution molecular dynamics (MD) simulations of short DNA oligomers immersed in explicit solvent. The Kullback-Leibler divergence between probability density functions is used to make several quantitative assessments of our nearest-neighbor, dimer-dependent model, which is compared against others in the hierarchy to assess various assumptions pertaining both to the locality of the energetic couplings and to the level of sequence dependence of its parameters. It is also compared directly against all-atom MD simulation to assess its predictive capabilities. The results show that the nearest-neighbor, dimer-dependent model can successfully resolve sequence effects both within and between oligomers. For example, due to the presence of frustration, the model can successfully predict the nonlocal changes in the minimum energy configuration of an oligomer that are consequent upon a local change of sequence at the level of a single point mutation.

A sequence-dependent rigid-base model of DNA.

PubMed

Gonzalez, O; Petkevičiūtė, D; Maddocks, J H

2013-02-07

A novel hierarchy of coarse-grain, sequence-dependent, rigid-base models of B-form DNA in solution is introduced. The hierarchy depends on both the assumed range of energetic couplings, and the extent of sequence dependence of the model parameters. A significant feature of the models is that they exhibit the phenomenon of frustration: each base cannot simultaneously minimize the energy of all of its interactions. As a consequence, an arbitrary DNA oligomer has an intrinsic or pre-existing stress, with the level of this frustration dependent on the particular sequence of the oligomer. Attention is focussed on the particular model in the hierarchy that has nearest-neighbor interactions and dimer sequence dependence of the model parameters. For a Gaussian version of this model, a complete coarse-grain parameter set is estimated. The parameterized model allows, for an oligomer of arbitrary length and sequence, a simple and explicit construction of an approximation to the configuration-space equilibrium probability density function for the oligomer in solution. The training set leading to the coarse-grain parameter set is itself extracted from a recent and extensive database of a large number of independent, atomic-resolution molecular dynamics (MD) simulations of short DNA oligomers immersed in explicit solvent. The Kullback-Leibler divergence between probability density functions is used to make several quantitative assessments of our nearest-neighbor, dimer-dependent model, which is compared against others in the hierarchy to assess various assumptions pertaining both to the locality of the energetic couplings and to the level of sequence dependence of its parameters. It is also compared directly against all-atom MD simulation to assess its predictive capabilities. The results show that the nearest-neighbor, dimer-dependent model can successfully resolve sequence effects both within and between oligomers. For example, due to the presence of frustration, the model can successfully predict the nonlocal changes in the minimum energy configuration of an oligomer that are consequent upon a local change of sequence at the level of a single point mutation.

Theory of interaction-induced renormalization of Drude weight and plasmon frequency in chiral multilayer graphene

NASA Astrophysics Data System (ADS)

Li, Xiao; Tse, Wang-Kong

2017-02-01

We develop a theory for the optical conductivity of doped ABC-stacked multilayer graphene including the effects of electron-electron interactions. Applying the quantum kinetic formalism, we formulate a set of pseudospin Bloch equations that govern the dynamics of the nonequilibrium density matrix driven by an external ac electric field under the influence of Coulomb interactions. These equations reveal a dynamical mechanism that couples the Drude and interband responses arising from the chirality of pseudospin textures in multilayer graphene systems. We demonstrate that this results in an interaction-induced enhancement of the Drude weight and plasmon frequency strongly dependent on the pseudospin winding number. Using bilayer graphene as an example, we also study the influence of higher-energy bands and find that they contribute considerable renormalization effects not captured by a low-energy two-band description. We argue that this enhancement of Drude weight and plasmon frequency occurs generally in materials characterized by electronic chirality.

Correlational Effects of the Molecular-Tilt Configuration and the Intermolecular van der Waals Interaction on the Charge Transport in the Molecular Junction.

PubMed

Shin, Jaeho; Gu, Kyungyeol; Yang, Seunghoon; Lee, Chul-Ho; Lee, Takhee; Jang, Yun Hee; Wang, Gunuk

2018-06-25

Molecular conformation, intermolecular interaction, and electrode-molecule contacts greatly affect charge transport in molecular junctions and interfacial properties of organic devices by controlling the molecular orbital alignment. Here, we statistically investigated the charge transport in molecular junctions containing self-assembled oligophenylene molecules sandwiched between an Au probe tip and graphene according to various tip-loading forces ( F L ) that can control the molecular-tilt configuration and the van der Waals (vdW) interactions. In particular, the molecular junctions exhibited two distinct transport regimes according to the F L dependence (i.e., F L -dependent and F L -independent tunneling regimes). In addition, the charge-injection tunneling barriers at the junction interfaces are differently changed when the F L ≤ 20 nN. These features are associated to the correlation effects between the asymmetry-coupling factor (η), the molecular-tilt angle (θ), and the repulsive intermolecular vdW force ( F vdW ) on the molecular-tunneling barriers. A more-comprehensive understanding of these charge transport properties was thoroughly developed based on the density functional theory calculations in consideration of the molecular-tilt configuration and the repulsive vdW force between molecules.

Coinfection with Plasmodium falciparum and Schistosoma haematobium: Additional Evidence of the Protective Effect of Schistosomiasis on Malaria in Senegalese Children

PubMed Central

Lemaitre, Magali; Watier, Laurence; Briand, Valérie; Garcia, André; Le Hesran, Jean Yves; Cot, Michel

2014-01-01

Parasitic infections are associated with high morbidity and mortality in developing countries. Several studies focused on the influence of helminth infections on malaria but the nature of the biological interaction is under debate. Our objective was to undertake a study to explore the influence of the measure of excreted egg load caused by Schistosoma haematobium on Plasmodium falciparum parasite densities. Ten measures of malaria parasite density and two measures of schistosomiasis egg urinary excretion over a 2-year follow-up period on 178 Senegalese children were considered. A linear mixed-effect model was developed to take data dependence into account. This work showed that children with a light S. haematobium infection (1–9 eggs/mL of urine) presented lower P. falciparum parasite densities than children not infected by S. haematobium (P < 0.04). Possible changes caused by parasite coinfections should be considered in the anti-helminth treatment of children and in malaria vaccination development. PMID:24323515

Coinfection with Plasmodium falciparum and Schistosoma haematobium: additional evidence of the protective effect of Schistosomiasis on malaria in Senegalese children.

PubMed

Lemaitre, Magali; Watier, Laurence; Briand, Valérie; Garcia, André; Le Hesran, Jean Yves; Cot, Michel

2014-02-01

Parasitic infections are associated with high morbidity and mortality in developing countries. Several studies focused on the influence of helminth infections on malaria but the nature of the biological interaction is under debate. Our objective was to undertake a study to explore the influence of the measure of excreted egg load caused by Schistosoma haematobium on Plasmodium falciparum parasite densities. Ten measures of malaria parasite density and two measures of schistosomiasis egg urinary excretion over a 2-year follow-up period on 178 Senegalese children were considered. A linear mixed-effect model was developed to take data dependence into account. This work showed that children with a light S. haematobium infection (1-9 eggs/mL of urine) presented lower P. falciparum parasite densities than children not infected by S. haematobium (P < 0.04). Possible changes caused by parasite coinfections should be considered in the anti-helminth treatment of children and in malaria vaccination development.

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

Filinov, A.V.; Golubnychiy, V.O.; Bonitz, M.

Extending our previous work [A.V. Filinov et al., J. Phys. A 36, 5957 (2003)], we present a detailed discussion of accuracy and practical applications of finite-temperature pseudopotentials for two-component Coulomb systems. Different pseudopotentials are discussed: (i) the diagonal Kelbg potential, (ii) the off-diagonal Kelbg potential, (iii) the improved diagonal Kelbg potential, (iv) an effective potential obtained with the Feynman-Kleinert variational principle, and (v) the 'exact' quantum pair potential derived from the two-particle density matrix. For the improved diagonal Kelbg potential, a simple temperature-dependent fit is derived which accurately reproduces the 'exact' pair potential in the whole temperature range. The derivedmore » pseudopotentials are then used in path integral Monte Carlo and molecular-dynamics (MD) simulations to obtain thermodynamical properties of strongly coupled hydrogen. It is demonstrated that classical MD simulations with spin-dependent interaction potentials for the electrons allow for an accurate description of the internal energy of hydrogen in the difficult regime of partial ionization down to the temperatures of about 60 000 K. Finally, we point out an interesting relationship between the quantum potentials and the effective potentials used in density-functional theory.« less

Poisson-Boltzmann theory of the charge-induced adsorption of semi-flexible polyelectrolytes.

PubMed

Ubbink, Job; Khokhlov, Alexei R

2004-03-15

A model is suggested for the structure of an adsorbed layer of a highly charged semi-flexible polyelectrolyte on a weakly charged surface of opposite charge sign. The adsorbed phase is thin, owing to the effective reversal of the charge sign of the surface upon adsorption, and ordered, owing to the high surface density of polyelectrolyte strands caused by the generally strong binding between polyelectrolyte and surface. The Poisson-Boltzmann equation for the electrostatic interaction between the array of adsorbed polyelectrolytes and the charged surface is solved for a cylindrical geometry, both numerically, using a finite element method, and analytically within the weak curvature limit under the assumption of excess monovalent salt. For small separations, repulsive surface polarization and counterion osmotic pressure effects dominate over the electrostatic attraction and the resulting electrostatic interaction curve shows a minimum at nonzero separations on the Angstrom scale. The equilibrium density of the adsorbed phase is obtained by minimizing the total free energy under the condition of equality of chemical potential and osmotic pressure of the polyelectrolyte in solution and in the adsorbed phase. For a wide range of ionic conditions and charge densities of the charged surface, the interstrand separation as predicted by the Poisson-Boltzmann model and the analytical theory closely agree. For low to moderate charge densities of the adsorbing surface, the interstrand spacing decreases as a function of the charge density of the charged surface. Above about 0.1 M excess monovalent salt, it is only weakly dependent on the ionic strength. At high charge densities of the adsorbing surface, the interstrand spacing increases with increasing ionic strength, in line with the experiments by Fang and Yang [J. Phys. Chem. B 101, 441 (1997)]. (c) 2004 American Institute of Physics.

High-power, kilojoule laser interactions with near-critical density plasma

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

Willingale, L.; Thomas, A. G. R.; Maksimchuk, A.

Experiments were performed using the Omega EP laser, which provided pulses containing 1kJ of energy in 9ps and was used to investigate high-power, relativistic intensity laser interactions with near-critical density plasmas, created from foam targets with densities of 3-100 mg/cm{sup 3}. The effect of changing the plasma density on both the laser light transmitted through the targets and the proton beam accelerated from the interaction was investigated. Two-dimensional particle-in-cell simulations enabled the interaction dynamics and laser propagation to be studied in detail. The effect of the laser polarization and intensity in the two-dimensional simulations on the channel formation and electronmore » heating are discussed. In this regime, where the plasma density is above the critical density, but below the relativistic critical density, the channel formation speed and therefore length are inversely proportional to the plasma density, which is faster than the hole boring model prediction. A general model is developed to describe the channel length in this regime.« less

Determination of the surface charge density and temperature dependence of purple membrane by electric force microscopy.

PubMed

Du, Huiwen; Li, Denghua; Wang, Yibing; Wang, Chenxuan; Zhang, Dongdong; Yang, Yan-lian; Wang, Chen

2013-08-29

We report here the measurement of the temperature-dependent surface charge density of purple membrane (PM) by using electrostatic force microscopy (EFM). The surface charge density was measured to be 3.4 × 10(5) e/cm(2) at room temperature and reaches the minimum at around 52 °C. The initial decrease of the surface charge density could be attributed to the reduced dipole alignment because of the thermally induced protein mobility in PM. The increase of charge density at higher temperature could be ascribed to the weakened interaction between proteins and the lipids, which leads to the exposure of the charged amino acids. This work could be a benefit to the direct assessment of the structural stability and electric properties of biological membranes at the nanoscale.

Linear entropy and collapse–revival phenomenon for a general formalism N-type four-level atom interacting with a single-mode field

NASA Astrophysics Data System (ADS)

Eied, A. A.

2018-05-01

In this paper, the linear entropy and collapse-revival phenomenon through the relation (< {\\hat{a}}+{\\hat{a}} > -{\\bar{n}}) in a system of N-configuration four-level atom interacting with a single-mode field with additional forms of nonlinearities of both the field and the intensity-dependent atom-field coupling functional are investigated. A factorization of the initial density operator is assumed, considering the field to be initially in a squeezed coherent states and the atom initially in its most upper excited state. The dynamical behavior of the linear entropy and the time evolution of (< {\\hat{a}}+ {\\hat{a}} > -{\\bar{n}}) are analyzed. In particular, the effects of the mean photon number, detuning, Kerr-like medium and the intensity-dependent coupling functional on the entropy and the evolution of (< {\\hat{a}}+ {\\hat{a}} > -{\\bar{n}}) are examined.

Mesoscale spatiotemporal variability in a complex host-parasite system influenced by intermediate host body size

PubMed Central

2017-01-01

Background Parasites are essential components of natural communities, but the factors that generate skewed distributions of parasite occurrences and abundances across host populations are not well understood. Methods Here, we analyse at a seascape scale the spatiotemporal relationships of parasite exposure and host body-size with the proportion of infected hosts (i.e., prevalence) and aggregation of parasite burden across ca. 150 km of the coast and over 22 months. We predicted that the effects of parasite exposure on prevalence and aggregation are dependent on host body-sizes. We used an indirect host-parasite interaction in which migratory seagulls, sandy-shore molecrabs, and an acanthocephalan worm constitute the definitive hosts, intermediate hosts, and endoparasite, respectively. In such complex systems, increments in the abundance of definitive hosts imply increments in intermediate hosts’ exposure to the parasite’s dispersive stages. Results Linear mixed-effects models showed a significant, albeit highly variable, positive relationship between seagull density and prevalence. This relationship was stronger for small (cephalothorax length >15 mm) than large molecrabs (<15 mm). Independently of seagull density, large molecrabs carried significantly more parasites than small molecrabs. The analysis of the variance-to-mean ratio of per capita parasite burden showed no relationship between seagull density and mean parasite aggregation across host populations. However, the amount of unexplained variability in aggregation was strikingly higher in larger than smaller intermediate hosts. This unexplained variability was driven by a decrease in the mean-variance scaling in heavily infected large molecrabs. Conclusions These results show complex interdependencies between extrinsic and intrinsic population attributes on the structure of host-parasite interactions. We suggest that parasite accumulation—a characteristic of indirect host-parasite interactions—and subsequent increasing mortality rates over ontogeny underpin size-dependent host-parasite dynamics. PMID:28828270

Entanglement Dynamics of Linear and Nonlinear Interaction of Two Two-Level Atoms with a Quantized Phase-Damped Field in the Dispersive Regime

NASA Astrophysics Data System (ADS)

Tavassoly, M. K.; Daneshmand, R.; Rustaee, N.

2018-06-01

In this paper we study the linear and nonlinear (intensity-dependent) interactions of two two-level atoms with a single-mode quantized field far from resonance, while the phase-damping effect is also taken into account. To find the analytical solution of the atom-field state vector corresponding to the considered model, after deducing the effective Hamiltonian we evaluate the time-dependent elements of the density operator using the master equation approach and superoperator method. Consequently, we are able to study the influences of the special nonlinearity function f (n) = √ {n}, the intensity of the initial coherent state field and the phase-damping parameter on the degree of entanglement of the whole system as well as the field and atom. It is shown that in the presence of damping, by passing time, the amount of entanglement of each subsystem with the rest of system, asymptotically reaches to its stationary and maximum value. Also, the nonlinear interaction does not have any effect on the entanglement of one of the atoms with the rest of system, but it changes the amplitude and time period of entanglement oscillations of the field and the other atom. Moreover, this may cause that, the degree of entanglement which may be low (high) at some moments of time becomes high (low) by entering the intensity-dependent function in the atom-field coupling.

Ballistic magnetotransport and spin-orbit interaction in indium antimonide and indium arsenide quantum wells

NASA Astrophysics Data System (ADS)

Peters, John Archibald

While charge transport in a two-dimensional electron system (2DES) is fairly well understood, many open experimental and theoretical questions related to the spin of electrons remain. The standard 2DES embedded in Alx Ga1-xAs/GaAs heterostructures is most likely not the optimal candidate for such investigations, since spin effects as well as spin-orbit interactions are small perturbations compared to other effects. This has brought InSb- and InAs-based material systems into focus due to the possibility of large spin-orbit interactions. By utilizing elastic scattering off a lithographic barrier, we investigate the consequence of spin on different electron trajectories observed in InSb and InAs quantum wells. We focus on the physical properties of spin-dependent reflection in a 2DES and we present experimental results demonstrating a method to create spin-polarized beams of ballistic electrons in the presence of a lateral potential barrier. Spatial separation of electron spins using cyclotron motion in a weak magnetic is also achieved via transverse magnetic focusing. We also explore electrostatic gating effects in InSb/InAlSb heterostructures and demonstrate the effective use of polymethylglutarimide (PMGI) as a gate dielectric for InSb. The dependence on temperature and on front gate voltage of mobility and density are also examined, revealing a strong dependence of mobility on density. As regards front gate action, there is saturation in the density once it reaches a limiting value. Further, we investigate antidot lattices patterned on InSb/InAlSb and InAs/AlGaSb heterostructures. At higher magnetic fields, ballistic commensurability features are displayed while at smaller magnetic fields localization and quantized oscillatory phenomena appear, with marked differences between InSb and InAs. Interesting localization behavior is exhibited in InSb, with the strength of the localization peak decreasing exponentially with temperature between 0.4 K and 50 K. InAs on the other hand show a strikingly modified antilocalization behavior, with small-period oscillations in magnetic field superposed. We also observe Altshuler-Aronov-Spivak oscillations in InSb and InAs antidot lattices and extract the phase and spin coherence lengths in InAs. Our experimental results are discussed in the light of localization and anti localization as probes of disorder and of spin dephasing mechanisms, modified by the artificial potential of the antidot lattice.

Nuclear ``pasta'' formation

NASA Astrophysics Data System (ADS)

Schneider, A. S.; Horowitz, C. J.; Hughto, J.; Berry, D. K.

2013-12-01

The formation of complex nonuniform phases of nuclear matter, known as nuclear pasta, is studied with molecular dynamics (MD) simulations containing 51200 nucleons. A phenomenological nuclear interaction is used that reproduces the saturation binding energy and density of nuclear matter. Systems are prepared at an initial density of 0.10fm-3 and then the density is decreased by expanding the simulation volume at different rates to densities of 0.01fm-3 or less. An originally uniform system of nuclear matter is observed to form spherical bubbles (“swiss cheese”), hollow tubes, flat plates (“lasagna”), thin rods (“spaghetti”) and, finally, nearly spherical nuclei with decreasing density. We explicitly observe nucleation mechanisms, with decreasing density, for these different pasta phase transitions. Topological quantities known as Minkowski functionals are obtained to characterize the pasta shapes. Different pasta shapes are observed depending on the expansion rate. This indicates nonequilibrium effects. We use this to determine the best ways to obtain lower energy states of the pasta system from MD simulations and to place constraints on the equilibration time of the system.

Body mass of prefledging Emperor Geese Chen canagica: Large-scale effects of interspecific densities and food availability

USGS Publications Warehouse

Lake, B.C.; Schmutz, J.A.; Lindberg, M.S.; Ely, Craig R.; Eldridge, W.D.; Broerman, F.J.

2008-01-01

We studied body mass of prefledging Emperor Geese Chen canagica at three locations across the Yukon-Kuskokwim Delta, Alaska, during 1990-2004 to investigate whether large-scale variation in body mass was related to interspecific competition for food. From 1990 to 2004, densities of Cackling Geese Branta hutchinsii minima more than doubled and were c. 2-5?? greater than densities of Emperor Geese, which were relatively constant over time. Body mass of prefledging Emperor Geese was strongly related (negatively) to interspecific densities of geese (combined density of Cackling and Emperor Geese) and positively related to measures of food availability (grazing lawn extent and net above-ground primary productivity (NAPP)). Grazing by geese resulted in consumption of ??? 90% of the NAPP that occurred in grazing lawns during the brood-rearing period, suggesting that density-dependent interspecific competition was from exploitation of common food resources. Efforts to increase the population size of Emperor Geese would benefit from considering competitive interactions among goose species and with forage plants. ?? 2008 The Authors.

Solvation effect of bacteriochlorophyll excitons in light-harvesting complex LH2.

PubMed

Urboniene, V; Vrublevskaja, O; Trinkunas, G; Gall, A; Robert, B; Valkunas, L

2007-09-15

We have characterized the influence of the protein environment on the spectral properties of the bacteriochlorophyll (Bchl) molecules of the peripheral light-harvesting (or LH2) complex from Rhodobacter sphaeroides. The spectral density functions of the pigments responsible for the 800 and 850 nm electronic transitions were determined from the temperature dependence of the Bchl absorption spectra in different environments (detergent micelles and native membranes). The spectral density function is virtually independent of the hydrophobic support that the protein experiences. The reorganization energy for the B850 Bchls is 220 cm(-1), which is almost twice that of the B800 Bchls, and its Huang-Rhys factor reaches 8.4. Around the transition point temperature, and at higher temperatures, both the static spectral inhomogeneity and the resonance interactions become temperature-dependent. The inhomogeneous distribution function of the transitions exhibits less temperature dependence when LH2 is embedded in membranes, suggesting that the lipid phase protects the protein. However, the temperature dependence of the fluorescence spectra of LH2 cannot be fitted using the same parameters determined from the analysis of the absorption spectra. Correct fitting requires the lowest exciton states to be additionally shifted to the red, suggesting the reorganization of the exciton spectrum.

Time-dependent MHD modeling of the global structure of the heliosphere

NASA Technical Reports Server (NTRS)

Liewer, P. C.; Brackbill, J. U.; Karmesin, S. Roy

1995-01-01

We present results from time-dependent modeling of the global structure of the heliosphere with neutral and magnetic field effects included. The magnetic field is assumed parallel to the interstellar flow in this two-dimensional axisymmetric model; the neutrals are treated as a fluid. The effects of interstellar neutrals and the interplanetary magnetic field on the location of the termination shock are studied using the most recent estimate of the interstellar medium parameters, results will be compared to those of Baranov and Zaitsev. The effect of the solar wind - VLISM interaction on the density and velocity of interstellar neutrals within the heliosphere will also be presented and related to observations. The response of the termination shock to the solar cycle variation in the solar wind will be compared to the response found previously using an axisymmetric hydrodynamic model without neutrals.

Relationship between anode material, supporting electrolyte and current density during electrochemical degradation of organic compounds in water.

PubMed

Guzmán-Duque, Fernando L; Palma-Goyes, Ricardo E; González, Ignacio; Peñuela, Gustavo; Torres-Palma, Ricardo A

2014-08-15

Taking crystal violet (CV) dye as pollutant model, the electrode, electrolyte and current density (i) relationship for electro-degrading organic molecules is discussed. Boron-doped diamond (BDD) or Iridium dioxide (IrO2) used as anode materials were tested with Na2SO4 or NaCl as electrolytes. CV degradation and generated oxidants showed that degradation pathways and efficiency are strongly linked to the current density-electrode-electrolyte interaction. With BDD, the degradation pathway depends on i: If ii(lim), generated oxidants play a major role in the CV elimination. When IrO2 was used, CV removal was not dependent on i, but on the electrolyte. Pollutant degradation in Na2SO4 on IrO2 seems to occur via IrO3; however, in the presence of NaCl, degradation was dependent on the chlorinated oxidative species generated. In terms of efficiency, the Na2SO4 electrolyte showed better results than NaCl when BDD anodes were employed. On the contrary, NaCl was superior when combined with IrO2. Thus, the IrO2/Cl(-) and BDD/SO4(2-) systems were better at removing the pollutant, being the former the most effective. On the other hand, pollutant degradation with the BDD/SO4(2-) and IrO2/Cl(-) systems is favored at low and high current densities, respectively. Copyright © 2014 Elsevier B.V. All rights reserved.

Complexity in African savannas: Direct, indirect, and cascading effects of animal densities, rainfall and vegetation availability

PubMed Central

Leeuwis, Tim; Peel, Mike

2018-01-01

Savanna ecosystems are popular subjects for interaction studies. Multiple studies have been done on the impact of elephants on vegetation, the impact of grass and browse availability on animal densities or on competition between herbivore species. Previous studies showed that elephant densities are frequently negatively correlated with densities of tall trees, and that browse and grass availability are correlated with browser and grazer density respectively. Additionally, a competition effect between browse and grass availability has been reported. These relationships are usually analysed by testing direct relationships between e.g., herbivore densities and food availability, without addressing competition effects or other indirect effects. In this study, multiple interactions in a savanna system have been analysed simultaneously using Partial Least Square-Path Modelling (PLS-PM) using mammal and vegetation data from three different wildlife reserves in southern KwaZulu-Natal. The results showed that the processes that three separate models for the three areas provided the best understanding of the importance of the different interactions. These models suggest that elephants had a negative impact on trees, but also on grass availability. The impact is stronger when elephants are not able to migrate during the dry season. Browsers and grazers were correlated with browse and grass availability, but competition between browse and grass was not detected. This study shows that due to the complexity of the interactions in an ecosystem and differences in environmental factors, these interactions are best studied per area. PLS-PM can be a useful tool for estimating direct, indirect, and cascading effects of changing animal densities in conservation areas. PMID:29768481

Quantum transport through a deformable molecular transistor

NASA Astrophysics Data System (ADS)

Cornaglia, P. S.; Grempel, D. R.; Ness, H.

2005-02-01

The linear transport properties of a model molecular transistor with electron-electron and electron-phonon interactions were investigated analytically and numerically. The model takes into account phonon modulation of the electronic energy levels and of the tunneling barrier between the molecule and the electrodes. When both effects are present they lead to asymmetries in the dependence of the conductance on gate voltage. The Kondo effect is observed in the presence of electron-phonon interactions. There are important qualitative differences between the cases of weak and strong coupling. In the first case the standard Kondo effect driven by spin fluctuations occurs. In the second case, it is driven by charge fluctuations. The Fermi-liquid relation between the spectral density of the molecule and its charge is altered by electron-phonon interactions. Remarkably, the relation between the zero-temperature conductance and the charge remains unchanged. Therefore, there is perfect transmission in all regimes whenever the average number of electrons in the molecule is an odd integer.

Correlation Imaging Reveals Specific Crowding Dynamics of Kinesin Motor Proteins

NASA Astrophysics Data System (ADS)

Miedema, Daniël M.; Kushwaha, Vandana S.; Denisov, Dmitry V.; Acar, Seyda; Nienhuis, Bernard; Peterman, Erwin J. G.; Schall, Peter

2017-10-01

Molecular motor proteins fulfill the critical function of transporting organelles and other building blocks along the biopolymer network of the cell's cytoskeleton, but crowding effects are believed to crucially affect this motor-driven transport due to motor interactions. Physical transport models, like the paradigmatic, totally asymmetric simple exclusion process (TASEP), have been used to predict these crowding effects based on simple exclusion interactions, but verifying them in experiments remains challenging. Here, we introduce a correlation imaging technique to precisely measure the motor density, velocity, and run length along filaments under crowding conditions, enabling us to elucidate the physical nature of crowding and test TASEP model predictions. Using the kinesin motor proteins kinesin-1 and OSM-3, we identify crowding effects in qualitative agreement with TASEP predictions, and we achieve excellent quantitative agreement by extending the model with motor-specific interaction ranges and crowding-dependent detachment probabilities. These results confirm the applicability of basic nonequilibrium models to the intracellular transport and highlight motor-specific strategies to deal with crowding.

Coulomb coupling effects in the gigahertz complex admittance of a quantum R–L circuit

NASA Astrophysics Data System (ADS)

Song, L.; Yin, J. Z.; Chen, S. W.

2018-05-01

We report on the gigahertz admittance measurements of a quantum conductor, i.e. a quantum R–L circuit, to probe the intrinsic dynamic of the conductor. The magnetic field dependence of the admittance phase provides us with an effective way to study the role of Coulomb interaction between counterpropagating edge channels. In addition, there is a small jump in the admittance phase when the transmitted modes are changed. This is because the gate voltage leads to a static potential shift of the quantum channel, then a quantum capacitance related to the density of states of the edge channels are influenced. Our study has made new discoveries of the dynamic transport in a quantum conductor, finding evidence for the deviations from quantum chiral transport associated with Coulomb interactions.

Local cellular neighborhood controls proliferation in cell competition

PubMed Central

Bove, Anna; Gradeci, Daniel; Fujita, Yasuyuki; Banerjee, Shiladitya; Charras, Guillaume; Lowe, Alan R.

2017-01-01

Cell competition is a quality-control mechanism through which tissues eliminate unfit cells. Cell competition can result from short-range biochemical inductions or long-range mechanical cues. However, little is known about how cell-scale interactions give rise to population shifts in tissues, due to the lack of experimental and computational tools to efficiently characterize interactions at the single-cell level. Here, we address these challenges by combining long-term automated microscopy with deep-learning image analysis to decipher how single-cell behavior determines tissue makeup during competition. Using our high-throughput analysis pipeline, we show that competitive interactions between MDCK wild-type cells and cells depleted of the polarity protein scribble are governed by differential sensitivity to local density and the cell type of each cell’s neighbors. We find that local density has a dramatic effect on the rate of division and apoptosis under competitive conditions. Strikingly, our analysis reveals that proliferation of the winner cells is up-regulated in neighborhoods mostly populated by loser cells. These data suggest that tissue-scale population shifts are strongly affected by cellular-scale tissue organization. We present a quantitative mathematical model that demonstrates the effect of neighbor cell–type dependence of apoptosis and division in determining the fitness of competing cell lines. PMID:28931601

An open-source framework for analyzing N-electron dynamics. II. Hybrid density functional theory/configuration interaction methodology.

PubMed

Hermann, Gunter; Pohl, Vincent; Tremblay, Jean Christophe

2017-10-30

In this contribution, we extend our framework for analyzing and visualizing correlated many-electron dynamics to non-variational, highly scalable electronic structure method. Specifically, an explicitly time-dependent electronic wave packet is written as a linear combination of N-electron wave functions at the configuration interaction singles (CIS) level, which are obtained from a reference time-dependent density functional theory (TDDFT) calculation. The procedure is implemented in the open-source Python program detCI@ORBKIT, which extends the capabilities of our recently published post-processing toolbox (Hermann et al., J. Comput. Chem. 2016, 37, 1511). From the output of standard quantum chemistry packages using atom-centered Gaussian-type basis functions, the framework exploits the multideterminental structure of the hybrid TDDFT/CIS wave packet to compute fundamental one-electron quantities such as difference electronic densities, transient electronic flux densities, and transition dipole moments. The hybrid scheme is benchmarked against wave function data for the laser-driven state selective excitation in LiH. It is shown that all features of the electron dynamics are in good quantitative agreement with the higher-level method provided a judicious choice of functional is made. Broadband excitation of a medium-sized organic chromophore further demonstrates the scalability of the method. In addition, the time-dependent flux densities unravel the mechanistic details of the simulated charge migration process at a glance. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Influence of the aggregate state on band structure and optical properties of C60 computed with different methods

NASA Astrophysics Data System (ADS)

Pal, Amrita; Arabnejad, Saeid; Yamashita, Koichi; Manzhos, Sergei

2018-05-01

C60 and C60 based molecules are efficient acceptors and electron transport layers for planar perovskite solar cells. While properties of these molecules are well studied by ab initio methods, those of solid C60, specifically its optical absorption properties, are not. We present a combined density functional theory-Density Functional Tight Binding (DFTB) study of the effect of solid state packing on the band structure and optical absorption of C60. The valence and conduction band edge energies of solid C60 differ on the order of 0.1 eV from single molecule frontier orbital energies. We show that calculations of optical properties using linear response time dependent-DFT(B) or the imaginary part of the dielectric constant (dipole approximation) can result in unrealistically large redshifts in the presence of intermolecular interactions compared to available experimental data. We show that optical spectra computed from the frequency-dependent real polarizability can better reproduce the effect of C60 aggregation on optical absorption, specifically with a generalized gradient approximation functional, and may be more suited to study effects of molecular aggregation.

Average-atom model for two-temperature states and ionic transport properties of aluminum in the warm dense matter regime

NASA Astrophysics Data System (ADS)

Hou, Yong; Fu, Yongsheng; Bredow, Richard; Kang, Dongdong; Redmer, Ronald; Yuan, Jianmin

2017-03-01

The average-atom model combined with the hyper-netted chain approximation is an efficient tool for electronic and ionic structure calculations for warm dense matter. Here we generalize this method in order to describe non-equilibrium states with different electron and ion temperature as produced in laser-matter interactions on ultra-short time scales. In particular, the electron-ion and ion-ion correlation effects are considered when calculating the electron structure. We derive an effective ion-ion pair-potential using the electron densities in the framework of temperature-depended density functional theory. Using this ion-ion potential we perform molecular dynamics simulations in order to determine the ionic transport properties such as the ionic diffusion coefficient and the shear viscosity through the ionic velocity autocorrelation functions.

Environmental Dependence of Warps in Spiral Galaxies

NASA Astrophysics Data System (ADS)

Ann, Hong Bae; Bae, Hyun Jeong

2016-12-01

We determined the warp parameters of 192 warped galaxies which are selected from 340 edge-on galaxies using color images as well as r-band isophotal maps. We derive the local background density (Σ_{n}) to examine the dependence of the warp amplitudes on the galaxy environment. We find a clear trend that strongly warped galaxies are likely to be found in high density regions where tidal interactions are supposed to be frequent. However, the correlation between α_{w} and Σ_{n} is too weak for weakly warped galaxies (α_{w} < 4°) and the cumulative distributions of weakly warped galaxies are not significantly different from those of galaxies with no detectable warps. This suggests that tidal interactions do not play a decisive role in the formation of weak warps.}

Plant diversity increases with the strength of negative density dependence at the global scale

USGS Publications Warehouse

LaManna, Joseph A.; Mangan, Scott A.; Alonso, Alfonso; Bourg, Norman; Brockelman, Warren Y.; Bunyavejchewin, Sarayudh; Chang, Li-Wan; Chiang, Jyh-Min; Chuyong, George B.; Clay, Keith; Condit, Richard; Cordell, Susan; Davies, Stuart J.; Furniss, Tucker J.; Giardina, Christian P.; Gunatilleke, I.A.U. Nimal; Gunatilleke, C.V. Savitri; He, Fangliang; Howe, Robert W.; Hubbell, Stephen P.; Hsieh, Chang-Fu; Inman-Narahari, Faith M.; Janik, David; Johnson, Daniel J.; Kenfack, David; Korte, Lisa; Kral, Kamil; Larson, Andrew J.; Lutz, James A.; McMahon, Sean M.; McShea, William J.; Memiaghe, Herve R.; Nathalang, Anuttara; Novotny, Vojtech; Ong, Perry S.; Orwig, David A.; Ostertag, Rebecca; Parker, Geoffrey G.; Phillips, Richard P.; Sack, Lawren; Sun, I-Fang; Tello, J. Sebastian; Thomas, Duncan W.; Turner, Benjamin L.; Vela Diaz, Dilys M.; Vrska, Tomas; Weiblen, George D.; Wolf, Amy; Yap, Sandra; Myers, Jonathan A.

2017-01-01

Theory predicts that higher biodiversity in the tropics is maintained by specialized interactions among plants and their natural enemies that result in conspecific negative density dependence (CNDD). By using more than 3000 species and nearly 2.4 million trees across 24 forest plots worldwide, we show that global patterns in tree species diversity reflect not only stronger CNDD at tropical versus temperate latitudes but also a latitudinal shift in the relationship between CNDD and species abundance. CNDD was stronger for rare species at tropical versus temperate latitudes, potentially causing the persistence of greater numbers of rare species in the tropics. Our study reveals fundamental differences in the nature of local-scale biotic interactions that contribute to the maintenance of species diversity across temperate and tropical communities.

Role of small-norm components in extended random-phase approximation

NASA Astrophysics Data System (ADS)

Tohyama, Mitsuru

2017-09-01

The role of the small-norm amplitudes in extended random-phase approximation (RPA) theories such as the particle-particle and hole-hole components of one-body amplitudes and the two-body amplitudes other than two-particle/two-hole components are investigated for the one-dimensional Hubbard model using an extended RPA derived from the time-dependent density matrix theory. It is found that these amplitudes cannot be neglected in strongly interacting regions where the effects of ground-state correlations are significant.

Quasiparticle interference, quasiparticle interactions, and the origin of the charge density wave in 2 H – NbSe 2

DOE PAGES

Arguello, C. J.; Rosenthal, E. P.; Andrade, E. F.; ...

2015-01-21

We show that a small number of intentionally introduced defects can be used as a spectroscopic tool to amplify quasiparticle interference in 2H-NbSe₂ that we measure by scanning tunneling spectroscopic imaging. We show, from the momentum and energy dependence of the quasiparticle interference, that Fermi surface nesting is inconsequential to charge density wave formation in 2H-NbSe₂. We demonstrate that, by combining quasiparticle interference data with additional knowledge of the quasiparticle band structure from angle resolved photoemission measurements, one can extract the wave vector and energy dependence of the important electronic scattering processes thereby obtaining direct information both about the fermiologymore » and the interactions. In 2H-NbSe₂, we use this combination to confirm that the important near-Fermi-surface electronic physics is dominated by the coupling of the quasiparticles to soft mode phonons at a wave vector different from the charge density wave ordering wave vector.« less

Quasiparticle interference, quasiparticle interactions, and the origin of the charge density wave in 2H-NbSe2.

PubMed

Arguello, C J; Rosenthal, E P; Andrade, E F; Jin, W; Yeh, P C; Zaki, N; Jia, S; Cava, R J; Fernandes, R M; Millis, A J; Valla, T; Osgood, R M; Pasupathy, A N

2015-01-23

We show that a small number of intentionally introduced defects can be used as a spectroscopic tool to amplify quasiparticle interference in 2H-NbSe2 that we measure by scanning tunneling spectroscopic imaging. We show, from the momentum and energy dependence of the quasiparticle interference, that Fermi surface nesting is inconsequential to charge density wave formation in 2H-NbSe2. We demonstrate that, by combining quasiparticle interference data with additional knowledge of the quasiparticle band structure from angle resolved photoemission measurements, one can extract the wave vector and energy dependence of the important electronic scattering processes thereby obtaining direct information both about the fermiology and the interactions. In 2H-NbSe2, we use this combination to confirm that the important near-Fermi-surface electronic physics is dominated by the coupling of the quasiparticles to soft mode phonons at a wave vector different from the charge density wave ordering wave vector.

Structure-based coarse-graining for inhomogeneous liquid polymer systems.

PubMed

Fukuda, Motoo; Zhang, Hedong; Ishiguro, Takahiro; Fukuzawa, Kenji; Itoh, Shintaro

2013-08-07

The iterative Boltzmann inversion (IBI) method is used to derive interaction potentials for coarse-grained (CG) systems by matching structural properties of a reference atomistic system. However, because it depends on such thermodynamic conditions as density and pressure of the reference system, the derived CG nonbonded potential is probably not applicable to inhomogeneous systems containing different density regimes. In this paper, we propose a structure-based coarse-graining scheme to devise CG nonbonded potentials that are applicable to different density bulk systems and inhomogeneous systems with interfaces. Similar to the IBI, the radial distribution function (RDF) of a reference atomistic bulk system is used for iteratively refining the CG nonbonded potential. In contrast to the IBI, however, our scheme employs an appropriately estimated initial guess and a small amount of refinement to suppress transfer of the many-body interaction effects included in the reference RDF into the CG nonbonded potential. To demonstrate the application of our approach to inhomogeneous systems, we perform coarse-graining for a liquid perfluoropolyether (PFPE) film coated on a carbon surface. The constructed CG PFPE model favorably reproduces structural and density distribution functions, not only for bulk systems, but also at the liquid-vacuum and liquid-solid interfaces, demonstrating that our CG scheme offers an easy and practical way to accurately determine nonbonded potentials for inhomogeneous systems.

Collective interaction of microscale matters in natural analogy: human cancer cells vs. microspheres

NASA Astrophysics Data System (ADS)

Ahn, Sungsook; Lee, Sang Joon; Postech Team

2014-11-01

Collective behaviors have been considered both in living and lifeless things as a natural phenomenon. During the ordering process, a sudden and spontaneous transition is typically generated between an order and a disorder according to the population density of interacting elements. In a cellular level collective behavior, the cells are distributed in the characteristic patterns according to the population density and the mutual interaction of the individual cells undergo density-dependent diffusive motion. On the other hand, density-controlled surface-modified hollow microsphere suspension induces an overpopulation via buoyancy which provides a driving force to induce an assembly. The collective behaviors of the cells and microspheres in a designed liquid medium are explained in terms of the deviation from the interparticle distance distribution and the induced strength to organize the particle position in a specific distance range. as a result, microscale particulate matters exhibit high resemblance in their pair correlation and dynamical heterogeneity in the intermediate range between a single individual and an agglomerate. Therefore, it is suggested that biological systems are analogically explained to be dominated by physically interactive aspects.

Feasibility of constraining the curvature parameter of the symmetry energy using elliptic flow data

NASA Astrophysics Data System (ADS)

Cozma, M. D.

2018-03-01

A QMD transport model that employs a modified momentum dependent interaction (MDI2) potential, supplemented by a phase-space coalescence model fitted to FOPI experimental multiplicities of free nucleons and light clusters is used to study the density dependence of the symmetry energy above the saturation point by a comparison with experimental elliptic flow ratios measured by the FOPI-LAND and ASYEOS Collaborations in 197Au + 197Au collisions at 400 MeV/nucleon impact energy. A previous calculation using the same model has proven that neutron-to-proton and neutron-to-charged-particles elliptic flow ratios probe on average different densities allowing in principle the extraction of both the slope L and curvature K_{sym} parameters of the symmetry energy. To make use of this result a Gogny interaction inspired potential is modified by the addition of a density dependent, momentum independent term, while enforcing a close description of the empirical nucleon optical potential, allowing independent modifications of L and Ksym. Comparing theoretical predictions with experimental data for neutron-to-proton and neutron-to-charged-particles elliptic flow ratios the following constraint is extracted: L = 85 ± 22(exp) ± 20(th) ± 12(sys) MeV and K_{sym} = 96 ± 315(exp) ± 170(th) ± 166(sys) MeV. Theoretical errors include effects due to uncertainties in the isoscalar part of the equation of state, value of the isovector neutron-proton effective mass splitting, in-medium effects on the elastic nucleon-nucleon cross-sections, Pauli blocking algorithm variants and scenario considered for the conservation of the total energy of the system. Systematical uncertainties are generated by the inability of the transport model to reproduce experimental light-cluster-to-proton multiplicity ratios. A value for L free of systematical theoretical uncertainties can be extracted from the neutron-to-proton elliptic flow ratio alone: L = 84 ± 30(exp) ± 19(th) MeV. It is demonstrated that elliptic flow ratios reach a maximum sensitivity on the K_{sym} parameter in heavy-ion collisions of about 250 MeV/nucleon impact energy, allowing a reduction of its experimental component of uncertainty to about 150 MeV.

Solving the Nose-Hoover thermostat for Nuclear Pasta

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

Perez Garcia, M. Angeles

2006-06-19

At densities just below nuclear saturation density, there may be possible non-uniform spatial configurations of neutron rich matter. In this work we present a calculation using molecular dynamics techniques for a nuclear system interacting via a semiclassical potential depending on both positions and momenta and kept at fixed temperature by using the Nose-Hoover Thermostat.

A model of urban scaling laws based on distance dependent interactions

NASA Astrophysics Data System (ADS)

Ribeiro, Fabiano L.; Meirelles, Joao; Ferreira, Fernando F.; Neto, Camilo Rodrigues

2017-03-01

Socio-economic related properties of a city grow faster than a linear relationship with the population, in a log-log plot, the so-called superlinear scaling. Conversely, the larger a city, the more efficient it is in the use of its infrastructure, leading to a sublinear scaling on these variables. In this work, we addressed a simple explanation for those scaling laws in cities based on the interaction range between the citizens and on the fractal properties of the cities. To this purpose, we introduced a measure of social potential which captured the influence of social interaction on the economic performance and the benefits of amenities in the case of infrastructure offered by the city. We assumed that the population density depends on the fractal dimension and on the distance-dependent interactions between individuals. The model suggests that when the city interacts as a whole, and not just as a set of isolated parts, there is improvement of the socio-economic indicators. Moreover, the bigger the interaction range between citizens and amenities, the bigger the improvement of the socio-economic indicators and the lower the infrastructure costs of the city. We addressed how public policies could take advantage of these properties to improve cities development, minimizing negative effects. Furthermore, the model predicts that the sum of the scaling exponents of social-economic and infrastructure variables are 2, as observed in the literature. Simulations with an agent-based model are confronted with the theoretical approach and they are compatible with the empirical evidences.

A model of urban scaling laws based on distance dependent interactions.

PubMed

Ribeiro, Fabiano L; Meirelles, Joao; Ferreira, Fernando F; Neto, Camilo Rodrigues

2017-03-01

Socio-economic related properties of a city grow faster than a linear relationship with the population, in a log-log plot, the so-called superlinear scaling . Conversely, the larger a city, the more efficient it is in the use of its infrastructure, leading to a sublinear scaling on these variables. In this work, we addressed a simple explanation for those scaling laws in cities based on the interaction range between the citizens and on the fractal properties of the cities. To this purpose, we introduced a measure of social potential which captured the influence of social interaction on the economic performance and the benefits of amenities in the case of infrastructure offered by the city. We assumed that the population density depends on the fractal dimension and on the distance-dependent interactions between individuals. The model suggests that when the city interacts as a whole, and not just as a set of isolated parts, there is improvement of the socio-economic indicators. Moreover, the bigger the interaction range between citizens and amenities, the bigger the improvement of the socio-economic indicators and the lower the infrastructure costs of the city. We addressed how public policies could take advantage of these properties to improve cities development, minimizing negative effects. Furthermore, the model predicts that the sum of the scaling exponents of social-economic and infrastructure variables are 2, as observed in the literature. Simulations with an agent-based model are confronted with the theoretical approach and they are compatible with the empirical evidences.

Elliptic flow from Coulomb interaction and low density elastic scattering

NASA Astrophysics Data System (ADS)

Sun, Yuliang; Li, Qingfeng; Wang, Fuqiang

2018-04-01

In high energy heavy ion collisions and interacting cold atom systems, large elliptic flow anisotropies have been observed. For the large opacity (ρ σ L ˜103 ) of the latter hydrodynamics is a natural consequence, but for the small opacity (ρ σ L ˜1 ) of the former the hydrodynamic description is questionable. To shed light onto the situation, we simulate the expansion of a low density argon ion (or atom) system, initially trapped in an elliptical region, under the Coulomb interaction (or elastic scattering). Significant elliptic anisotropy is found in both cases, and the anisotropy depends on the initial spatial eccentricity and the density of the system. The results may provide insights into the physics of anisotropic flow in high energy heavy ion collisions and its role in the study of quantum chromodynamics.

Amino Acid Side Chain Interactions in the Presence of Salts

PubMed Central

Hassan, Sergio A.

2005-01-01

The effects of salt on the intermolecular interactions between polar/charged amino acids are investigated through molecular dynamics simulations. The mean forces and associated potentials are calculated for NaCl salt in the 0–2 M concentration range at 298 K. It is found that the addition of salt may stabilize or destabilize the interactions, depending on the nature of the interacting molecules. The degree of (de)stabilization is quantified, and the origin of the salt-dependent modulation is discussed based upon an analysis of solvent density profiles. To gain insight into the molecular origin of the salt modulation, spatial distribution functions (sdf’s) are calculated, revealing a high degree of solvent structuredness in all cases. The peaks in the sdf’s are consistent with long-range hydrogen-bonding networks connecting the solute hydrophilic groups, and that contribute to their intermolecular solvent-induced forces. The restructuring of water around the solutes as they dissociate from close contact is analyzed. This analysis offers clues on how the solvent structure modulates the effective intermolecular interactions in complex solutes. This modulation results from a critical balance between bulk electrostatic forces and those exerted by (i) the water molecules in the structured region between the monomers, which is disrupted by ions that transiently enter the hydration shells, and (ii) the ions in the hydration shells in direct interactions with the solutes. The implications of these findings in protein/ligand (noncovalent) association/dissociation mechanisms are briefly discussed. PMID:16479276

Interactions between genetic variation and cellular environment in skeletal muscle gene expression.

PubMed

Taylor, D Leland; Knowles, David A; Scott, Laura J; Ramirez, Andrea H; Casale, Francesco Paolo; Wolford, Brooke N; Guan, Li; Varshney, Arushi; Albanus, Ricardo D'Oliveira; Parker, Stephen C J; Narisu, Narisu; Chines, Peter S; Erdos, Michael R; Welch, Ryan P; Kinnunen, Leena; Saramies, Jouko; Sundvall, Jouko; Lakka, Timo A; Laakso, Markku; Tuomilehto, Jaakko; Koistinen, Heikki A; Stegle, Oliver; Boehnke, Michael; Birney, Ewan; Collins, Francis S

2018-01-01

From whole organisms to individual cells, responses to environmental conditions are influenced by genetic makeup, where the effect of genetic variation on a trait depends on the environmental context. RNA-sequencing quantifies gene expression as a molecular trait, and is capable of capturing both genetic and environmental effects. In this study, we explore opportunities of using allele-specific expression (ASE) to discover cis-acting genotype-environment interactions (GxE)-genetic effects on gene expression that depend on an environmental condition. Treating 17 common, clinical traits as approximations of the cellular environment of 267 skeletal muscle biopsies, we identify 10 candidate environmental response expression quantitative trait loci (reQTLs) across 6 traits (12 unique gene-environment trait pairs; 10% FDR per trait) including sex, systolic blood pressure, and low-density lipoprotein cholesterol. Although using ASE is in principle a promising approach to detect GxE effects, replication of such signals can be challenging as validation requires harmonization of environmental traits across cohorts and a sufficient sampling of heterozygotes for a transcribed SNP. Comprehensive discovery and replication will require large human transcriptome datasets, or the integration of multiple transcribed SNPs, coupled with standardized clinical phenotyping.

Finite metapopulation models with density-dependent migration and stochastic local dynamics

PubMed Central

Saether, B.-E.; Engen, S.; Lande, R.

1999-01-01

The effects of small density-dependent migration on the dynamics of a metapopulation are studied in a model with stochastic local dynamics. We use a diffusion approximation to study how changes in the migration rate and habitat occupancy affect the rates of local colonization and extinction. If the emigration rate increases or if the immigration rate decreases with local population size, a positive expected rate of change in habitat occupancy is found for a greater range of habitat occupancies than when the migration is density-independent. In contrast, the reverse patterns of density dependence in respective emigration and immigration reduce the range of habitat occupancies where the metapopulation will be viable. This occurs because density-dependent migration strongly influences both the establishment and rescue effects in the local dynamics of metapopulations.

Potassium-induced effect on structure and chemical activity of Cu xO/Cu(111) (x≤2) surface: A combined scanning tunneling microscopy and density functional theory study

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

Liu, Ping; An, Wei; Stacchiola, Dario

2015-10-16

Potassium (K) plays an essential role in promoting catalytic reaction in many established industrial catalytic processes. Here, we report a combined study using scanning tunneling microscopy (STM) and density functional theory (DFT) in understanding the effect of depositing K on the atomic and electronic structures as well as chemical activities of Cu xO/Cu(111) (x≤2). The DFT calculations observe a pseudomorphic growth of K on Cu xO/Cu(111) up to 0.19 monolayer (ML) of coverage, where K binds the surface via strong ionic interaction with chemisorbed oxygen and the relatively weak electrostatic interactions with copper ions, lower and upper oxygen on themore » Cu xO rings. The simulated STM pattern based on the DFT results agrees well with the experimental observations. The deposited K displays great impact on the surface electronic structure of Cu xO/Cu(111), which induces significant reduction in work function and leads to a strong electron polarization on the surface. The promotion of K on the surface binding properties is selective. It varies depending on the nature of adsorbates. According to our results, K has little effect on surface acidity, while it enhances the surface basicity significantly. As a consequence, the presence of K does not help for CO adsorption on Cu xO/Cu(111), but being able to accelerate the activation of CO 2. Thus, such promotion strongly depends on the combinations from both geometric and electronic effects. Our results highlight the origin of promoting effect of alkalis in the design of catalysts for the complex reactions.« less

Charge Transfer Enhancement in the D-π-A Type Porphyrin Dyes: A Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TD-DFT) Study.

PubMed

Kang, Guo-Jun; Song, Chao; Ren, Xue-Feng

2016-11-25

The electronic geometries and optical properties of two D-π-A type zinc porphyrin dyes (NCH₃-YD2 and TPhe-YD) were systematically investigated by density functional theory (DFT) and time-dependent density functional theory (TD-DFT) to reveal the origin of significantly altered charge transfer enhancement by changing the electron donor of the famous porphyrin-based sensitizer YD2-o-C8. The molecular geometries and photophysical properties of dyes before and after binding to the TiO₂ cluster were fully investigated. From the analyses of natural bond orbital (NBO), extended charge decomposition analysis (ECDA), and electron density variations (Δρ) between the excited state and ground state, it was found that the introduction of N(CH₃)₂ and 1,1,2-triphenylethene groups enhanced the intramolecular charge-transfer (ICT) character compared to YD2-o-C8. The absorption wavelength and transition possess character were significantly influenced by N(CH₃)₂ and 1,1,2-triphenylethene groups. NCH₃-YD2 with N(CH₃)₂ groups in the donor part is an effective way to improve the interactions between the dyes and TiO₂ surface, light having efficiency (LHE), and free energy change (ΔG inject ), which is expected to be an efficient dye for use in dye-sensitized solar cells (DSSCs).

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

PubMed Central

Vander Wal, Eric; van Beest, Floris M.; Brook, Ryan K.

2013-01-01

Density dependence can have marked effects on social behaviors such as group size. We tested whether changes in population density of a large herbivore (elk, Cervus canadensis) affected sex-specific group size and whether the response was density- or frequency-dependent. We quantified the probability and strength of changes in group sizes and dispersion as population density changed for each sex. We used group size data from a population of elk in Manitoba, Canada, that was experimentally reduced from 1.20 to 0.67 elk/km2 between 2002 and 2009. Our results indicated that functional responses of group size to population density are sex-specific. Females showed a positive density-dependent response in group size at population densities ≥0.70 elk/km2 and we found evidence for a minimum group size at population density ≤0.70 elk/km2. Changes in male group size were also density-dependent; however, the strength of the relationship was lower than for females. Density dependence in male group size was predominantly a result of fusion of solitary males into larger groups, rather than fusion among existing groups. Our study revealed that density affects group size of a large herbivore differently between males and females, which has important implications for the benefits e.g., alleviating predation risk, and costs of social behaviors e.g., competition for resources and mates, and intra-specific pathogen transmission. PMID:23326502

First-principles supercell calculations of small polarons with proper account for long-range polarization effects

NASA Astrophysics Data System (ADS)

Kokott, Sebastian; Levchenko, Sergey V.; Rinke, Patrick; Scheffler, Matthias

2018-03-01

We present a density functional theory (DFT) based supercell approach for modeling small polarons with proper account for the long-range elastic response of the material. Our analysis of the supercell dependence of the polaron properties (e.g., atomic structure, binding energy, and the polaron level) reveals long-range electrostatic effects and the electron–phonon (el–ph) interaction as the two main contributors. We develop a correction scheme for DFT polaron calculations that significantly reduces the dependence of polaron properties on the DFT exchange-correlation functional and the size of the supercell in the limit of strong el–ph coupling. Using our correction approach, we present accurate all-electron full-potential DFT results for small polarons in rocksalt MgO and rutile TiO2.

Nonadiabatic Dynamics in Single-Electron Tunneling Devices with Time-Dependent Density-Functional Theory

NASA Astrophysics Data System (ADS)

Dittmann, Niklas; Splettstoesser, Janine; Helbig, Nicole

2018-04-01

We simulate the dynamics of a single-electron source, modeled as a quantum dot with on-site Coulomb interaction and tunnel coupling to an adjacent lead in time-dependent density-functional theory. Based on this system, we develop a time-nonlocal exchange-correlation potential by exploiting analogies with quantum-transport theory. The time nonlocality manifests itself in a dynamical potential step. We explicitly link the time evolution of the dynamical step to physical relaxation timescales of the electron dynamics. Finally, we discuss prospects for simulations of larger mesoscopic systems.

Nonadiabatic Dynamics in Single-Electron Tunneling Devices with Time-Dependent Density-Functional Theory.

PubMed

Dittmann, Niklas; Splettstoesser, Janine; Helbig, Nicole

2018-04-13

We simulate the dynamics of a single-electron source, modeled as a quantum dot with on-site Coulomb interaction and tunnel coupling to an adjacent lead in time-dependent density-functional theory. Based on this system, we develop a time-nonlocal exchange-correlation potential by exploiting analogies with quantum-transport theory. The time nonlocality manifests itself in a dynamical potential step. We explicitly link the time evolution of the dynamical step to physical relaxation timescales of the electron dynamics. Finally, we discuss prospects for simulations of larger mesoscopic systems.

Dissipation-induced dipole blockade and antiblockade in driven Rydberg systems

NASA Astrophysics Data System (ADS)

Young, Jeremy T.; Boulier, Thomas; Magnan, Eric; Goldschmidt, Elizabeth A.; Wilson, Ryan M.; Rolston, Steven L.; Porto, James V.; Gorshkov, Alexey V.

2018-02-01

We study theoretically and experimentally the competing blockade and antiblockade effects induced by spontaneously generated contaminant Rydberg atoms in driven Rydberg systems. These contaminant atoms provide a source of strong dipole-dipole interactions and play a crucial role in the system's behavior. We study this problem theoretically using two different approaches. The first is a cumulant expansion approximation, in which we ignore third-order and higher connected correlations. Using this approach for the case of resonant drive, a many-body blockade radius picture arises, and we find qualitative agreement with previous experimental results. We further predict that as the atomic density is increased, the Rydberg population's dependence on Rabi frequency will transition from quadratic to linear dependence at lower Rabi frequencies. We study this behavior experimentally by observing this crossover at two different atomic densities. We confirm that the larger density system has a smaller crossover Rabi frequency than the smaller density system. The second theoretical approach is a set of phenomenological inhomogeneous rate equations. We compare the results of our rate-equation model to the experimental observations [E. A. Goldschmidt et al., Phys. Rev. Lett. 116, 113001 (2016), 10.1103/PhysRevLett.116.113001] and find that these rate equations provide quantitatively good scaling behavior of the steady-state Rydberg population for both resonant and off-resonant drives.

Evolutionary stability of mutualism: interspecific population regulation as an evolutionarily stable strategy.

PubMed

Holland, J Nathaniel; DeAngelis, Donald L; Schultz, Stewart T

2004-09-07

Interspecific mutualisms are often vulnerable to instability because low benefit : cost ratios can rapidly lead to extinction or to the conversion of mutualism to parasite-host or predator-prey interactions. We hypothesize that the evolutionary stability of mutualism can depend on how benefits and costs to one mutualist vary with the population density of its partner, and that stability can be maintained if a mutualist can influence demographic rates and regulate the population density of its partner. We test this hypothesis in a model of mutualism with key features of senita cactus (Pachycereus schottii)-senita moth (Upiga virescens) interactions, in which benefits of pollination and costs of larval seed consumption to plant fitness depend on pollinator density. We show that plants can maximize their fitness by allocating resources to the production of excess flowers at the expense of fruit. Fruit abortion resulting from excess flower production reduces pre-adult survival of the pollinating seed-consumer, and maintains its density beneath a threshold that would destabilize the mutualism. Such a strategy of excess flower production and fruit abortion is convergent and evolutionarily stable against invasion by cheater plants that produce few flowers and abort few to no fruit. This novel mechanism of achieving evolutionarily stable mutualism, namely interspecific population regulation, is qualitatively different from other mechanisms invoking partner choice or selective rewards, and may be a general process that helps to preserve mutualistic interactions in nature.

Effects of dispersal, shrubs, and density-dependent morality on seed and seedling distributions in temperate forests

Treesearch

Janneke Hille Ris Lambers; James S. Clark

2003-01-01

Processes limiting recruitment of trees may have large impacts on forest dynamics. In this paper, we determined the effects of dispersal, shrubs (Rhododendron maximum), and density-dependent mortality on seed and seedling distributions of Southern Appalachian trees. We quantified the spatial distribution of seed rain, seed bank densities, first-year...

Interspecific competition and allelopathic interaction between Karenia mikimotoi and Dunaliella salina in laboratory culture

NASA Astrophysics Data System (ADS)

He, Dong; Liu, Jiao; Hao, Qiang; Ran, Lihua; Zhou, Bin; Tang, Xuexi

2016-03-01

Algal allelopathy is a manifold ecological/physiological phenomenon that is focused on chemical interactions and autotoxicity. We investigated the allelopathic interactions between Karenia mikimotoi and Dunaliella salina in laboratory cultures based on diff erent temperature (15°C, 20°C, and 25°C) and lighting (40, 80, and 160 μmol/(m2·s)) conditions. The growth of D. salina in bi-algae culture (1:1 size/density) was significantly restrained. The results of cell-free filtrate culture indicate that direct cell-tocell contact was not necessary in interspecific competition. Further experimental results demonstrated that allelochemicals released from K. mikimotoi were markedly influenced by both temperature ( P =0.013) and irradiance ( P =0.003), resulting in diff erent growth characteristics of D. salina in filtrate mediums. Compared with the plateau period, K. mikimotoi exudates in the exponential phase had a stronger short-term inhibition effect on D. salina in normal conditions. A clear concentration-dependent relationship was observed in the effect of allelochemicals released from K. mikimotoi with low-promoting and high-repressing effects on D. Salina in a short time-scale. In addition, allelopathic substances remain stable and effective under high temperature and pressure stress. Many flocculent sediments adhering with D. salina cells were observed in all filtrate mediums, while the quantity and color depended on the original culture conditions.

Microscopic analysis of homogeneous electron gas by considering dipole-dipole interaction

NASA Astrophysics Data System (ADS)

Bordbar, G. H.; Pouresmaeeli, F.

2017-12-01

Implying perturbation theory, the impact of the dipole-dipole interaction (DDI) on the thermodynamic properties of a homogeneous electron gas at zero temperature is investigated. Through the second quantization formalism, the analytic expressions for the ground state energy and the DDI energy are obtained. In this paper, the DDI energy has similarities with the previous works done by others. We show that its general behavior depends on density and the total angular momentum. Especially, it is found that the DDI energy has a highly state-dependent behavior. With the growth of density, the magnitude of DDI energy, which is found to be the summation of all energy contributions of the states with even and odd total angular momenta, grows linearly. It is also found that for the states with even and odd total angular momenta, the DDI energy contributions are corresponding to the positive and negative values, respectively. In particular, an increase of total angular momentum leads to decline in the magnitude of energy contribution. Therefore, the dipole-dipole interaction reveals distinct characteristics in comparison with central-like interactions.

Liquid-liquid critical point in a simple analytical model of water.

PubMed

Urbic, Tomaz

2016-10-01

A statistical model for a simple three-dimensional Mercedes-Benz model of water was used to study phase diagrams. This model on a simple level describes the thermal and volumetric properties of waterlike molecules. A molecule is presented as a soft sphere with four directions in which hydrogen bonds can be formed. Two neighboring waters can interact through a van der Waals interaction or an orientation-dependent hydrogen-bonding interaction. For pure water, we explored properties such as molar volume, density, heat capacity, thermal expansion coefficient, and isothermal compressibility and found that the volumetric and thermal properties follow the same trends with temperature as in real water and are in good general agreement with Monte Carlo simulations. The model exhibits also two critical points for liquid-gas transition and transition between low-density and high-density fluid. Coexistence curves and a Widom line for the maximum and minimum in thermal expansion coefficient divides the phase space of the model into three parts: in one part we have gas region, in the second a high-density liquid, and the third region contains low-density liquid.

Liquid-liquid critical point in a simple analytical model of water

NASA Astrophysics Data System (ADS)

Urbic, Tomaz

2016-10-01

A statistical model for a simple three-dimensional Mercedes-Benz model of water was used to study phase diagrams. This model on a simple level describes the thermal and volumetric properties of waterlike molecules. A molecule is presented as a soft sphere with four directions in which hydrogen bonds can be formed. Two neighboring waters can interact through a van der Waals interaction or an orientation-dependent hydrogen-bonding interaction. For pure water, we explored properties such as molar volume, density, heat capacity, thermal expansion coefficient, and isothermal compressibility and found that the volumetric and thermal properties follow the same trends with temperature as in real water and are in good general agreement with Monte Carlo simulations. The model exhibits also two critical points for liquid-gas transition and transition between low-density and high-density fluid. Coexistence curves and a Widom line for the maximum and minimum in thermal expansion coefficient divides the phase space of the model into three parts: in one part we have gas region, in the second a high-density liquid, and the third region contains low-density liquid.

The investigation of the lateral interaction effect's on traffic flow behavior under open boundaries

NASA Astrophysics Data System (ADS)

Bouadi, M.; Jetto, K.; Benyoussef, A.; El Kenz, A.

2017-11-01

In this paper, an open boundaries traffic flow system is studied by taking into account the lateral interaction with spatial defects. For a random defects distribution, if the vehicles velocities are weakly correlated, the traffic phases can be predicted by considering the corresponding inflow and outflow functions. Conversely, if the vehicles velocities are strongly correlated, a phase segregation appears inside the system's bulk which induces the maximum current appearance. Such velocity correlation depends mainly on the defects densities and the probabilities of lateral deceleration. However, for a compact defects distribution, the traffic phases are predictable by using the inflow in the system beginning, the inflow entering the defects zone and the outflow function.

Proximity effects in cold gases of multiply charged atoms (Review)

NASA Astrophysics Data System (ADS)

Chikina, I.; Shikin, V.

2016-07-01

Possible proximity effects in gases of cold, multiply charged atoms are discussed. Here we deal with rarefied gases with densities nd of multiply charged (Z ≫ 1) atoms at low temperatures in the well-known Thomas-Fermi (TF) approximation, which can be used to evaluate the statistical properties of single atoms. In order to retain the advantages of the TF formalism, which is successful for symmetric problems, the external boundary conditions accounting for the finiteness of the density of atoms (donors), nd ≠ 0, are also symmetrized (using a spherical Wigner-Seitz cell) and formulated in a standard way that conserves the total charge within the cell. The model shows that at zero temperature in a rarefied gas of multiply charged atoms there is an effective long-range interaction Eproxi(nd), the sign of which depends on the properties of the outer shells of individual atoms. The long-range character of the interaction Eproxi is evaluated by comparing it with the properties of the well-known London dispersive attraction ELond(nd) < 0, which is regarded as a long-range interaction in gases. For the noble gases argon, krypton, and xenon Eproxi>0 and for the alkali and alkaline-earth elements Eproxi < 0. At finite temperatures, TF statistics manifests a new, anomalously large proximity effect, which reflects the tendency of electrons localized at Coulomb centers to escape into the continuum spectrum. The properties of thermal decay are interesting in themselves as they determine the important phenomenon of dissociation of neutral complexes into charged fragments. This phenomenon appears consistently in the TF theory through the temperature dependence of the different versions of Eproxi. The anomaly in the thermal proximity effect shows up in the following way: for T ≠ 0 there is no equilibrium solution of TS statistics for single multiply charged atoms in a vacuum when the effect is present. Instability is suppressed in a Wigner-Seitz model under the assumption that there are no electron fluxes through the outer boundary R3 ∝ n-1d of a Wigner-Seitz cell. Eproxi corresponds to the definition of the correlation energy in a gas of interacting particles. This review is written so as to enable comparison of the results of the TF formalism with the standard assumptions of the correlation theory for classical plasmas. The classic example from work on weak solutions (including charged solutions)—the use of semi-impermeable membranes for studies of osmotic pressure—is highly appropriate for problems involving Eproxi. Here we are speaking of one or more sharp boundaries formed by the ionic component of a many-particle problem. These may be a metal-vacuum boundary in a standard Casimir cell in a study of the vacuum properties in the 2l gap between conducting media of different kinds or different layered systems (quantum wells) in semiconductors, etc. As the mobile part of the equilibrium near a sharp boundary, electrons can (should) escape beyond the confines of the ion core into a gap 2l with a probability that depends, among other factors, on the properties of Eproxi for the electron cloud inside the conducting walls of the Casimir cell (quantum well). The analog of the Casimir sandwich in semiconductors is the widely used multilayer heterostructures referred to as quantum wells of width 2l with sides made of suitable doped materials, which ensure statistical equilibrium exchange of electrons between the layers of the multilayer structure. The thermal component of the proximity effects in semiconducting quantum wells provides an idea of many features of the dissociation process in doped semiconductors. In particular, a positive Eproxi > 0 (relative to the bottom of the conduction band) indicates that TF donors with a finite density nd ≠ 0 form a degenerate, semiconducting state in the semiconductor. At zero temperature, there is a finite density of free carriers which increases with a power-law dependence on T.

Does Mutual Interference Affect the Feeding Rate of Aphidophagous Coccinellids? A Modeling Perspective.

PubMed

Papanikolaou, Nikos E; Demiris, Nikos; Milonas, Panagiotis G; Preston, Simon; Kypraios, Theodore

2016-01-01

Mutual interference involves direct interactions between individuals of the same species that may alter their foraging success. Larvae of aphidophagous coccinellids typically stay within a patch during their lifetime, displaying remarkable aggregation to their prey. Thus, as larvae are exposed to each other, frequent encounters may affect their foraging success. A study was initiated in order to determine the effect of mutual interference in the coccinellids' feeding rate. One to four 4th larval instars of the fourteen-spotted ladybird beetle Propylea quatuordecimpunctata were exposed for 6 hours into plastic containers with different densities of the black bean aphid, Aphis fabae, on potted Vicia faba plants. The data were used to fit a purely prey-dependent Holling type II model and its alternatives which account for interference competition and have thus far been underutilized, i.e. the Beddington-DeAngelis, the Crowley-Martin and a modified Hassell-Varley model. The Crowley-Martin mechanistic model appeared to be slightly better among the competing models. The results showed that although the feeding rate became approximately independent of predator density at high prey density, some predator dependence in the coccinellid's functional response was observed at the low prey-high predator density combination. It appears that at low prey densities, digestion breaks are negligible so that the predators do waste time interfering with each other, whereas at high prey densities time loss during digestion breaks may fully accommodate the cost of interference, so that the time cost may be negligible.

Numerical simulation of freshwater/seawater interaction in a dual-permeability karst system with conduits: the development of discrete-continuum VDFST-CFP model

NASA Astrophysics Data System (ADS)

Xu, Zexuan; Hu, Bill

2016-04-01

Dual-permeability karst aquifers of porous media and conduit networks with significant different hydrological characteristics are widely distributed in the world. Discrete-continuum numerical models, such as MODFLOW-CFP and CFPv2, have been verified as appropriate approaches to simulate groundwater flow and solute transport in numerical modeling of karst hydrogeology. On the other hand, seawater intrusion associated with fresh groundwater resources contamination has been observed and investigated in numbers of coastal aquifers, especially under conditions of sea level rise. Density-dependent numerical models including SEAWAT are able to quantitatively evaluate the seawater/freshwater interaction processes. A numerical model of variable-density flow and solute transport - conduit flow process (VDFST-CFP) is developed to provide a better description of seawater intrusion and submarine groundwater discharge in a coastal karst aquifer with conduits. The coupling discrete-continuum VDFST-CFP model applies Darcy-Weisbach equation to simulate non-laminar groundwater flow in the conduit system in which is conceptualized and discretized as pipes, while Darcy equation is still used in continuum porous media. Density-dependent groundwater flow and solute transport equations with appropriate density terms in both conduit and porous media systems are derived and numerically solved using standard finite difference method with an implicit iteration procedure. Synthetic horizontal and vertical benchmarks are created to validate the newly developed VDFST-CFP model by comparing with other numerical models such as variable density SEAWAT, couplings of constant density groundwater flow and solute transport MODFLOW/MT3DMS and discrete-continuum CFPv2/UMT3D models. VDFST-CFP model improves the simulation of density dependent seawater/freshwater mixing processes and exchanges between conduit and matrix. Continuum numerical models greatly overestimated the flow rate under turbulent flow condition but discrete-continuum models provide more accurate results. Parameters sensitivities analysis indicates that conduit diameter and friction factor, matrix hydraulic conductivity and porosity are important parameters that significantly affect variable-density flow and solute transport simulation. The pros and cons of model assumptions, conceptual simplifications and numerical techniques in VDFST-CFP are discussed. In general, the development of VDFST-CFP model is an innovation in numerical modeling methodology and could be applied to quantitatively evaluate the seawater/freshwater interaction in coastal karst aquifers. Keywords: Discrete-continuum numerical model; Variable density flow and transport; Coastal karst aquifer; Non-laminar flow

Genetic variation in foundation species governs the dynamics of trophic interactions

PubMed Central

Valencia-Cuevas, Leticia; Mussali-Galante, Patricia; Cano-Santana, Zenón; Pujade-Villar, Juli; Equihua-Martínez, Armando

2018-01-01

Abstract Various studies have demonstrated that the foundation species genetic diversity can have direct effects that extend beyond the individual or population level, affecting the dependent communities. Additionally, these effects may be indirectly extended to higher trophic levels throughout the entire community. Quercus castanea is an oak species with characteristics of foundation species beyond presenting a wide geographical distribution and being a dominant element of Mexican temperate forests. In this study, we analyzed the influence of population (He) and individual (HL) genetic diversity of Q. castanea on its canopy endophagous insect community and associated parasitoids. Specifically, we studied the composition, richness (S) and density of leaf-mining moths (Lepidoptera: Tischeridae, Citheraniidae), gall-forming wasps (Hymenoptera: Cynipidae), and canopy parasitoids of Q. castanea. We sampled 120 trees belonging to six populations (20/site) through the previously recognized gradient of genetic diversity. In total, 22 endophagous insect species belonging to three orders (Hymenoptera, Lepidoptera, and Diptera) and 20 parasitoid species belonging to 13 families were identified. In general, we observed that the individual genetic diversity of the host plant (HL) has a significant positive effect on the S and density of the canopy endophagous insect communities. In contrast, He has a significant negative effect on the S of endophagous insects. Additionally, indirect effects of HL were observed, affecting the S and density of parasitoid insects. Our results suggest that genetic variation in foundation species can be one of the most important factors governing the dynamics of tritrophic interactions that involve oaks, herbivores, and parasitoids. PMID:29492034

Alcohol prevention on college campuses: the moderating effect of the alcohol environment on the effectiveness of social norms marketing campaigns.

PubMed

Scribner, Richard A; Theall, Katherine P; Mason, Karen; Simonsen, Neal; Schneider, Shari Kessel; Towvim, Laura Gomberg; DeJong, William

2011-03-01

Evaluations of social norms marketing campaigns to reduce college student drinking have produced conflicting results. This study examines whether the effectiveness of such campaigns may be moderated by on-premise alcohol outlet density in the surrounding community. Multilevel analyses were conducted of student survey responses (N= 19,838) from 32 U.S. colleges that took part in one of two 4-year randomized, controlled trials completed for the Social Norms Marketing Research Project (SNMRP). In the models, students by year were nested within treatment (n = 16) and control group (n = 16) campuses, which were characterized by the on-premise outlet density in their surrounding community. The moderating effect of outlet density was introduced into the models as an interaction between the treatment effect (i.e., the effect of the social norms marketing campaigns over time) and outlet density. The models were also stratified by campus alcohol outlet density (high vs. low) to examine the effect of the intervention in each type of setting. There was a significant interaction between the treatment effect and on-premise alcohol outlet density for one of the drinking outcomes targeted by the SNMRP intervention, the number of drinks when partying, and marginal evidence of interaction effects for two other outcomes, maximum recent consumption and a composite drinking scale. In stratified analyses, an intervention effect was observed for three of the four outcomes among students from campuses with lower on-premise alcohol outlet density, whereas no intervention effect was observed among students from campuses with higher on-premise alcohol outlet density. The findings suggest that the campus alcohol environment moderates the effect of social norms marketing interventions. Social norms marketing intervention may be less effective on campuses with higher densities of on-sale alcohol outlets.

Theory of molecular crowding in Brownian hard-sphere liquids.

PubMed

Zaccone, Alessio; Terentjev, Eugene M

2012-06-01

We derive an analytical pair potential of mean force for Brownian molecules in the liquid state. Our approach accounts for many-particle correlations of crowding particles of the liquid and for diffusive transport across the spatially modulated local density of crowders in the dense environment. Focusing on the limit of equal-size particles, we show that this diffusive transport leads to additional density- and structure-dependent terms in the interaction potential and to a much stronger attraction (by a factor of ≈4 at average volume fraction of crowders φ{0}=0.25) than in the standard depletion interaction where the diffusive effects are neglected. As an illustration of the theory, we use it to study the size of a polymer chain in a solution of inert crowders. Even in the case of an athermal background solvent, when a classical chain should be fully swollen, we find a sharp coil-globule transition of the ideal chain collapsing at a critical value of the crowder volume fraction φ{c}≈0.145.

Classical density-functional theory of inhomogeneous water including explicit molecular structure and nonlinear dielectric response.

PubMed

Lischner, Johannes; Arias, T A

2010-02-11

We present an accurate free-energy functional for liquid water written in terms of a set of effective potential fields in which fictitious noninteracting water molecules move. The functional contains an exact expression of the entropy of noninteracting molecules and thus provides an ideal starting point for the inclusion of complex intermolecular interactions which depend on the orientation of the interacting molecules. We show how an excess free-energy functional can be constructed to reproduce the following properties of water: the dielectric response; the experimental site-site correlation functions; the surface tension; the bulk modulus of the liquid and the variation of this modulus with pressure; the density of the liquid and the vapor phase; and liquid-vapor coexistence. As a demonstration, we present results for the application of this theory to the behavior of liquid water in a parallel plate capacitor. In particular, we make predictions for the dielectric response of water in the nonlinear regime, finding excellent agreement with known data.

Thermal Conductivity and Thermopower near the 2D Metal-Insulator transition, Final Technical Report

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

Sarachik, Myriam P.

2015-02-20

STUDIES OF STRONGLY-INTERACTING 2D ELECTRON SYSTEMS – There is a great deal of current interest in the properties of systems in which the interaction between electrons (their potential energy) is large compared to their kinetic energy. We have investigated an apparent, unexpected metal-insulator transition inferred from the behavior of the temperature-dependence of the resistivity; moreover, detailed analysis of the behavior of the magnetoresistance suggests that the electrons’ effective mass diverges, supporting this scenario. Whether this is a true phase transition or crossover behavior has been strenuously debated over the past 20 years. Our measurements have now shown that the thermoelectricmore » power of these 2D materials diverges at a finite density, providing clear evidence that this is, in fact, a phase transition to a new low-density phase which may be a precursor or a direct transition to the long sought-after electronic crystal predicted by Eugene Wigner in 1934.« less

Quench dynamics of the spin-imbalanced Fermi-Hubbard model in one dimension

NASA Astrophysics Data System (ADS)

Yin, Xiao; Radzihovsky, Leo

2016-12-01

We study a nonequilibrium dynamics of a one-dimensional spin-imbalanced Fermi-Hubbard model following a quantum quench of on-site interaction, realizable, for example, in Feshbach-resonant atomic Fermi gases. We focus on the post-quench evolution starting from the initial BCS and Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) ground states and analyze the corresponding spin-singlet, spin-triplet, density-density, and magnetization-magnetization correlation functions. We find that beyond a light-cone crossover time, rich post-quench dynamics leads to thermalized and pre-thermalized stationary states that display strong dependence on the initial ground state. For initially gapped BCS state, the long-time stationary state resembles thermalization with the effective temperature set by the initial value of the Hubbard interaction. In contrast, while the initial gapless FFLO state reaches a stationary pre-thermalized form, it remains far from equilibrium. We suggest that such post-quench dynamics can be used as a fingerprint for identification and study of the FFLO phase.

Fundamental population-productivity relationships can be modified through density-dependent feedbacks of life-history evolution.

PubMed

Kuparinen, Anna; Stenseth, Nils Christian; Hutchings, Jeffrey A

2014-12-01

The evolution of life histories over contemporary time scales will almost certainly affect population demography. One important pathway for such eco-evolutionary interactions is the density-dependent regulation of population dynamics. Here, we investigate how fisheries-induced evolution (FIE) might alter density-dependent population-productivity relationships. To this end, we simulate the eco-evolutionary dynamics of an Atlantic cod (Gadus morhua) population under fishing, followed by a period of recovery in the absence of fishing. FIE is associated with increases in juvenile production, the ratio of juveniles to mature population biomass, and the ratio of the mature population biomass relative to the total population biomass. In contrast, net reproductive rate (R 0 ) and per capita population growth rate (r) decline concomitantly with evolution. Our findings suggest that FIE can substantially modify the fundamental population-productivity relationships that underlie density-dependent population regulation and that form the primary population-dynamical basis for fisheries stock-assessment projections. From a conservation and fisheries-rebuilding perspective, we find that FIE reduces R 0 and r, the two fundamental correlates of population recovery ability and inversely extinction probability.

Huntingtin interacting protein 1 can regulate neurogenesis in Drosophila.

PubMed

Moores, Justin N; Roy, Sophie; Nicholson, Donald W; Staveley, Brian E

2008-08-01

Huntington's disease (HD) is associated with a range of cellular consequences including selective neuronal death and decreased levels of neurogenesis. Ultimately, these altered processes are dependent upon proteins that interact with Huntingtin (Htt) such as the Huntingtin-interacting protein 1 (Hip1) which has a reduced binding preference to expanded Htt. These effects are similar to those observed with modified Notch signal transduction. As Hip1 plays a key role in endocytosis and intracellular transport, and activation of the Notch signal requires both, we investigated putative links between Hip1 and Notch signaling in flies. We have identified two forms of Hip1 that may be produced through the use of alternative first exons: a version of Hip1 with a lipid-binding ANTH domain and Hip1DeltaANTH lacking this domain. The directed expression of Hip1 decreases, while expression of Hip1DeltaANTH increases, the density of sensory microchaetae on the dorsal notum, a classical model of neurogenesis. A reduction in microchaetae density associated with Notch(Microchaetae Deficient (MCD)) (N(MCD) ) alleles is sensitive to both Hip1 and Hip1DeltaANTH levels, as are the bristle phenotypes generated by misexpression of deltex, a key mediator of Notch signaling. Genetic studies further demonstrate that the observed effects of Hip1 and of Hip1DeltaANTH are sensitive to achaete gene dosage while insensitive to the levels of E(Spl), suggesting a non-canonical Notch neurogenic signal through a deltex-dependent pathway. The novel role we describe for Hip1 in Notch-mediated neurogenesis provides a functional link between Notch signaling and proteins related to HD.

Angle-adjustable density field formulation for the modeling of crystalline microstructure

NASA Astrophysics Data System (ADS)

Wang, Zi-Le; Liu, Zhirong; Huang, Zhi-Feng

2018-05-01

A continuum density field formulation with particle-scale resolution is constructed to simultaneously incorporate the orientation dependence of interparticle interactions and the rotational invariance of the system, a fundamental but challenging issue in modeling the structure and dynamics of a broad range of material systems across variable scales. This generalized phase field crystal-type approach is based upon the complete expansion of particle direct correlation functions and the concept of isotropic tensors. Through applications to the modeling of various two- and three-dimensional crystalline structures, our study demonstrates the capability of bond-angle control in this continuum field theory and its effects on the emergence of ordered phases, and provides a systematic way of performing tunable angle analyses for crystalline microstructures.

Modeling turbulent/chemistry interactions using assumed pdf methods

NASA Technical Reports Server (NTRS)

Gaffney, R. L, Jr.; White, J. A.; Girimaji, S. S.; Drummond, J. P.

1992-01-01

Two assumed probability density functions (pdfs) are employed for computing the effect of temperature fluctuations on chemical reaction. The pdfs assumed for this purpose are the Gaussian and the beta densities of the first kind. The pdfs are first used in a parametric study to determine the influence of temperature fluctuations on the mean reaction-rate coefficients. Results indicate that temperature fluctuations significantly affect the magnitude of the mean reaction-rate coefficients of some reactions depending on the mean temperature and the intensity of the fluctuations. The pdfs are then tested on a high-speed turbulent reacting mixing layer. Results clearly show a decrease in the ignition delay time due to increases in the magnitude of most of the mean reaction rate coefficients.

Exploring the effect of oxygen coverage on the electronic, magnetic and chemical properties of Ni(111) supported h-BN sheet: A density functional study

NASA Astrophysics Data System (ADS)

Wasey, A. H. M. Abdul; Das, G. P.; Majumder, C.

2017-05-01

Traditionally, h-BN is used as coating material to prevent corrosion on the metal surface. In sharp contrast to this, here we show catalytic behavior of h-BN monolayer deposited on Ni(111) surface, clearly demonstrating the influence of the support in modulation of h-BN electronic structure. Using first principles density functional theory we have studied the interaction of O2 molecules with the h-BN/Ni(111) surface. The activation of Osbnd O bond, which is the most important step for oxidative catalysis, showed dependence on the O2 coverage. Thus this study is extremely important to predict the optimum O2 pressure in reaction chamber for efficient catalysis.

Characterization of hot dense plasma with plasma parameters

NASA Astrophysics Data System (ADS)

Singh, Narendra; Goyal, Arun; Chaurasia, S.

2018-05-01

Characterization of hot dense plasma (HDP) with its parameters temperature, electron density, skin depth, plasma frequency is demonstrated in this work. The dependence of HDP parameters on temperature and electron density is discussed. The ratio of the intensities of spectral lines within HDP is calculated as a function of electron temperature. The condition of weakly coupled for HDP is verified by calculating coupling constant. Additionally, atomic data such as transition wavelength, excitation energies, line strength, etc. are obtained for Be-like ions on the basis of MCDHF method. In atomic data calculations configuration interaction and relativistic effects QED and Breit corrections are newly included for HDP characterization and this is first result of HDP parameters from extreme ultraviolet (EUV) radiations.

Anisotropy and temperature dependence of structural, thermodynamic, and elastic properties of crystalline cellulose Iβ: a first-principles investigation

Treesearch

ShunLi Shang; Louis G. Hector Jr.; Paul Saxe; Zi-Kui Liu; Robert J. Moon; Pablo D. Zavattieri

2014-01-01

Anisotropy and temperature dependence of structural, thermodynamic and elastic properties of crystalline cellulose Iβ were computed with first-principles density functional theory (DFT) and a semi-empirical correction for van der Waals interactions. Specifically, we report the computed temperature variation (up to 500...

Intertwined order in a frustrated four-leg t - J cylinder

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

Dodaro, John F.; Jiang, Hong -Chen; Kivelson, Steven A.

Here, we report a density-matrix renormalization group study of the t–J model with nearest (t 1 and J 1) and next-nearest (t 2 and J 2) interactions on a four-leg cylinder with concentration δ=1/8 of doped holes. We observe an astonishingly complex interplay between uniform d-wave superconductivity (SC) and strong spin and charge-density wave ordering tendencies (SDW and CDW). Depending on parameters, the CDWs can be commensurate with period 4 or 8. By comparing the charge ordering vectors with 2k F, we rule out Fermi surface nesting-induced density wave order in our model. Magnetic frustration (i.e., J 2/J 1~1/2) significantlymore » quenches SDW correlations with little effect on the CDW. Typically, the SC order is strongly modulated at the CDW ordering vector and exhibits d-wave symmetry around the cylinder. There is no evidence of a near-degenerate tendency to pair-density wave (PDW) ordering, charge 4e SC, or orbital current order.« less