Thermal Density Functional Theory: Time-Dependent Linear Response and Approximate Functionals from the Fluctuation-Dissipation Theorem

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

Pribram-Jones, Aurora; Grabowski, Paul E.; Burke, Kieron

We present that the van Leeuwen proof of linear-response time-dependent density functional theory (TDDFT) is generalized to thermal ensembles. This allows generalization to finite temperatures of the Gross-Kohn relation, the exchange-correlation kernel of TDDFT, and fluctuation dissipation theorem for DFT. Finally, this produces a natural method for generating new thermal exchange-correlation approximations.

Thermal Density Functional Theory: Time-Dependent Linear Response and Approximate Functionals from the Fluctuation-Dissipation Theorem

DOE PAGES

Pribram-Jones, Aurora; Grabowski, Paul E.; Burke, Kieron

2016-06-08

We present that the van Leeuwen proof of linear-response time-dependent density functional theory (TDDFT) is generalized to thermal ensembles. This allows generalization to finite temperatures of the Gross-Kohn relation, the exchange-correlation kernel of TDDFT, and fluctuation dissipation theorem for DFT. Finally, this produces a natural method for generating new thermal exchange-correlation approximations.

The Havriliak-Negami relaxation and its relatives: the response, relaxation and probability density functions

NASA Astrophysics Data System (ADS)

Górska, K.; Horzela, A.; Bratek, Ł.; Dattoli, G.; Penson, K. A.

2018-04-01

We study functions related to the experimentally observed Havriliak-Negami dielectric relaxation pattern proportional in the frequency domain to [1+(iωτ0){\\hspace{0pt}}α]-β with τ0 > 0 being some characteristic time. For α = l/k< 1 (l and k being positive and relatively prime integers) and β > 0 we furnish exact and explicit expressions for response and relaxation functions in the time domain and suitable probability densities in their domain dual in the sense of the inverse Laplace transform. All these functions are expressed as finite sums of generalized hypergeometric functions, convenient to handle analytically and numerically. Introducing a reparameterization β = (2-q)/(q-1) and τ0 = (q-1){\\hspace{0pt}}1/α (1 < q < 2) we show that for 0 < α < 1 the response functions fα, β(t/τ0) go to the one-sided Lévy stable distributions when q tends to one. Moreover, applying the self-similarity property of the probability densities gα, β(u) , we introduce two-variable densities and show that they satisfy the integral form of the evolution equation.

Functional response of ungulate browsers in disturbed eastern hemlock forests

USGS Publications Warehouse

DeStefano, Stephen

2015-01-01

Ungulate browsing in predator depleted North American landscapes is believed to be causing widespread tree recruitment failures. However, canopy disturbances and variations in ungulate densities are sources of heterogeneity that can buffer ecosystems against herbivory. Relatively little is known about the functional response (the rate of consumption in relation to food availability) of ungulates in eastern temperate forests, and therefore how “top down” control of vegetation may vary with disturbance type, intensity, and timing. This knowledge gap is relevant in the Northeastern United States today with the recent arrival of hemlock woolly adelgid (HWA; Adelges tsugae) that is killing eastern hemlocks (Tsuga canadensis) and initiating salvage logging as a management response. We used an existing experiment in central New England begun in 2005, which simulated severe adelgid infestation and intensive logging of intact hemlock forest, to examine the functional response of combined moose (Alces americanus) and white-tailed deer (Odocoileus virginianus) foraging in two different time periods after disturbance (3 and 7 years). We predicted that browsing impacts would be linear or accelerating (Type I or Type III response) in year 3 when regenerating stem densities were relatively low and decelerating (Type II response) in year 7 when stem densities increased. We sampled and compared woody regeneration and browsing among logged and simulated insect attack treatments and two intact controls (hemlock and hardwood forest) in 2008 and again in 2012. We then used AIC model selection to compare the three major functional response models (Types I, II, and III) of ungulate browsing in relation to forage density. We also examined relative use of the different stand types by comparing pellet group density and remote camera images. In 2008, total and proportional browse consumption increased with stem density, and peaked in logged plots, revealing a Type I response. In 2012, stem densities were greatest in girdled plots, but proportional browse consumption was highest at intermediate stem densities in logged plots, exhibiting a Type III (rather than a Type II) functional response. Our results revealed shifting top–down control by herbivores at different stages of stand recovery after disturbance and in different understory conditions resulting from logging vs. simulated adelgid attack. If forest managers wish to promote tree regeneration in hemlock stands that is more resistant to ungulate browsers, leaving HWA-infested stands unmanaged may be a better option than preemptively logging them.

Thermo-mechanical characterization of silicone foams

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

Rangaswamy, Partha; Smith, Nickolaus A.; Cady, Carl M.

Cellular solids such as elastomeric foams are used in many structural applications to absorb and dissipate energy, due to their light weight (low density) and high energy absorption capability. In this paper we will discuss foams derived from S5370, a silicone foam formulation developed by Dow Corning. In the application presented, the foam is consolidated into a cushion component of constant thickness but variable density. A mechanical material model developed by Lewis (2013), predicts material response, in part, as a function of relative density. To determine the required parameters for this model we have obtained the mechanical response in compressionmore » for ambient, cold and hot temperatures. The variable density cushion provided samples sufficient samples so that the effect of sample initial density on the mechanical response could be studied. The mechanical response data showed extreme sensitivity to relative density. We also observed at strains corresponding to 1 MPa a linear relationship between strain and initial density for all temperatures. Samples taken from parts with a history of thermal cycling demonstrated a stiffening response that was a function of temperature, with the trend of more stiffness as temperature increased above ambient. This observation is in agreement with the entropic effects on the thermo-mechanical behavior of silicone polymers. In this study, we present the experimental methods necessary for the development of a material model, the testing protocol, analysis of test data, and a discussion of load (stress) and gap (strain) as a function of sample initial densities and temperatures« less

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.

Characterization of nonGaussian atmospheric turbulence for prediction of aircraft response statistics

NASA Technical Reports Server (NTRS)

Mark, W. D.

1977-01-01

Mathematical expressions were derived for the exceedance rates and probability density functions of aircraft response variables using a turbulence model that consists of a low frequency component plus a variance modulated Gaussian turbulence component. The functional form of experimentally observed concave exceedance curves was predicted theoretically, the strength of the concave contribution being governed by the coefficient of variation of the time fluctuating variance of the turbulence. Differences in the functional forms of response exceedance curves and probability densities also were shown to depend primarily on this same coefficient of variation. Criteria were established for the validity of the local stationary assumption that is required in the derivations of the exceedance curves and probability density functions. These criteria are shown to depend on the relative time scale of the fluctuations in the variance, the fluctuations in the turbulence itself, and on the nominal duration of the relevant aircraft impulse response function. Metrics that can be generated from turbulence recordings for testing the validity of the local stationary assumption were developed.

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...

The energy dependence of the lateral dose response functions of detectors with various densities in photon-beam dosimetry.

PubMed

Looe, Hui Khee; Harder, Dietrich; Poppe, Björn

2017-02-07

The lateral dose response function is a general characteristic of the volume effect of a detector used for photon dosimetry in a water phantom. It serves as the convolution kernel transforming the true absorbed dose to water profile, which would be produced within the undisturbed water phantom, into the detector-measured signal profile. The shape of the lateral dose response function characterizes (i) the volume averaging attributable to the detector's size and (ii) the disturbance of the secondary electron field associated with the deviation of the electron density of the detector material from the surrounding water. In previous work, the characteristic dependence of the shape of the lateral dose response function upon the electron density of the detector material was studied for 6 MV photons by Monte Carlo simulation of a wall-less voxel-sized detector (Looe et al 2015 Phys. Med. Biol. 60 6585-07). This study is here continued for 60 Co gamma rays and 15 MV photons in comparison with 6 MV photons. It is found (1) that throughout these photon spectra the shapes of the lateral dose response functions are retaining their characteristic dependence on the detector's electron density, and (2) that their energy-dependent changes are only moderate. This appears as a practical advantage because the lateral dose response function can then be treated as practically invariant across a clinical photon beam in spite of the known changes of the photon spectrum with increasing distance from the beam axis.

A Patch Density Recommendation based on Convergence Studies for Vehicle Panel Vibration Response resulting from Excitation by a Diffuse Acoustic Field

NASA Technical Reports Server (NTRS)

Smith, Andrew; LaVerde, Bruce; Jones, Douglas; Towner, Robert; Waldon, James; Hunt, Ron

2013-01-01

Producing fluid structural interaction estimates of panel vibration from an applied pressure field excitation are quite dependent on the spatial correlation of the pressure field. There is a danger of either over estimating a low frequency response or under predicting broad band panel response in the more modally dense bands if the pressure field spatial correlation is not accounted for adequately. It is a useful practice to simulate the spatial correlation of the applied pressure field over a 2d surface using a matrix of small patch area regions on a finite element model (FEM). Use of a fitted function for the spatial correlation between patch centers can result in an error if the choice of patch density is not fine enough to represent the more continuous spatial correlation function throughout the intended frequency range of interest. Several patch density assumptions to approximate the fitted spatial correlation function are first evaluated using both qualitative and quantitative illustrations. The actual response of a typical vehicle panel system FEM is then examined in a convergence study where the patch density assumptions are varied over the same model. The convergence study results illustrate the impacts possible from a poor choice of patch density on the analytical response estimate. The fitted correlation function used in this study represents a diffuse acoustic field (DAF) excitation of the panel to produce vibration response.

Density-functional expansion methods: Grand challenges.

PubMed

Giese, Timothy J; York, Darrin M

2012-03-01

We discuss the source of errors in semiempirical density functional expansion (VE) methods. In particular, we show that VE methods are capable of well-reproducing their standard Kohn-Sham density functional method counterparts, but suffer from large errors upon using one or more of these approximations: the limited size of the atomic orbital basis, the Slater monopole auxiliary basis description of the response density, and the one- and two-body treatment of the core-Hamiltonian matrix elements. In the process of discussing these approximations and highlighting their symptoms, we introduce a new model that supplements the second-order density-functional tight-binding model with a self-consistent charge-dependent chemical potential equalization correction; we review our recently reported method for generalizing the auxiliary basis description of the atomic orbital response density; and we decompose the first-order potential into a summation of additive atomic components and many-body corrections, and from this examination, we provide new insights and preliminary results that motivate and inspire new approximate treatments of the core-Hamiltonian.

The role of relativity in the optical response of gold within the time-dependent current-density-functional theory.

PubMed

Romaniello, P; de Boeij, P L

2005-04-22

We included relativistic effects in the formulation of the time-dependent current-density-functional theory for the calculation of linear response properties of metals [P. Romaniello and P. L. de Boeij, Phys. Rev. B (to be published)]. We treat the dominant scalar-relativistic effects using the zeroth-order regular approximation in the ground-state density-functional theory calculations, as well as in the time-dependent response calculations. The results for the dielectric function of gold calculated in the spectral range of 0-10 eV are compared with experimental data reported in literature and recent ellipsometric measurements. As well known, relativistic effects strongly influence the color of gold. We find that the onset of interband transitions is shifted from around 3.5 eV, obtained in a nonrelativistic calculation, to around 1.9 eV when relativity is included. With the inclusion of the scalar-relativistic effects there is an overall improvement of both real and imaginary parts of the dielectric function over the nonrelativistic ones. Nevertheless some important features in the absorption spectrum are not well reproduced, but can be explained in terms of spin-orbit coupling effects. The remaining deviations are attributed to the underestimation of the interband gap (5d-6sp band gap) in the local-density approximation and to the use of the adiabatic local-density approximation in the response calculation.

A predator-prey model with a holling type I functional response including a predator mutual interference

USGS Publications Warehouse

Seo, G.; DeAngelis, D.L.

2011-01-01

The most widely used functional response in describing predator-prey relationships is the Holling type II functional response, where per capita predation is a smooth, increasing, and saturating function of prey density. Beddington and DeAngelis modified the Holling type II response to include interference of predators that increases with predator density. Here we introduce a predator-interference term into a Holling type I functional response. We explain the ecological rationale for the response and note that the phase plane configuration of the predator and prey isoclines differs greatly from that of the Beddington-DeAngelis response; for example, in having three possible interior equilibria rather than one. In fact, this new functional response seems to be quite unique. We used analytical and numerical methods to show that the resulting system shows a much richer dynamical behavior than the Beddington-DeAngelis response, or other typically used functional responses. For example, cyclic-fold, saddle-fold, homoclinic saddle connection, and multiple crossing bifurcations can all occur. We then use a smooth approximation to the Holling type I functional response with predator mutual interference to show that these dynamical properties do not result from the lack of smoothness, but rather from subtle differences in the functional responses. ?? 2011 Springer Science+Business Media, LLC.

Time dependent density functional calculation of plasmon response in clusters

NASA Astrophysics Data System (ADS)

Wang, Feng; Zhang, Feng-Shou; Eric, Suraud

2003-02-01

We have introduced a theoretical scheme for the efficient description of the optical response of a cluster based on the time-dependent density functional theory. The practical implementation is done by means of the fully fledged time-dependent local density approximation scheme, which is solved directly in the time domain without any linearization. As an example we consider the simple Na2 cluster and compute its surface plasmon photoabsorption cross section, which is in good agreement with the experiments.

Air density dependence of the response of the PTW SourceCheck 4pi ionization chamber for 125I brachytherapy seeds.

PubMed

Torres Del Río, J; Tornero-López, A M; Guirado, D; Pérez-Calatayud, J; Lallena, A M

2017-06-01

To analyze the air density dependence of the response of the new SourceCheck 4pi ionization chamber, manufactured by PTW. The air density dependence of three different SourceCheck 4pi chambers was studied by measuring 125 I sources. Measurements were taken by varying the pressure from 746.6 to 986.6hPa in a pressure chamber. Three different HDR 1000 Plus ionization chambers were also analyzed under similar conditions. A linear and a potential-like function of the air density were fitted to experimental data and their achievement in describing them was analyzed. SourceCheck 4pi chamber response showed a residual dependence on the air density once the standard pressure and temperature factor was applied. The chamber response was overestimated when the air density was below that under normal atmospheric conditions. A similar dependence was found for the HDR 1000 Plus chambers analyzed. A linear function of the air density permitted a very good description of this residual dependence, better than with a potential function. No significant variability between the different specimens of the same chamber model studied was found. The effect of overestimation observed in the chamber responses once they are corrected for the standard pressure and temperature may represent a non-negligible ∼4% overestimation in high altitude cities as ours (700m AMSL). This overestimation behaves linearly with the air density in all cases analyzed. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

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

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

Tabacchi, G; Hutter, J; Mundy, C

2005-04-07

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

On the subsystem formulation of linear-response time-dependent DFT.

PubMed

Pavanello, Michele

2013-05-28

A new and thorough derivation of linear-response subsystem time-dependent density functional theory (TD-DFT) is presented and analyzed in detail. Two equivalent derivations are presented and naturally yield self-consistent subsystem TD-DFT equations. One reduces to the subsystem TD-DFT formalism of Neugebauer [J. Chem. Phys. 126, 134116 (2007)]. The other yields Dyson type equations involving three types of subsystem response functions: coupled, uncoupled, and Kohn-Sham. The Dyson type equations for subsystem TD-DFT are derived here for the first time. The response function formalism reveals previously hidden qualities and complications of subsystem TD-DFT compared with the regular TD-DFT of the supersystem. For example, analysis of the pole structure of the subsystem response functions shows that each function contains information about the electronic spectrum of the entire supersystem. In addition, comparison of the subsystem and supersystem response functions shows that, while the correlated response is subsystem additive, the Kohn-Sham response is not. Comparison with the non-subjective partition DFT theory shows that this non-additivity is largely an artifact introduced by the subjective nature of the density partitioning in subsystem DFT.

Nonlocal and Nonadiabatic Effects in the Charge-Density Response of Solids: A Time-Dependent Density-Functional Approach

NASA Astrophysics Data System (ADS)

Panholzer, Martin; Gatti, Matteo; Reining, Lucia

2018-04-01

The charge-density response of extended materials is usually dominated by the collective oscillation of electrons, the plasmons. Beyond this feature, however, intriguing many-body effects are observed. They cannot be described by one of the most widely used approaches for the calculation of dielectric functions, which is time-dependent density functional theory (TDDFT) in the adiabatic local density approximation (ALDA). Here, we propose an approximation to the TDDFT exchange-correlation kernel which is nonadiabatic and nonlocal. It is extracted from correlated calculations in the homogeneous electron gas, where we have tabulated it for a wide range of wave vectors and frequencies. A simple mean density approximation allows one to use it in inhomogeneous materials where the density varies on a scale of 1.6 rs or faster. This kernel contains effects that are completely absent in the ALDA; in particular, it correctly describes the double plasmon in the dynamic structure factor of sodium, and it shows the characteristic low-energy peak that appears in systems with low electronic density. It also leads to an overall quantitative improvement of spectra.

Nonlocal and Nonadiabatic Effects in the Charge-Density Response of Solids: A Time-Dependent Density-Functional Approach.

PubMed

Panholzer, Martin; Gatti, Matteo; Reining, Lucia

2018-04-20

The charge-density response of extended materials is usually dominated by the collective oscillation of electrons, the plasmons. Beyond this feature, however, intriguing many-body effects are observed. They cannot be described by one of the most widely used approaches for the calculation of dielectric functions, which is time-dependent density functional theory (TDDFT) in the adiabatic local density approximation (ALDA). Here, we propose an approximation to the TDDFT exchange-correlation kernel which is nonadiabatic and nonlocal. It is extracted from correlated calculations in the homogeneous electron gas, where we have tabulated it for a wide range of wave vectors and frequencies. A simple mean density approximation allows one to use it in inhomogeneous materials where the density varies on a scale of 1.6 r_{s} or faster. This kernel contains effects that are completely absent in the ALDA; in particular, it correctly describes the double plasmon in the dynamic structure factor of sodium, and it shows the characteristic low-energy peak that appears in systems with low electronic density. It also leads to an overall quantitative improvement of spectra.

Multireference Density Functional Theory with Generalized Auxiliary Systems for Ground and Excited States.

PubMed

Chen, Zehua; Zhang, Du; Jin, Ye; Yang, Yang; Su, Neil Qiang; Yang, Weitao

2017-09-21

To describe static correlation, we develop a new approach to density functional theory (DFT), which uses a generalized auxiliary system that is of a different symmetry, such as particle number or spin, from that of the physical system. The total energy of the physical system consists of two parts: the energy of the auxiliary system, which is determined with a chosen density functional approximation (DFA), and the excitation energy from an approximate linear response theory that restores the symmetry to that of the physical system, thus rigorously leading to a multideterminant description of the physical system. The electron density of the physical system is different from that of the auxiliary system and is uniquely determined from the functional derivative of the total energy with respect to the external potential. Our energy functional is thus an implicit functional of the physical system density, but an explicit functional of the auxiliary system density. We show that the total energy minimum and stationary states, describing the ground and excited states of the physical system, can be obtained by a self-consistent optimization with respect to the explicit variable, the generalized Kohn-Sham noninteracting density matrix. We have developed the generalized optimized effective potential method for the self-consistent optimization. Among options of the auxiliary system and the associated linear response theory, reformulated versions of the particle-particle random phase approximation (pp-RPA) and the spin-flip time-dependent density functional theory (SF-TDDFT) are selected for illustration of principle. Numerical results show that our multireference DFT successfully describes static correlation in bond dissociation and double bond rotation.

A Keystone Ant Species Provides Robust Biological Control of the Coffee Berry Borer Under Varying Pest Densities.

PubMed

Morris, Jonathan R; Vandermeer, John; Perfecto, Ivette

2015-01-01

Species' functional traits are an important part of the ecological complexity that determines the provisioning of ecosystem services. In biological pest control, predator response to pest density variation is a dynamic trait that impacts the provision of this service in agroecosystems. When pest populations fluctuate, farmers relying on biocontrol services need to know how natural enemies respond to these changes. Here we test the effect of variation in coffee berry borer (CBB) density on the biocontrol efficiency of a keystone ant species (Azteca sericeasur) in a coffee agroecosystem. We performed exclosure experiments to measure the infestation rate of CBB released on coffee branches in the presence and absence of ants at four different CBB density levels. We measured infestation rate as the number of CBB bored into fruits after 24 hours, quantified biocontrol efficiency (BCE) as the proportion of infesting CBB removed by ants, and estimated functional response from ant attack rates, measured as the difference in CBB infestation between branches. Infestation rates of CBB on branches with ants were significantly lower (71%-82%) than on those without ants across all density levels. Additionally, biocontrol efficiency was generally high and did not significantly vary across pest density treatments. Furthermore, ant attack rates increased linearly with increasing CBB density, suggesting a Type I functional response. These results demonstrate that ants can provide robust biological control of CBB, despite variation in pest density, and that the response of predators to pest density variation is an important factor in the provision of biocontrol services. Considering how natural enemies respond to changes in pest densities will allow for more accurate biocontrol predictions and better-informed management of this ecosystem service in agroecosystems.

A Keystone Ant Species Provides Robust Biological Control of the Coffee Berry Borer Under Varying Pest Densities

PubMed Central

Morris, Jonathan R.; Vandermeer, John; Perfecto, Ivette

2015-01-01

Species’ functional traits are an important part of the ecological complexity that determines the provisioning of ecosystem services. In biological pest control, predator response to pest density variation is a dynamic trait that impacts the provision of this service in agroecosystems. When pest populations fluctuate, farmers relying on biocontrol services need to know how natural enemies respond to these changes. Here we test the effect of variation in coffee berry borer (CBB) density on the biocontrol efficiency of a keystone ant species (Azteca sericeasur) in a coffee agroecosystem. We performed exclosure experiments to measure the infestation rate of CBB released on coffee branches in the presence and absence of ants at four different CBB density levels. We measured infestation rate as the number of CBB bored into fruits after 24 hours, quantified biocontrol efficiency (BCE) as the proportion of infesting CBB removed by ants, and estimated functional response from ant attack rates, measured as the difference in CBB infestation between branches. Infestation rates of CBB on branches with ants were significantly lower (71%-82%) than on those without ants across all density levels. Additionally, biocontrol efficiency was generally high and did not significantly vary across pest density treatments. Furthermore, ant attack rates increased linearly with increasing CBB density, suggesting a Type I functional response. These results demonstrate that ants can provide robust biological control of CBB, despite variation in pest density, and that the response of predators to pest density variation is an important factor in the provision of biocontrol services. Considering how natural enemies respond to changes in pest densities will allow for more accurate biocontrol predictions and better-informed management of this ecosystem service in agroecosystems. PMID:26562676

Magnetic field influences on the lateral dose response functions of photon-beam detectors: MC study of wall-less water-filled detectors with various densities.

PubMed

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

2017-06-21

The distortion of detector reading profiles across photon beams in the presence of magnetic fields is a developing subject of clinical photon-beam dosimetry. The underlying modification by the Lorentz force of a detector's lateral dose response function-the convolution kernel transforming the true cross-beam dose profile in water into the detector reading profile-is here studied for the first time. The three basic convolution kernels, the photon fluence response function, the dose deposition kernel, and the lateral dose response function, of wall-less cylindrical detectors filled with water of low, normal and enhanced density are shown by Monte Carlo simulation to be distorted in the prevailing direction of the Lorentz force. The asymmetric shape changes of these convolution kernels in a water medium and in magnetic fields of up to 1.5 T are confined to the lower millimetre range, and they depend on the photon beam quality, the magnetic flux density and the detector's density. The impact of this distortion on detector reading profiles is demonstrated using a narrow photon beam profile. For clinical applications it appears as favourable that the magnetic flux density dependent distortion of the lateral dose response function, as far as secondary electron transport is concerned, vanishes in the case of water-equivalent detectors of normal water density. By means of secondary electron history backtracing, the spatial distribution of the photon interactions giving rise either directly to secondary electrons or to scattered photons further downstream producing secondary electrons which contribute to the detector's signal, and their lateral shift due to the Lorentz force is elucidated. Electron history backtracing also serves to illustrate the correct treatment of the influences of the Lorentz force in the EGSnrc Monte Carlo code applied in this study.

Differential growth responses to water balance of coexisting deciduous tree species are linked to wood density in a Bolivian tropical dry forest.

PubMed

Mendivelso, Hooz A; Camarero, J Julio; Royo Obregón, Oriol; Gutiérrez, Emilia; Toledo, Marisol

2013-01-01

A seasonal period of water deficit characterizes tropical dry forests (TDFs). There, sympatric tree species exhibit a diversity of growth rates, functional traits, and responses to drought, suggesting that each species may possess different strategies to grow under different conditions of water availability. The evaluation of the long-term growth responses to changes in the soil water balance should provide an understanding of how and when coexisting tree species respond to water deficit in TDFs. Furthermore, such differential growth responses may be linked to functional traits related to water storage and conductance. We used dendrochronology and climate data to retrospectively assess how the radial growth of seven coexisting deciduous tree species responded to the seasonal soil water balance in a Bolivian TDF. Linear mixed-effects models were used to quantify the relationships between basal area increment and seasonal water balance. We related these relationships with wood density and sapwood production to assess if they affect the growth responses to climate. The growth of all species responded positively to water balance during the wet season, but such responses differed among species as a function of their wood density. For instance, species with a strong growth response to water availability averaged a low wood density which may facilitate the storage of water in the stem. By contrast, species with very dense wood were those whose growth was less sensitive to water availability. Coexisting tree species thus show differential growth responses to changes in soil water balance during the wet season. Our findings also provide a link between wood density, a trait related to the ability of trees to store water in the stem, and wood formation in response to water availability.

Differential Growth Responses to Water Balance of Coexisting Deciduous Tree Species Are Linked to Wood Density in a Bolivian Tropical Dry Forest

PubMed Central

Mendivelso, Hooz A.; Camarero, J. Julio; Royo Obregón, Oriol; Gutiérrez, Emilia; Toledo, Marisol

2013-01-01

A seasonal period of water deficit characterizes tropical dry forests (TDFs). There, sympatric tree species exhibit a diversity of growth rates, functional traits, and responses to drought, suggesting that each species may possess different strategies to grow under different conditions of water availability. The evaluation of the long-term growth responses to changes in the soil water balance should provide an understanding of how and when coexisting tree species respond to water deficit in TDFs. Furthermore, such differential growth responses may be linked to functional traits related to water storage and conductance. We used dendrochronology and climate data to retrospectively assess how the radial growth of seven coexisting deciduous tree species responded to the seasonal soil water balance in a Bolivian TDF. Linear mixed-effects models were used to quantify the relationships between basal area increment and seasonal water balance. We related these relationships with wood density and sapwood production to assess if they affect the growth responses to climate. The growth of all species responded positively to water balance during the wet season, but such responses differed among species as a function of their wood density. For instance, species with a strong growth response to water availability averaged a low wood density which may facilitate the storage of water in the stem. By contrast, species with very dense wood were those whose growth was less sensitive to water availability. Coexisting tree species thus show differential growth responses to changes in soil water balance during the wet season. Our findings also provide a link between wood density, a trait related to the ability of trees to store water in the stem, and wood formation in response to water availability. PMID:24116001

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.

Nonlocal kinetic energy functional from the jellium-with-gap model: Applications to orbital-free density functional theory

NASA Astrophysics Data System (ADS)

Constantin, Lucian A.; Fabiano, Eduardo; Della Sala, Fabio

2018-05-01

Orbital-free density functional theory (OF-DFT) promises to describe the electronic structure of very large quantum systems, being its computational cost linear with the system size. However, the OF-DFT accuracy strongly depends on the approximation made for the kinetic energy (KE) functional. To date, the most accurate KE functionals are nonlocal functionals based on the linear-response kernel of the homogeneous electron gas, i.e., the jellium model. Here, we use the linear-response kernel of the jellium-with-gap model to construct a simple nonlocal KE functional (named KGAP) which depends on the band-gap energy. In the limit of vanishing energy gap (i.e., in the case of metals), the KGAP is equivalent to the Smargiassi-Madden (SM) functional, which is accurate for metals. For a series of semiconductors (with different energy gaps), the KGAP performs much better than SM, and results are close to the state-of-the-art functionals with sophisticated density-dependent kernels.

An uncertainty model of acoustic metamaterials with random parameters

NASA Astrophysics Data System (ADS)

He, Z. C.; Hu, J. Y.; Li, Eric

2018-01-01

Acoustic metamaterials (AMs) are man-made composite materials. However, the random uncertainties are unavoidable in the application of AMs due to manufacturing and material errors which lead to the variance of the physical responses of AMs. In this paper, an uncertainty model based on the change of variable perturbation stochastic finite element method (CVPS-FEM) is formulated to predict the probability density functions of physical responses of AMs with random parameters. Three types of physical responses including the band structure, mode shapes and frequency response function of AMs are studied in the uncertainty model, which is of great interest in the design of AMs. In this computation, the physical responses of stochastic AMs are expressed as linear functions of the pre-defined random parameters by using the first-order Taylor series expansion and perturbation technique. Then, based on the linear function relationships of parameters and responses, the probability density functions of the responses can be calculated by the change-of-variable technique. Three numerical examples are employed to demonstrate the effectiveness of the CVPS-FEM for stochastic AMs, and the results are validated by Monte Carlo method successfully.

First-passage problems: A probabilistic dynamic analysis for degraded structures

NASA Technical Reports Server (NTRS)

Shiao, Michael C.; Chamis, Christos C.

1990-01-01

Structures subjected to random excitations with uncertain system parameters degraded by surrounding environments (a random time history) are studied. Methods are developed to determine the statistics of dynamic responses, such as the time-varying mean, the standard deviation, the autocorrelation functions, and the joint probability density function of any response and its derivative. Moreover, the first-passage problems with deterministic and stationary/evolutionary random barriers are evaluated. The time-varying (joint) mean crossing rate and the probability density function of the first-passage time for various random barriers are derived.

On the calculation of charge transfer transitions with standard density functionals using constrained variational density functional theory.

PubMed

Ziegler, Tom; Krykunov, Mykhaylo

2010-08-21

It is well known that time-dependent density functional theory (TD-DFT) based on standard gradient corrected functionals affords both a quantitative and qualitative incorrect picture of charge transfer transitions between two spatially separated regions. It is shown here that the well known failure can be traced back to the use of linear response theory. Further, it is demonstrated that the inclusion of higher order terms readily affords a qualitatively correct picture even for simple functionals based on the local density approximation. The inclusion of these terms is done within the framework of a newly developed variational approach to excitation energies called constrained variational density functional theory (CV-DFT). To second order [CV(2)-DFT] this theory is identical to adiabatic TD-DFT within the Tamm-Dancoff approximation. With inclusion of fourth order corrections [CV(4)-DFT] it affords a qualitative correct description of charge transfer transitions. It is finally demonstrated that the relaxation of the ground state Kohn-Sham orbitals to first order in response to the change in density on excitation together with CV(4)-DFT affords charge transfer excitations in good agreement with experiment. The new relaxed theory is termed R-CV(4)-DFT. The relaxed scheme represents an effective way in which to introduce double replacements into the description of single electron excitations, something that would otherwise require a frequency dependent kernel.

In vitro cell-mediated immunity after thermal injury is not impaired. Density gradient purification of mononuclear cells is associated with spurious (artifactual) immunosuppression.

PubMed Central

Xu, D Z; Deitch, E A; Sittig, K; Qi, L; McDonald, J C

1988-01-01

Mononuclear cells isolated by density gradient centrifugation from the peripheral blood of burn patients, but not healthy volunteers, are contaminated with large numbers of nonmononuclear cells. These contaminating leukocytes could cause artifactual alterations in standard in vitro tests of lymphocyte function. Thus, we compared the in vitro blastogenic response of density gradient purified leukocytes and T-cell purified lymphocytes from 13 burn patients to mitogenic (PHA) and antigenic stimuli. The mitogenic and antigenic response of the patients' density gradient purified leukocytes were impaired compared to healthy volunteers (p less than 0.01). However, when the contaminating nonlymphocytes were removed, the patients' cells responded normally to both stimuli. Thus, density gradient purified mononuclear cells from burn patients are contaminated by leukocytes that are not phenotypically or functionally lymphocytes. Since the lymphocytes from burn patients respond normally to PHA and alloantigens after the contaminating nonlymphocyte cell population has been removed, it appears that in vitro assays of lymphocyte function using density gradient purified leukocytes may give spurious results. PMID:2973771

Multiresolution quantum chemistry in multiwavelet bases: excited states from time-dependent Hartree–Fock and density functional theory via linear response

DOE PAGES

Yanai, Takeshi; Fann, George I.; Beylkin, Gregory; ...

2015-02-25

Using the fully numerical method for time-dependent Hartree–Fock and density functional theory (TD-HF/DFT) with the Tamm–Dancoff (TD) approximation we use a multiresolution analysis (MRA) approach to present our findings. From a reformulation with effective use of the density matrix operator, we obtain a general form of the HF/DFT linear response equation in the first quantization formalism. It can be readily rewritten as an integral equation with the bound-state Helmholtz (BSH) kernel for the Green's function. The MRA implementation of the resultant equation permits excited state calculations without virtual orbitals. Moreover, the integral equation is efficiently and adaptively solved using amore » numerical multiresolution solver with multiwavelet bases. Our implementation of the TD-HF/DFT methods is applied for calculating the excitation energies of H 2, Be, N 2, H 2O, and C 2H 4 molecules. The numerical errors of the calculated excitation energies converge in proportion to the residuals of the equation in the molecular orbitals and response functions. The energies of the excited states at a variety of length scales ranging from short-range valence excitations to long-range Rydberg-type ones are consistently accurate. It is shown that the multiresolution calculations yield the correct exponential asymptotic tails for the response functions, whereas those computed with Gaussian basis functions are too diffuse or decay too rapidly. Finally, we introduce a simple asymptotic correction to the local spin-density approximation (LSDA) so that in the TDDFT calculations, the excited states are correctly bound.« less

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.

Linear and quadratic static response functions and structure functions in Yukawa liquids.

PubMed

Magyar, Péter; Donkó, Zoltán; Kalman, Gabor J; Golden, Kenneth I

2014-08-01

We compute linear and quadratic static density response functions of three-dimensional Yukawa liquids by applying an external perturbation potential in molecular dynamics simulations. The response functions are also obtained from the equilibrium fluctuations (static structure factors) in the system via the fluctuation-dissipation theorems. The good agreement of the quadratic response functions, obtained in the two different ways, confirms the quadratic fluctuation-dissipation theorem. We also find that the three-point structure function may be factorizable into two-point structure functions, leading to a cluster representation of the equilibrium triplet correlation function.

Photoionization of Atoms and Ions: Application of Time-Dependent Response Method within the Density Functional Theory.

DTIC Science & Technology

1987-10-13

AD-A±95 686 PHOTOIONIZATION OF ATOMS AND IONS: APPLICATION OF III TIME-DEPENDENT RESPONSE..(U) NAVAL RESEARCH LAB WASHINGTON DC U GUPTA ET AL. 13 OCT...on revere if ncemy and idmntify by block number) FIELD GROUP SUBGROUP Photoionization Density functional Atoms Time dependent 1 S. (Continue on...reverse if necenary and identify by block numnbw) The photoionization cross-section of several atoms (AT, Xe, Rn, Cs) and ions (Ne-like Ar, H-like and Li

Underscreening in ionic liquids: a first principles analysis.

PubMed

Rotenberg, Benjamin; Bernard, Olivier; Hansen, Jean-Pierre

2018-02-07

An attempt is made to understand the underscreening effect, observed in concentrated electrolyte solutions or melts, on the basis of simple, admittedly crude models involving charged (for the ions) and neutral (for the solvent molecules) hard spheres. The thermodynamic and structural properties of these 'primitive' and 'semi-primitive' models are calculated within mean spherical approximation, which provides the basic input required to determine the partial density response functions. The screening length [Formula: see text], which is unambiguously defined in terms of the wave-number-dependent response functions, exhibits a cross-over from a low density, Debye-like regime, to a regime where [Formula: see text] increases with density beyond a critical density at which the Debye length [Formula: see text] becomes comparable to the ion diameter. In this high density regime the ratio [Formula: see text] increases according to a power law, in qualitative agreement with experimental measurements, albeit at a much slower rate.

Underscreening in ionic liquids: a first principles analysis

NASA Astrophysics Data System (ADS)

Rotenberg, Benjamin; Bernard, Olivier; Hansen, Jean-Pierre

2018-02-01

An attempt is made to understand the underscreening effect, observed in concentrated electrolyte solutions or melts, on the basis of simple, admittedly crude models involving charged (for the ions) and neutral (for the solvent molecules) hard spheres. The thermodynamic and structural properties of these ‘primitive’ and ‘semi-primitive’ models are calculated within mean spherical approximation, which provides the basic input required to determine the partial density response functions. The screening length λS , which is unambiguously defined in terms of the wave-number-dependent response functions, exhibits a cross-over from a low density, Debye-like regime, to a regime where λS increases with density beyond a critical density at which the Debye length λD becomes comparable to the ion diameter. In this high density regime the ratio λ_S/λD increases according to a power law, in qualitative agreement with experimental measurements, albeit at a much slower rate.

Functional differentiability in time-dependent quantum mechanics.

PubMed

Penz, Markus; Ruggenthaler, Michael

2015-03-28

In this work, we investigate the functional differentiability of the time-dependent many-body wave function and of derived quantities with respect to time-dependent potentials. For properly chosen Banach spaces of potentials and wave functions, Fréchet differentiability is proven. From this follows an estimate for the difference of two solutions to the time-dependent Schrödinger equation that evolve under the influence of different potentials. Such results can be applied directly to the one-particle density and to bounded operators, and present a rigorous formulation of non-equilibrium linear-response theory where the usual Lehmann representation of the linear-response kernel is not valid. Further, the Fréchet differentiability of the wave function provides a new route towards proving basic properties of time-dependent density-functional theory.

Application of information theory to the design of line-scan imaging systems

NASA Technical Reports Server (NTRS)

Huck, F. O.; Park, S. K.; Halyo, N.; Stallman, S.

1981-01-01

Information theory is used to formulate a single figure of merit for assessing the performance of line scan imaging systems as a function of their spatial response (point spread function or modulation transfer function), sensitivity, sampling and quantization intervals, and the statistical properties of a random radiance field. Computational results for the information density and efficiency (i.e., the ratio of information density to data density) are intuitively satisfying and compare well with experimental and theoretical results obtained by earlier investigators concerned with the performance of TV systems.

Relations among several nuclear and electronic density functional reactivity indexes

NASA Astrophysics Data System (ADS)

Torrent-Sucarrat, Miquel; Luis, Josep M.; Duran, Miquel; Toro-Labbé, Alejandro; Solà, Miquel

2003-11-01

An expansion of the energy functional in terms of the total number of electrons and the normal coordinates within the canonical ensemble is presented. A comparison of this expansion with the expansion of the energy in terms of the total number of electrons and the external potential leads to new relations among common density functional reactivity descriptors. The formulas obtained provide explicit links between important quantities related to the chemical reactivity of a system. In particular, the relation between the nuclear and the electronic Fukui functions is recovered. The connection between the derivatives of the electronic energy and the nuclear repulsion energy with respect to the external potential offers a proof for the "Quantum Chemical le Chatelier Principle." Finally, the nuclear linear response function is defined and the relation of this function with the electronic linear response function is given.

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

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

Attarian Shandiz, M., E-mail: mohammad.attarianshandiz@mail.mcgill.ca; Gauvin, R.

The temperature and pressure dependency of the volume plasmon energy of solids was investigated by density functional theory calculations. The volume change of crystal is the major factor responsible for the variation of valence electron density and plasmon energy in the free electron model. Hence, to introduce the effect of temperature and pressure for the density functional theory calculations of plasmon energy, the temperature and pressure dependency of lattice parameter was used. Also, by combination of the free electron model and the equation of state based on the pseudo-spinodal approach, the temperature and pressure dependency of the plasmon energy wasmore » modeled. The suggested model is in good agreement with the results of density functional theory calculations and available experimental data for elements with the free electron behavior.« less

Item Response Theory with Estimation of the Latent Population Distribution Using Spline-Based Densities

ERIC Educational Resources Information Center

Woods, Carol M.; Thissen, David

2006-01-01

The purpose of this paper is to introduce a new method for fitting item response theory models with the latent population distribution estimated from the data using splines. A spline-based density estimation system provides a flexible alternative to existing procedures that use a normal distribution, or a different functional form, for the…

Relationship between symbiont density and photosynthetic carbon acquisition in the temperate coral Cladocora caespitosa

NASA Astrophysics Data System (ADS)

Hoogenboom, M.; Beraud, E.; Ferrier-Pagès, C.

2010-03-01

This study quantified variation in net photosynthetic carbon gain in response to natural fluctuations in symbiont density for the Mediterranean coral Cladocora caespitosa, and evaluated which density maximized photosynthetic carbon acquisition. To do this, carbon acquisition was modeled as an explicit function of symbiont density. The model was parameterized using measurements of rates of photosynthesis and respiration for small colonies with a broad range of zooxanthella concentrations. Results demonstrate that rates of net photosynthesis increase asymptotically with symbiont density, whereas rates of respiration increase linearly. In combination, these functional responses meant that colony energy acquisition decreased at both low and at very high zooxanthella densities. However, there was a wide range of symbiont densities for which net daily photosynthesis was approximately equivalent. Therefore, significant changes in symbiont density do not necessarily cause a change in autotrophic energy acquisition by the colony. Model estimates of the optimal range of cell densities corresponded well with independent observations of symbiont concentrations obtained from field and laboratory studies of healthy colonies. Overall, this study demonstrates that the seasonal fluctuations, in symbiont numbers observed in healthy colonies of the Mediterranean coral investigated, do not have a strong effect on photosynthetic energy acquisition.

The ethological trap: functional and numerical responses of highly efficient invasive predators driving prey extinctions.

PubMed

Spencer, Ricky-John; Van Dyke, James U; Thompson, Michael B

2016-10-01

Ecological traps are threats to organisms, and exist in a range of biological systems. A subset of ecological trap theory is the "ethological trap," whereby behaviors canalized by past natural selection become traps when environments change rapidly. Invasive predators are major threats to imperiled species and their ability to exploit canalized behaviors of naive prey is particularly important for the establishment of the predator and the decline of the native prey. Our study uses ecological theory to demonstrate that invasive predator controls require shifts in management priorities. Total predation rate (i.e., total response) is the product of both the functional response and numerical response of predators to prey. Functional responses are the changes in the rate of prey consumption by individual predators, relative to prey abundance. Numerical responses are the aggregative rates of prey consumption by all predators relative to prey density, which change with predator density via reproduction or migration, in response to changes in prey density. Traditional invasive predator management methods focus on reducing predator populations, and thus manage for numerical responses. These management efforts fail to manage for functional responses, and may not eliminate impacts of highly efficient individual predators. We explore this problem by modeling the impacts of functional and numerical responses of invasive foxes depredating imperiled Australian turtle nests. Foxes exhibit exceptionally efficient functional responses. A single fox can destroy >95% of turtle nests in a nesting area, which eliminates juvenile recruitment. In this case, the ethological trap is the "Arribada" nesting strategy, an emergent behavior whereby most turtles in a population nest simultaneously in the same nesting grounds. Our models show that Arribada nesting events do not oversaturate foxes, and small numbers of foxes depredate all of the nests in a given Arribada. Widely scattering nests may reduce fox predation rates, but the long generation times of turtles combined with their rapid recent decline suggests that evolutionary responses in nesting strategy may be unlikely. Our study demonstrates that reducing populations of highly efficient invasive predators is insufficient for preserving native prey species. Instead, management must reduce individual predator efficiency, independent of reducing predator population size. © 2016 by the Ecological Society of America.

Predator-dependent functional response in wolves: from food limitation to surplus killing.

PubMed

Zimmermann, Barbara; Sand, Håkan; Wabakken, Petter; Liberg, Olof; Andreassen, Harry Peter

2015-01-01

The functional response of a predator describes the change in per capita kill rate to changes in prey density. This response can be influenced by predator densities, giving a predator-dependent functional response. In social carnivores which defend a territory, kill rates also depend on the individual energetic requirements of group members and their contribution to the kill rate. This study aims to provide empirical data for the functional response of wolves Canis lupus to the highly managed moose Alces alces population in Scandinavia. We explored prey and predator dependence, and how the functional response relates to the energetic requirements of wolf packs. Winter kill rates of GPS-collared wolves and densities of cervids were estimated for a total of 22 study periods in 15 wolf territories. The adult wolves were identified as the individuals responsible for providing kills to the wolf pack, while pups could be described as inept hunters. The predator-dependent, asymptotic functional response models (i.e. Hassell-Varley type II and Crowley-Martin) performed best among a set of 23 competing linear, asymptotic and sigmoid models. Small wolf packs acquired >3 times as much moose biomass as required to sustain their field metabolic rate (FMR), even at relatively low moose abundances. Large packs (6-9 wolves) acquired less biomass than required in territories with low moose abundance. We suggest the surplus killing by small packs is a result of an optimal foraging strategy to consume only the most nutritious parts of easy accessible prey while avoiding the risk of being detected by humans. Food limitation may have a stabilizing effect on pack size in wolves, as supported by the observed negative relationship between body weight of pups and pack size. © 2014 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.

Influence of spatial heterogeneity on the type of zooplankton functional response: A study based on field observations

NASA Astrophysics Data System (ADS)

Morozov, Andrew; Arashkevich, Elena; Reigstad, Marit; Falk-Petersen, Stig

2008-10-01

Mathematical models of plankton dynamics are sensitive to the choice of type of zooplankton functional response, i.e., to how the rate of intake of food varies with the food density. Conventionally, the conclusion on the actual type of functional response for a given zooplankton species is made based upon laboratory analysis on experimental feeding. In this paper, we show that such an approach can be too simplistic and misleading. Based on real ocean data obtained from three expeditions of R/V Jan Mayen in the Barents Sea in 2003-2005, we demonstrate that vertical heterogeneity in algal distribution as well as active vertical movement of herbivorous zooplankton can modify the type of trophic response completely. In particular, we found that the rate of average intake of algae by Calanus glacialis exhibits a Holling type III response, instead of Holling type I or II found previously in laboratory experiments. We argue that this conceptual discrepancy is due to the ability of the zooplankton to feed in layers with high algal density and to avoid depths with lower algal density. Since theoretical studies would predict enhancing in system stability in the case of Holling type III, our results may be of importance for understanding the main factors controlling plankton dynamics.

Thermal and active fluctuations of a compressible bilayer vesicle

NASA Astrophysics Data System (ADS)

Sachin Krishnan, T. V.; Yasuda, Kento; Okamoto, Ryuichi; Komura, Shigeyuki

2018-05-01

We discuss thermal and active fluctuations of a compressible bilayer vesicle by using the results of hydrodynamic theory for vesicles. Coupled Langevin equations for the membrane deformation and the density fields are employed to calculate the power spectral density matrix of membrane fluctuations. Thermal contribution is obtained by means of the fluctuation dissipation theorem, whereas active contribution is calculated from exponentially decaying time correlation functions of active random forces. We obtain the total power spectral density as a sum of thermal and active contributions. An apparent response function is further calculated in order to compare with the recent microrheology experiment on red blood cells. An enhanced response is predicted in the low-frequency regime for non-thermal active fluctuations.

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

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

Rüger, Robert, E-mail: rueger@scm.com; Department of Theoretical Chemistry, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam; Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Linnéstr. 2, 04103 Leipzig

2016-05-14

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

Functional imaging of the human brain using a modular, fibre-less, high-density diffuse optical tomography system.

PubMed

Chitnis, Danial; Cooper, Robert J; Dempsey, Laura; Powell, Samuel; Quaggia, Simone; Highton, David; Elwell, Clare; Hebden, Jeremy C; Everdell, Nicholas L

2016-10-01

We present the first three-dimensional, functional images of the human brain to be obtained using a fibre-less, high-density diffuse optical tomography system. Our technology consists of independent, miniaturized, silicone-encapsulated DOT modules that can be placed directly on the scalp. Four of these modules were arranged to provide up to 128, dual-wavelength measurement channels over a scalp area of approximately 60 × 65 mm 2 . Using a series of motor-cortex stimulation experiments, we demonstrate that this system can obtain high-quality, continuous-wave measurements at source-detector separations ranging from 14 to 55 mm in adults, in the presence of hair. We identify robust haemodynamic response functions in 5 out of 5 subjects, and present diffuse optical tomography images that depict functional haemodynamic responses that are well-localized in all three dimensions at both the individual and group levels. This prototype modular system paves the way for a new generation of wearable, wireless, high-density optical neuroimaging technologies.

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.

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.

Association Between Brain Activation and Functional Connectivity.

PubMed

Tomasi, Dardo; Volkow, Nora D

2018-04-13

The origin of the "resting-state" brain activity recorded with functional magnetic resonance imaging (fMRI) is still uncertain. Here we provide evidence for the neurovascular origins of the amplitude of the low-frequency fluctuations (ALFF) and the local functional connectivity density (lFCD) by comparing them with task-induced blood-oxygen level dependent (BOLD) responses, which are considered a proxy for neuronal activation. Using fMRI data for 2 different tasks (Relational and Social) collected by the Human Connectome Project in 426 healthy adults, we show that ALFF and lFCD have linear associations with the BOLD response. This association was significantly attenuated by a novel task signal regression (TSR) procedure, indicating that task performance enhances lFCD and ALFF in activated regions. We also show that lFCD predicts BOLD activation patterns, as was recently shown for other functional connectivity metrics, which corroborates that resting functional connectivity architecture impacts brain activation responses. Thus, our findings indicate a common source for BOLD responses, ALFF and lFCD, which is consistent with the neurovascular origin of local hemodynamic synchrony presumably reflecting coordinated fluctuations in neuronal activity. This study also supports the development of task-evoked functional connectivity density mapping.

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

Collagen Matrix Density Drives the Metabolic Shift in Breast Cancer Cells.

PubMed

Morris, Brett A; Burkel, Brian; Ponik, Suzanne M; Fan, Jing; Condeelis, John S; Aguirre-Ghiso, Julio A; Castracane, James; Denu, John M; Keely, Patricia J

2016-11-01

Increased breast density attributed to collagen I deposition is associated with a 4-6 fold increased risk of developing breast cancer. Here, we assessed cellular metabolic reprogramming of mammary carcinoma cells in response to increased collagen matrix density using an in vitro 3D model. Our initial observations demonstrated changes in functional metabolism in both normal mammary epithelial cells and mammary carcinoma cells in response to changes in matrix density. Further, mammary carcinoma cells grown in high density collagen matrices displayed decreased oxygen consumption and glucose metabolism via the tricarboxylic acid (TCA) cycle compared to cells cultured in low density matrices. Despite decreased glucose entry into the TCA cycle, levels of glucose uptake, cell viability, and ROS were not different between high and low density matrices. Interestingly, under high density conditions the contribution of glutamine as a fuel source to drive the TCA cycle was significantly enhanced. These alterations in functional metabolism mirrored significant changes in the expression of metabolic genes involved in glycolysis, oxidative phosphorylation, and the serine synthesis pathway. This study highlights the broad importance of the collagen microenvironment to cellular expression profiles, and shows that changes in density of the collagen microenvironment can modulate metabolic shifts of cancer cells. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

Functional Responses and Resilience of Boreal Forest Ecosystem after Reduction of Deer Density

PubMed Central

Bachand, Marianne; Pellerin, Stéphanie; Moretti, Marco; Aubin, Isabelle; Tremblay, Jean-Pierre; Côté, Steeve D.; Poulin, Monique

2014-01-01

The functional trait-based approach is increasingly used to predict responses of ecological communities to disturbances, but most studies target a single taxonomic group. Here, we assessed the resilience of a forest ecosystem to an overabundant herbivore population by assessing changes in 19 functional traits for plant, 13 traits for ground beetle and 16 traits for songbird communities after six years of controlled browsing on Anticosti Island (Quebec, Canada). Our results indicated that plants were more responsive to 6 years of reduced browsing pressure than ground beetles and songbirds. However, co-inertia analysis revealed that ground beetle communities responded in a similar way than plant communities with stronger relationships between plant and ground beetle traits at reduced deer density, a pattern not detected between plant and songbird. High deer density favored plants species that reproduce vegetatively and with abiotic pollination and seed dispersal, traits implying little interaction with animal. On the other hand, traits found at reduced deer density mostly involved trophic interaction. For example, plants in this treatment had fleshy fruits and large seeds dispersed by birds or other animals whereas ground beetle species were carnivorous. Overall, our results suggest that plant communities recovered some functional components to overabundant herbivore populations, since most traits associated with undisturbed forests were reestablished after six years of deer reduction. The re-establishment of functional plant communities with traits involving trophic interaction induces changes in the ground-beetle trait community, but forest structure remains likely insufficiently heterogeneous to shift the songbird trait community within six years. PMID:24587362

Gaussian polarizable-ion tight binding.

PubMed

Boleininger, Max; Guilbert, Anne Ay; Horsfield, Andrew P

2016-10-14

To interpret ultrafast dynamics experiments on large molecules, computer simulation is required due to the complex response to the laser field. We present a method capable of efficiently computing the static electronic response of large systems to external electric fields. This is achieved by extending the density-functional tight binding method to include larger basis sets and by multipole expansion of the charge density into electrostatically interacting Gaussian distributions. Polarizabilities for a range of hydrocarbon molecules are computed for a multipole expansion up to quadrupole order, giving excellent agreement with experimental values, with average errors similar to those from density functional theory, but at a small fraction of the cost. We apply the model in conjunction with the polarizable-point-dipoles model to estimate the internal fields in amorphous poly(3-hexylthiophene-2,5-diyl).

Gaussian polarizable-ion tight binding

NASA Astrophysics Data System (ADS)

Boleininger, Max; Guilbert, Anne AY; Horsfield, Andrew P.

2016-10-01

To interpret ultrafast dynamics experiments on large molecules, computer simulation is required due to the complex response to the laser field. We present a method capable of efficiently computing the static electronic response of large systems to external electric fields. This is achieved by extending the density-functional tight binding method to include larger basis sets and by multipole expansion of the charge density into electrostatically interacting Gaussian distributions. Polarizabilities for a range of hydrocarbon molecules are computed for a multipole expansion up to quadrupole order, giving excellent agreement with experimental values, with average errors similar to those from density functional theory, but at a small fraction of the cost. We apply the model in conjunction with the polarizable-point-dipoles model to estimate the internal fields in amorphous poly(3-hexylthiophene-2,5-diyl).

Amodal brain activation and functional connectivity in response to high-energy-density food cues in obesity.

PubMed

Carnell, Susan; Benson, Leora; Pantazatos, Spiro P; Hirsch, Joy; Geliebter, Allan

2014-11-01

The obesogenic environment is pervasive, yet only some people become obese. The aim was to investigate whether obese individuals show differential neural responses to visual and auditory food cues, independent of cue modality. Obese (BMI 29-41, n = 10) and lean (BMI 20-24, n = 10) females underwent fMRI scanning during presentation of auditory (spoken word) and visual (photograph) cues representing high-energy-density (ED) and low-ED foods. The effect of obesity on whole-brain activation, and on functional connectivity with the midbrain/VTA, was examined. Obese compared with lean women showed greater modality-independent activation of the midbrain/VTA and putamen in response to high-ED (vs. low-ED) cues, as well as relatively greater functional connectivity between the midbrain/VTA and cerebellum (P < 0.05 corrected). Heightened modality-independent responses to food cues within the midbrain/VTA and putamen, and altered functional connectivity between the midbrain/VTA and cerebellum, could contribute to excessive food intake in obese individuals. © 2014 The Obesity Society.

Four-Component Damped Density Functional Response Theory Study of UV/Vis Absorption Spectra and Phosphorescence Parameters of Group 12 Metal-Substituted Porphyrins.

PubMed

Fransson, Thomas; Saue, Trond; Norman, Patrick

2016-05-10

The influences of group 12 (Zn, Cd, Hg) metal-substitution on the valence spectra and phosphorescence parameters of porphyrins (P) have been investigated in a relativistic setting. In order to obtain valence spectra, this study reports the first application of the damped linear response function, or complex polarization propagator, in the four-component density functional theory framework [as formulated in Villaume et al. J. Chem. Phys. 2010 , 133 , 064105 ]. It is shown that the steep increase in the density of states as due to the inclusion of spin-orbit coupling yields only minor changes in overall computational costs involved with the solution of the set of linear response equations. Comparing single-frequency to multifrequency spectral calculations, it is noted that the number of iterations in the iterative linear equation solver per frequency grid-point decreases monotonously from 30 to 0.74 as the number of frequency points goes from one to 19. The main heavy-atom effect on the UV/vis-absorption spectra is indirect and attributed to the change of point group symmetry due to metal-substitution, and it is noted that substitutions using heavier atoms yield small red-shifts of the intense Soret-band. Concerning phosphorescence parameters, the adoption of a four-component relativistic setting enables the calculation of such properties at a linear order of response theory, and any higher-order response functions do not need to be considered-a real, conventional, form of linear response theory has been used for the calculation of these parameters. For the substituted porphyrins, electronic coupling between the lowest triplet states is strong and results in theoretical estimates of lifetimes that are sensitive to the wave function and electron density parametrization. With this in mind, we report our best estimates of the phosphorescence lifetimes to be 460, 13.8, 11.2, and 0.00155 s for H2P, ZnP, CdP, and HgP, respectively, with the corresponding transition energies being equal to 1.46, 1.50, 1.38, and 0.89 eV.

An evaluation of random analysis methods for the determination of panel damping

NASA Technical Reports Server (NTRS)

Bhat, W. V.; Wilby, J. F.

1972-01-01

An analysis is made of steady-state and non-steady-state methods for the measurement of panel damping. Particular emphasis is placed on the use of random process techniques in conjunction with digital data reduction methods. The steady-state methods considered use the response power spectral density, response autocorrelation, excitation-response crosspower spectral density, or single-sided Fourier transform (SSFT) of the response autocorrelation function. Non-steady-state methods are associated mainly with the use of rapid frequency sweep excitation. Problems associated with the practical application of each method are evaluated with specific reference to the case of a panel exposed to a turbulent airflow, and two methods, the power spectral density and the single-sided Fourier transform methods, are selected as being the most suitable. These two methods are demonstrated experimentally, and it is shown that the power spectral density method is satisfactory under most conditions, provided that appropriate corrections are applied to account for filter bandwidth and background noise errors. Thus, the response power spectral density method is recommended for the measurement of the damping of panels exposed to a moving airflow.

Molecular Electron Density Theory: A Modern View of Reactivity in Organic Chemistry.

PubMed

Domingo, Luis R

2016-09-30

A new theory for the study of the reactivity in Organic Chemistry, named Molecular Electron Density Theory (MEDT), is proposed herein. MEDT is based on the idea that while the electron density distribution at the ground state is responsible for physical and chemical molecular properties, as proposed by the Density Functional Theory (DFT), the capability for changes in electron density is responsible for molecular reactivity. Within MEDT, the reactivity in Organic Chemistry is studied through a rigorous quantum chemical analysis of the changes of the electron density as well as the energies associated with these changes along the reaction path in order to understand experimental outcomes. Studies performed using MEDT allow establishing a modern rationalisation and to gain insight into molecular mechanisms and reactivity in Organic Chemistry.

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.

Radiometric analysis of photographic data by the effective exposure method

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

Constantine, B J

1972-04-01

The effective exposure method provides for radiometric analysis of photographic data. A three-dimensional model, where density is a function of energy and wavelength, is postulated to represent the film response function. Calibration exposures serve to eliminate the other factors which affect image density. The effective exposure causing an image can be determined by comparing the image density with that of a calibration exposure. If the relative spectral distribution of the source is known, irradiance and/or radiance can be unfolded from the effective exposure expression.

Density-dependent adjustment of inducible defenses.

PubMed

Tollrian, Ralph; Duggen, Sonja; Weiss, Linda C; Laforsch, Christian; Kopp, Michael

2015-08-03

Predation is a major factor driving evolution, and organisms have evolved adaptations increasing their survival chances. However, most defenses incur trade-offs between benefits and costs. Many organisms save costs by employing inducible defenses as responses to fluctuating predation risk. The level of defense often increases with predator densities. However, individual predation risk should not only depend on predator density but also on the density of conspecifics. If the predator has a saturating functional response one would predict a negative correlation between prey density and individual predation risk and hence defense expression. Here, we tested this hypothesis using six model systems, covering a taxonomic range from protozoa to rotifers and crustaceans. In all six systems, we found that the level of defense expression increased with predator density but decreased with prey density. In one of our systems, i.e. in Daphnia, we further show that the response to prey density is triggered by a chemical cue released by conspecifics and congeners. Our results indicate that organisms adjust the degree of defense to the acute predation risk, rather than merely to predators' densities. Our study suggests that density-dependent defense expression reflects accurate predation-risk assessment and is a general principle in many inducible-defense systems.

Density-dependent adjustment of inducible defenses

PubMed Central

Tollrian, Ralph; Duggen, Sonja; Weiss, Linda C.; Laforsch, Christian; Kopp, Michael

2015-01-01

Predation is a major factor driving evolution, and organisms have evolved adaptations increasing their survival chances. However, most defenses incur trade-offs between benefits and costs. Many organisms save costs by employing inducible defenses as responses to fluctuating predation risk. The level of defense often increases with predator densities. However, individual predation risk should not only depend on predator density but also on the density of conspecifics. If the predator has a saturating functional response one would predict a negative correlation between prey density and individual predation risk and hence defense expression. Here, we tested this hypothesis using six model systems, covering a taxonomic range from protozoa to rotifers and crustaceans. In all six systems, we found that the level of defense expression increased with predator density but decreased with prey density. In one of our systems, i.e. in Daphnia, we further show that the response to prey density is triggered by a chemical cue released by conspecifics and congeners. Our results indicate that organisms adjust the degree of defense to the acute predation risk, rather than merely to predators’ densities. Our study suggests that density-dependent defense expression reflects accurate predation-risk assessment and is a general principle in many inducible-defense systems. PMID:26235428

Diagrammatic expansion for positive density-response spectra: Application to the electron gas

NASA Astrophysics Data System (ADS)

Uimonen, A.-M.; Stefanucci, G.; Pavlyukh, Y.; van Leeuwen, R.

2015-03-01

In a recent paper [Phys. Rev. B 90, 115134 (2014), 10.1103/PhysRevB.90.115134] we put forward a diagrammatic expansion for the self-energy which guarantees the positivity of the spectral function. In this work we extend the theory to the density-response function. We write the generic diagram for the density-response spectrum as the sum of "partitions." In a partition the original diagram is evaluated using time-ordered Green's functions on the left half of the diagram, antitime-ordered Green's functions on the right half of the diagram, and lesser or greater Green's function gluing the two halves. As there exists more than one way to cut a diagram in two halves, to every diagram corresponds more than one partition. We recognize that the most convenient diagrammatic objects for constructing a theory of positive spectra are the half-diagrams. Diagrammatic approximations obtained by summing the squares of half-diagrams do indeed correspond to a combination of partitions which, by construction, yield a positive spectrum. We develop the theory using bare Green's functions and subsequently extend it to dressed Green's functions. We further prove a connection between the positivity of the spectral function and the analytic properties of the polarizability. The general theory is illustrated with several examples and then applied to solve the long-standing problem of including vertex corrections without altering the positivity of the spectrum. In fact already the first-order vertex diagram, relevant to the study of gradient expansion, Friedel oscillations, etc., leads to spectra which are negative in certain frequency domain. We find that the simplest approximation to cure this deficiency is given by the sum of the zeroth-order bubble diagram, the first-order vertex diagram, and a partition of the second-order ladder diagram. We evaluate this approximation in the three-dimensional homogeneous electron gas and show the positivity of the spectrum for all frequencies and densities.

Effect of wetting-layer density of states on the gain and phase recovery dynamics of quantum-dot semiconductor optical amplifiers

NASA Astrophysics Data System (ADS)

Kim, Jungho; Yu, Bong-Ahn

2015-03-01

We numerically investigate the effect of the wetting-layer (WL) density of states on the gain and phase recovery dynamics of quantum-dot semiconductor optical amplifiers in both electrical and optical pumping schemes by solving 1088 coupled rate equations. The temporal variations of the ultrafast gain and phase recovery responses at the ground state (GS) are calculated as a function of the WL density of states. The ultrafast gain recovery responses do not significantly depend on the WL density of states in the electrical pumping scheme and the three optical pumping schemes such as the optical pumping to the WL, the optical pumping to the excited state ensemble, and the optical pumping to the GS ensemble. The ultrafast phase recovery responses are also not significantly affected by the WL density of states except the optical pumping to the WL, where the phase recovery component caused by the WL becomes slowed down as the WL density of states increases.

Global hybrids from the semiclassical atom theory satisfying the local density linear response.

PubMed

Fabiano, Eduardo; Constantin, Lucian A; Cortona, Pietro; Della Sala, Fabio

2015-01-13

We propose global hybrid approximations of the exchange-correlation (XC) energy functional which reproduce well the modified fourth-order gradient expansion of the exchange energy in the semiclassical limit of many-electron neutral atoms and recover the full local density approximation (LDA) linear response. These XC functionals represent the hybrid versions of the APBE functional [Phys. Rev. Lett. 2011, 106, 186406] yet employing an additional correlation functional which uses the localization concept of the correlation energy density to improve the compatibility with the Hartree-Fock exchange as well as the coupling-constant-resolved XC potential energy. Broad energetic and structural testing, including thermochemistry and geometry, transition metal complexes, noncovalent interactions, gold clusters and small gold-molecule interfaces, as well as an analysis of the hybrid parameters, show that our construction is quite robust. In particular, our testing shows that the resulting hybrid, including 20% of Hartree-Fock exchange and named hAPBE, performs remarkably well for a broad palette of systems and properties, being generally better than popular hybrids (PBE0 and B3LYP). Semiempirical dispersion corrections are also provided.

Seabirds as indicators of marine food supplies: Cairns revisited

USGS Publications Warehouse

Piatt, John F.; Harding, Ann M.A.; Shultz, Michael T.; Speckman, Suzann G.; van Pelt, Thomas I.; Drew, Gary S.; Kettle, Arthur B.

2007-01-01

In his seminal paper about using seabirds as indicators of marine food supplies, Cairns (1987, Biol Oceanogr 5:261–271) predicted that (1) parameters of seabird biology and behavior would vary in curvilinear fashion with changes in food supply, (2) the threshold of prey density over which birds responded would be different for each parameter, and (3) different seabird species would respond differently to variation in food availability depending on foraging behavior and ability to adjust time budgets. We tested these predictions using data collected at colonies of common murre Uria aalge and black-legged kittiwake Rissa tridactyla in Cook Inlet, Alaska. (1) Of 22 seabird responses fitted with linear and non-linear functions, 16 responses exhibited significant curvilinear shapes, and Akaike’s information criterion (AIC) analysis indicated that curvilinear functions provided the best-fitting model for 12 of those. (2) However, there were few differences among parameters in their threshold to prey density, presumably because most responses ultimately depend upon a single threshold for prey acquisition at sea. (3) There were similarities and some differences in how species responded to variability in prey density. Both murres and kittiwakes minimized variability (CV < 15%) in their own body condition and growth of chicks in the face of high annual variability (CV = 69%) in local prey density. Whereas kittiwake breeding success (CV = 63%, r2 = 0.89) reflected prey variability, murre breeding success did not (CV = 29%, r2< 0.00). It appears that murres were able to buffer breeding success by reallocating discretionary ‘loafing’ time to foraging effort in response (r2 = 0.64) to declining prey density. Kittiwakes had little or no discretionary time, so fledging success was a more direct function of local prey density. Implications of these results for using ‘seabirds as indicators’ are discussed.

Non-linear feeding functional responses in the Greater Flamingo (Phoenicopterus roseus) predict immediate negative impact of wetland degradation on this flagship species

PubMed Central

Deville, Anne-Sophie; Grémillet, David; Gauthier-Clerc, Michel; Guillemain, Matthieu; Von Houwald, Friederike; Gardelli, Bruno; Béchet, Arnaud

2013-01-01

Accurate knowledge of the functional response of predators to prey density is essential for understanding food web dynamics, to parameterize mechanistic models of animal responses to environmental change, and for designing appropriate conservation measures. Greater flamingos (Phoenicopterus roseus), a flagship species of Mediterranean wetlands, primarily feed on Artemias (Artemia spp.) in commercial salt pans, an industry which may collapse for economic reasons. Flamingos also feed on alternative prey such as Chironomid larvae (e.g., Chironomid spp.) and rice seeds (Oryza sativa). However, the profitability of these food items for flamingos remains unknown. We determined the functional responses of flamingos feeding on Artemias, Chironomids, or rice. Experiments were conducted on 11 captive flamingos. For each food item, we offered different ranges of food densities, up to 13 times natural abundance. Video footage allowed estimating intake rates. Contrary to theoretical predictions for filter feeders, intake rates did not increase linearly with increasing food density (type I). Intake rates rather increased asymptotically with increasing food density (type II) or followed a sigmoid shape (type III). Hence, flamingos were not able to ingest food in direct proportion to their abundance, possibly because of unique bill structure resulting in limited filtering capabilities. Overall, flamingos foraged more efficiently on Artemias. When feeding on Chironomids, birds had lower instantaneous rates of food discovery and required more time to extract food from the sediment and ingest it, than when filtering Artemias from the water column. However, feeding on rice was energetically more profitable for flamingos than feeding on Artemias or Chironomids, explaining their attraction for rice fields. Crucially, we found that food densities required for flamingos to reach asymptotic intake rates are rarely met under natural conditions. This allows us to predict an immediate negative effect of any decrease in prey density upon flamingo foraging performance. PMID:23762525

Semi-local machine-learned kinetic energy density functional with third-order gradients of electron density

NASA Astrophysics Data System (ADS)

Seino, Junji; Kageyama, Ryo; Fujinami, Mikito; Ikabata, Yasuhiro; Nakai, Hiromi

2018-06-01

A semi-local kinetic energy density functional (KEDF) was constructed based on machine learning (ML). The present scheme adopts electron densities and their gradients up to third-order as the explanatory variables for ML and the Kohn-Sham (KS) kinetic energy density as the response variable in atoms and molecules. Numerical assessments of the present scheme were performed in atomic and molecular systems, including first- and second-period elements. The results of 37 conventional KEDFs with explicit formulae were also compared with those of the ML KEDF with an implicit formula. The inclusion of the higher order gradients reduces the deviation of the total kinetic energies from the KS calculations in a stepwise manner. Furthermore, our scheme with the third-order gradient resulted in the closest kinetic energies to the KS calculations out of the presented functionals.

A recipe for free-energy functionals of polarizable molecular fluids

NASA Astrophysics Data System (ADS)

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Arias, T. A.

2014-04-01

Classical density-functional theory is the most direct approach to equilibrium structures and free energies of inhomogeneous liquids, but requires the construction of an approximate free-energy functional for each liquid of interest. We present a general recipe for constructing functionals for small-molecular liquids based only on bulk experimental properties and ab initio calculations of a single solvent molecule. This recipe combines the exact free energy of the non-interacting system with fundamental measure theory for the repulsive contribution and a weighted density functional for the short-ranged attractive interactions. We add to these ingredients a weighted polarization functional for the long-range correlations in both the rotational and molecular-polarizability contributions to the dielectric response. We also perform molecular dynamics calculations for the free energy of cavity formation and the high-field dielectric response, and show that our free-energy functional adequately describes these properties (which are key for accurate solvation calculations) for all three solvents in our study: water, chloroform, and carbon tetrachloride.

Finite-temperature dynamics of the Mott insulating Hubbard chain

NASA Astrophysics Data System (ADS)

Nocera, Alberto; Essler, Fabian H. L.; Feiguin, Adrian E.

2018-01-01

We study the dynamical response of the half-filled one-dimensional Hubbard model for a range of interaction strengths U and temperatures T by a combination of numerical and analytical techniques. Using time-dependent density matrix renormalization group computations we find that the single-particle spectral function undergoes a crossover to a spin-incoherent Luttinger liquid regime at temperatures T ˜J =4 t2/U for sufficiently large U >4 t . At smaller values of U and elevated temperatures the spectral function is found to exhibit two thermally broadened bands of excitations, reminiscent of what is found in the Hubbard-I approximation. The dynamical density-density response function is shown to exhibit a finite-temperature resonance at low frequencies inside the Mott gap, with a physical origin similar to the Villain mode in gapped quantum spin chains. We complement our numerical computations by developing an analytic strong-coupling approach to the low-temperature dynamics in the spin-incoherent regime.

Unveiling the nature of post-linear response Z-vector method for time-dependent density functional theory.

PubMed

Pastore, Mariachiara; Assfeld, Xavier; Mosconi, Edoardo; Monari, Antonio; Etienne, Thibaud

2017-07-14

We report a theoretical study on the analysis of the relaxed one-particle difference density matrix characterizing the passage from the ground to the excited state of a molecular system, as obtained from time-dependent density functional theory. In particular, this work aims at using the physics contained in the so-called Z-vector, which differentiates between unrelaxed and relaxed difference density matrices to analyze excited states' nature. For this purpose, we introduce novel quantum-mechanical quantities, based on the detachment/attachment methodology, for analysing the Z-vector transformation for different molecules and density functional theory functionals. A derivation pathway of these novel descriptors is reported, involving a numerical integration to be performed in the Euclidean space on the density functions. This topological analysis is then applied to two sets of chromophores, and the correlation between the level of theory and the behavior of our descriptors is properly rationalized. In particular, the effect of range-separation on the relaxation amplitude is discussed. The relaxation term is finally shown to be system-specific (for a given level of theory) and independent of the number of electrons (i.e., the relaxation amplitude is not simply the result of a collective phenomenon).

Excited State Studies of Polyacenes Using the All-Order Constricted Variational Density Functional Theory with Orbital Relaxation.

PubMed

Senn, Florian; Krykunov, Mykhaylo

2015-10-22

For the polyacenes series from naphthalene to hexacene, we present the vertical singlet excitation energies 1 (1)La and 1 (1)Lb, as well as the first triplet excitation energies obtained by the all-order constricted variational density functional theory with orbital relaxation (R-CV(∞)-DFT). R-CV(∞)-DFT is a further development of variational density functional theory (CV(∞)-DFT), which has already been successfully applied for the calculation of the vertical singlet excitation energies (1)La and (1)Lb for polyacenes,15 and we show that one obtains consistent excitation energies using the local density approximation as a functional for singlet as well as for triplet excitations when going beyond the linear response theory. Furthermore, we apply self-consistent field density functional theory (ΔSCF-DFT) and compare the obtained excitation energies for the first triplet excitations T1, where, due to the character of the transition, ΔSCF-DFT and R-CV(∞)-DFT become numerically equivalent, and for the singlet excitations 1 (1)La and 1 (1)Lb, where the two methods differ.

Detectability of auditory signals presented without defined observation intervals

NASA Technical Reports Server (NTRS)

Watson, C. S.; Nichols, T. L.

1976-01-01

Ability to detect tones in noise was measured without defined observation intervals. Latency density functions were estimated for the first response following a signal and, separately, for the first response following randomly distributed instances of background noise. Detection performance was measured by the maximum separation between the cumulative latency density functions for signal-plus-noise and for noise alone. Values of the index of detectability, estimated by this procedure, were approximately those obtained with a 2-dB weaker signal and defined observation intervals. Simulation of defined- and non-defined-interval tasks with an energy detector showed that this device performs very similarly to the human listener in both cases.

On the Gause predator-prey model with a refuge: a fresh look at the history.

PubMed

Křivan, Vlastimil

2011-04-07

This article re-analyses a prey-predator model with a refuge introduced by one of the founders of population ecology Gause and his co-workers to explain discrepancies between their observations and predictions of the Lotka-Volterra prey-predator model. They replaced the linear functional response used by Lotka and Volterra by a saturating functional response with a discontinuity at a critical prey density. At concentrations below this critical density prey were effectively in a refuge while at a higher densities they were available to predators. Thus, their functional response was of the Holling type III. They analyzed this model and predicted existence of a limit cycle in predator-prey dynamics. In this article I show that their model is ill posed, because trajectories are not well defined. Using the Filippov method, I define and analyze solutions of the Gause model. I show that depending on parameter values, there are three possibilities: (1) trajectories converge to a limit cycle, as predicted by Gause, (2) trajectories converge to an equilibrium, or (3) the prey population escapes predator control and grows to infinity. Copyright © 2011 Elsevier Ltd. All rights reserved.

Metabolites related to renal function, immune activation, and carbamylation are associated with muscle composition in older adults.

PubMed

Lustgarten, Michael S; Fielding, Roger A

2017-12-15

Reduced skeletal muscle density in older adults is associated with insulin resistance, decreased physical function, and an increased all-cause mortality risk. To elucidate mechanisms that may underlie the maintenance of skeletal muscle density, we conducted a secondary analysis of previously published muscle composition and serum metabolomic data in 73 older adults (average age, 78y). Multivariable-adjusted linear regression was used to examine associations between 321 metabolites with muscle composition, defined as the ratio between normal density (NDM) with low density (LDM) thigh muscle cross sectional area (NDM/LDM). Sixty metabolites were significantly (p≤0.05 and q<0.30) associated with NDM/LDM. Decreased renal function and the immune response have been previously linked with reduced muscle density, but the mechanisms underlying these connections are less clear. Metabolites that were significantly associated with muscle composition were then tested for their association with circulating markers of renal function (blood urea nitrogen, creatinine, uric acid), and with the immune response (neutrophils/lymphocytes) and activation (kynurenine/tryptophan). 43 significant NDM/LDM metabolites (including urea) were co-associated with at least 1 marker of renal function; 23 of these metabolites have been previously identified as uremic solutes. The neutrophil/lymphocyte ratio was significantly associated with NDM/LDM (β±SE: -0.3±0.1, p=0.01, q=0.04). 35 significant NDM/LDM metabolites were co-associated with immune activation. Carbamylation (defined as homocitrulline/lysine) was identified as a pathway that may link renal function and immune activation with muscle composition, as 29 significant NDM/LDM metabolites were co-associated with homocitrulline/lysine, with at least 2 markers of renal function, and with kynurenine/tryptophan. When considering that elevated urea and uremic metabolites have been linked with an increased systemic microbial burden, that antimicrobial defense can be reduced in the presence of carbamylation, and that adipocytes can promote host defense, we propose the novel hypothesis that the age-related increase in adipogenesis within muscle may be a compensatory antimicrobial response to protect against an elevated microbial burden. Copyright © 2017 Elsevier Inc. All rights reserved.

Human self-control and the density of reinforcement

PubMed Central

Flora, Stephen R.; Pavlik, William B.

1992-01-01

Choice responding in adult humans on a discrete-trial button-pressing task was examined as a function of amount, delay, and overall density (points per unit time) of reinforcement. Reinforcement consisted of points that were exchangeable for money. In T 0 conditions, an impulsive response produced 4 points immediately and a self-control response produced 10 points after a delay of 15 s. In T 15 conditions, a constant delay of 15 s was added to both prereinforcer delays. Postreinforcer delays, which consisted of 15 s added to the end of each impulsive trial, equated trial durations regardless of choice, and was manipulated in both T 0 and T 15 conditions. In all conditions, choice was predicted directly from the relative reinforcement densities of the alternatives. Self-control was observed in all conditions except T 0 without postreinforcer delays, where the impulsive choices produced the higher reinforcement density. These results support previous studies showing that choice is a direct function of the relative reinforcement densities when conditioned (point) reinforcers are used. In contrast, where responding produces intrinsic (immediately consumable) reinforcers, immediacy of reinforcement appears to account for preference when density does not. PMID:16812652

Cell size and wall dimensions drive distinct variability of earlywood and latewood density in Northern Hemisphere conifers.

PubMed

Björklund, Jesper; Seftigen, Kristina; Schweingruber, Fritz; Fonti, Patrick; von Arx, Georg; Bryukhanova, Marina V; Cuny, Henri E; Carrer, Marco; Castagneri, Daniele; Frank, David C

2017-11-01

Interannual variability of wood density - an important plant functional trait and environmental proxy - in conifers is poorly understood. We therefore explored the anatomical basis of density. We hypothesized that earlywood density is determined by tracheid size and latewood density by wall dimensions, reflecting their different functional tasks. To determine general patterns of variability, density parameters from 27 species and 349 sites across the Northern Hemisphere were correlated to tree-ring width parameters and local climate. We performed the same analyses with density and width derived from anatomical data comprising two species and eight sites. The contributions of tracheid size and wall dimensions to density were disentangled with sensitivity analyses. Notably, correlations between density and width shifted from negative to positive moving from earlywood to latewood. Temperature responses of density varied intraseasonally in strength and sign. The sensitivity analyses revealed tracheid size as the main determinant of earlywood density, while wall dimensions become more influential for latewood density. Our novel approach of integrating detailed anatomical data with large-scale tree-ring data allowed us to contribute to an improved understanding of interannual variations of conifer growth and to illustrate how conifers balance investments in the competing xylem functions of hydraulics and mechanical support. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Solvatochromic shifts from coupled-cluster theory embedded in density functional theory

NASA Astrophysics Data System (ADS)

Höfener, Sebastian; Gomes, André Severo Pereira; Visscher, Lucas

2013-09-01

Building on the framework recently reported for determining general response properties for frozen-density embedding [S. Höfener, A. S. P. Gomes, and L. Visscher, J. Chem. Phys. 136, 044104 (2012)], 10.1063/1.3675845, in this work we report a first implementation of an embedded coupled-cluster in density-functional theory (CC-in-DFT) scheme for electronic excitations, where only the response of the active subsystem is taken into account. The formalism is applied to the calculation of coupled-cluster excitation energies of water and uracil in aqueous solution. We find that the CC-in-DFT results are in good agreement with reference calculations and experimental results. The accuracy of calculations is mainly sensitive to factors influencing the correlation treatment (basis set quality, truncation of the cluster operator) and to the embedding treatment of the ground-state (choice of density functionals). This allows for efficient approximations at the excited state calculation step without compromising the accuracy. This approximate scheme makes it possible to use a first principles approach to investigate environment effects with specific interactions at coupled-cluster level of theory at a cost comparable to that of calculations of the individual subsystems in vacuum.

Observation of self-regulating response in Li xM yMn 2-yO 4 (M=Mn, Ni): A study using density functional theory

NASA Astrophysics Data System (ADS)

Ragavendran, K.; Sherwood, Daniel; Emmanuel, Bosco

2009-02-01

Density functional theory is used to understand the response of the transition metal-oxygen octahedra in Li xMn 2O 4 and Li xNi 0.5Mn 1.5O 4 to lithium intercalation and de-intercalation. Electronic structure computations on these compounds for x=0, 0.5 and 1 indicate that the 3d DOS of Mn is almost unaffected to variations in x. On the other hand, the oxygen 2p-DOS and to a lesser extent Ni 3d DOS are found to be sensitive to perturbation. The observations are explained on the grounds of self-regulating response, characteristic of systems having localized d states that communicate with a covalent manifold.

Simulation-based Bayesian inference for latent traits of item response models: Introduction to the ltbayes package for R.

PubMed

Johnson, Timothy R; Kuhn, Kristine M

2015-12-01

This paper introduces the ltbayes package for R. This package includes a suite of functions for investigating the posterior distribution of latent traits of item response models. These include functions for simulating realizations from the posterior distribution, profiling the posterior density or likelihood function, calculation of posterior modes or means, Fisher information functions and observed information, and profile likelihood confidence intervals. Inferences can be based on individual response patterns or sets of response patterns such as sum scores. Functions are included for several common binary and polytomous item response models, but the package can also be used with user-specified models. This paper introduces some background and motivation for the package, and includes several detailed examples of its use.

The response analysis of fractional-order stochastic system via generalized cell mapping method.

PubMed

Wang, Liang; Xue, Lili; Sun, Chunyan; Yue, Xiaole; Xu, Wei

2018-01-01

This paper is concerned with the response of a fractional-order stochastic system. The short memory principle is introduced to ensure that the response of the system is a Markov process. The generalized cell mapping method is applied to display the global dynamics of the noise-free system, such as attractors, basins of attraction, basin boundary, saddle, and invariant manifolds. The stochastic generalized cell mapping method is employed to obtain the evolutionary process of probability density functions of the response. The fractional-order ϕ 6 oscillator and the fractional-order smooth and discontinuous oscillator are taken as examples to give the implementations of our strategies. Studies have shown that the evolutionary direction of the probability density function of the fractional-order stochastic system is consistent with the unstable manifold. The effectiveness of the method is confirmed using Monte Carlo results.

Stochastic response and bifurcation of periodically driven nonlinear oscillators by the generalized cell mapping method

NASA Astrophysics Data System (ADS)

Han, Qun; Xu, Wei; Sun, Jian-Qiao

2016-09-01

The stochastic response of nonlinear oscillators under periodic and Gaussian white noise excitations is studied with the generalized cell mapping based on short-time Gaussian approximation (GCM/STGA) method. The solutions of the transition probability density functions over a small fraction of the period are constructed by the STGA scheme in order to construct the GCM over one complete period. Both the transient and steady-state probability density functions (PDFs) of a smooth and discontinuous (SD) oscillator are computed to illustrate the application of the method. The accuracy of the results is verified by direct Monte Carlo simulations. The transient responses show the evolution of the PDFs from being Gaussian to non-Gaussian. The effect of a chaotic saddle on the stochastic response is also studied. The stochastic P-bifurcation in terms of the steady-state PDFs occurs with the decrease of the smoothness parameter, which corresponds to the deterministic pitchfork bifurcation.

Intraspecific Relationships among Wood Density, Leaf Structural Traits and Environment in Four Co-Occurring Species of Nothofagus in New Zealand

PubMed Central

Richardson, Sarah J.; Allen, Robert B.; Buxton, Rowan P.; Easdale, Tomás A.; Hurst, Jennifer M.; Morse, Christopher W.; Smissen, Rob D.; Peltzer, Duane A.

2013-01-01

Plant functional traits capture important variation in plant strategy and function. Recent literature has revealed that within-species variation in traits is greater than previously supposed. However, we still have a poor understanding of how intraspecific variation is coordinated among different traits, and how it is driven by environment. We quantified intraspecific variation in wood density and five leaf traits underpinning the leaf economics spectrum (leaf dry matter content, leaf mass per unit area, size, thickness and density) within and among four widespread Nothofagus tree species in southern New Zealand. We tested whether intraspecific relationships between wood density and leaf traits followed widely reported interspecific relationships, and whether variation in these traits was coordinated through shared responses to environmental factors. Sample sites varied widely in environmental variables, including soil fertility (25–900 mg kg–1 total P), precipitation (668–4875 mm yr–1), temperature (5.2–12.4 °C mean annual temperature) and latitude (41–46 °S). Leaf traits were strongly correlated with one another within species, but not with wood density. There was some evidence for a positive relationship between wood density and leaf tissue density and dry matter content, but no evidence that leaf mass or leaf size were correlated with wood density; this highlights that leaf mass per unit area cannot be used as a surrogate for component leaf traits such as tissue density. Trait variation was predicted by environmental factors, but not consistently among different traits; e.g., only leaf thickness and leaf density responded to the same environmental cues as wood density. We conclude that although intraspecific variation in wood density and leaf traits is strongly driven by environmental factors, these responses are not strongly coordinated among functional traits even across co-occurring, closely-related plant species. PMID:23527041

Friedel oscillation near a van Hove singularity in two-dimensional Dirac materials

NASA Astrophysics Data System (ADS)

Lu, Chi-Ken

2016-02-01

We consider Friedel oscillation in the two-dimensional Dirac materials when the Fermi level is near the van Hove singularity. Twisted graphene bilayer and the surface state of topological crystalline insulator are the representative materials which show low-energy saddle points that are feasible to probe by gating. We approximate the Fermi surface near saddle point with a hyperbola and calculate the static Lindhard response function. Employing a theorem of Lighthill, the induced charge density δ n due to an impurity is obtained and the algebraic decay of δ n is determined by the singularity of the static response function. Although a hyperbolic Fermi surface is rather different from a circular one, the static Lindhard response function in the present case shows a singularity similar with the response function associated with circular Fermi surface, which leads to the δ n\\propto {{R}-2} at large distance R. The dependences of charge density on the Fermi energy are different. Consequently, it is possible to observe in twisted graphene bilayer the evolution that δ n\\propto {{R}-3} near Dirac point changes to δ n\\propto {{R}-2} above the saddle point. Measurements using scanning tunnelling microscopy around the impurity sites could verify the prediction.

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

Yanai, Takeshi; Fann, George I.; Beylkin, Gregory

Using the fully numerical method for time-dependent Hartree–Fock and density functional theory (TD-HF/DFT) with the Tamm–Dancoff (TD) approximation we use a multiresolution analysis (MRA) approach to present our findings. From a reformulation with effective use of the density matrix operator, we obtain a general form of the HF/DFT linear response equation in the first quantization formalism. It can be readily rewritten as an integral equation with the bound-state Helmholtz (BSH) kernel for the Green's function. The MRA implementation of the resultant equation permits excited state calculations without virtual orbitals. Moreover, the integral equation is efficiently and adaptively solved using amore » numerical multiresolution solver with multiwavelet bases. Our implementation of the TD-HF/DFT methods is applied for calculating the excitation energies of H 2, Be, N 2, H 2O, and C 2H 4 molecules. The numerical errors of the calculated excitation energies converge in proportion to the residuals of the equation in the molecular orbitals and response functions. The energies of the excited states at a variety of length scales ranging from short-range valence excitations to long-range Rydberg-type ones are consistently accurate. It is shown that the multiresolution calculations yield the correct exponential asymptotic tails for the response functions, whereas those computed with Gaussian basis functions are too diffuse or decay too rapidly. Finally, we introduce a simple asymptotic correction to the local spin-density approximation (LSDA) so that in the TDDFT calculations, the excited states are correctly bound.« less

Opiates and cerebral functional activity in rats

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

Trusk, T.C.

1986-01-01

Cerebral activity was measured using the free-fatty acid (1-/sup 14/C) octanoate as a fast functional tracer in conscious, unrestrained rats 5 minutes after intravenous injection of heroin, cocaine or saline vehicle. Regional changes of octanoate labeling density in the autoradiograms relative to saline-injected animals were used to determine the functional activity effects of each drug. Heroin and cocaine each produced a distinctive pattern of activity increases and suppression throughout the rat brain. Similar regional changes induced by both drugs were found in limbic brain regions implicated in drug reinforcement. Labeled octanoate autoradiography was used to measure the cerebral functional responsemore » to a tone that had previously been paired to heroin injections. Rats were trained in groups of three consisting of one heroin self-administration animal, and two animals receiving yoked infusion of heroin or saline. A tone was paired with each infusion during training. Behavioral experiments in similarly trained rats demonstrated that these training conditions impart secondary reinforcing properties to the tone in animals previously self-administering heroin, while the tone remains behaviorally neutral in yoked-infusion rats. Cerebral functional activity was measured during presentation of the tone without drug infusion. Octanoate labeling density changed in fifteen brain areas in response to the tone previously paired to heroin without response contingency. Labeling density was significantly modified in sixteen regions as a result of previously pairing the tone to response-contingent heroin infusions.« less

Kohn-Sham potentials from electron densities using a matrix representation within finite atomic orbital basis sets

NASA Astrophysics Data System (ADS)

Zhang, Xing; Carter, Emily A.

2018-01-01

We revisit the static response function-based Kohn-Sham (KS) inversion procedure for determining the KS effective potential that corresponds to a given target electron density within finite atomic orbital basis sets. Instead of expanding the potential in an auxiliary basis set, we directly update the potential in its matrix representation. Through numerical examples, we show that the reconstructed density rapidly converges to the target density. Preliminary results are presented to illustrate the possibility of obtaining a local potential in real space from the optimized potential in its matrix representation. We have further applied this matrix-based KS inversion approach to density functional embedding theory. A proof-of-concept study of a solvated proton transfer reaction demonstrates the method's promise.

Response of the Shockley surface state to an external electrical field: A density-functional theory study of Cu(111)

NASA Astrophysics Data System (ADS)

Berland, K.; Einstein, T. L.; Hyldgaard, P.

2012-01-01

The response of the Cu(111) Shockley surface state to an external electrical field is characterized by combining a density-functional theory calculation for a slab geometry with an analysis of the Kohn-Sham wave functions. Our analysis is facilitated by a decoupling of the Kohn-Sham states via a rotation in Hilbert space. We find that the surface state displays isotropic dispersion, quadratic until the Fermi wave vector but with a significant quartic contribution beyond. We calculate the shift in energetic position and effective mass of the surface state for an electrical field perpendicular to the Cu(111) surface; the response is linear over a broad range of field strengths. We find that charge transfer occurs beyond the outermost copper atoms and that accumulation of electrons is responsible for a quarter of the screening of the electrical field. This allows us to provide well converged determinations of the field-induced changes in the surface state for a moderate number of layers in the slab geometry.

Electron correlation and the self-interaction error of density functional theory

NASA Astrophysics Data System (ADS)

Polo, Victor; Kraka, Elfi; Cremer, Dieter

The self-interaction error (SIE) of commonly used DFT functionals has been systematically investigated by comparing the electron density distribution ρ( r ) generated by self-interaction corrected DFT (SIC-DFT) with a series of reference densities obtained by DFT or wavefunction theory (WFT) methods that cover typical electron correlation effects. Although the SIE of GGA functionals is considerably smaller than that of LDA functionals, it has significant consequences for the coverage of electron correlation effects at the DFT level of theory. The exchange SIE mimics long range (non-dynamic) pair correlation effects, and is responsible for the fact that the electron density of DFT exchange-only calculations resembles often that of MP4, MP2 or even CCSD(T) calculations. Changes in the electron density caused by SICDFT exchange are comparable with those that are associated with HF exchange. Correlation functionals contract the density towards the bond and the valence region, thus taking negative charge out of the van der Waals region where these effects are exaggerated by the influence of the SIE of the correlation functional. Hence, SIC-DFT leads in total to a relatively strong redistribution of negative charge from van der Waals, non-bonding, and valence regions of heavy atoms to the bond regions. These changes, although much stronger, resemble those obtained when comparing the densities of hybrid functionals such as B3LYP with the corresponding GGA functional BLYP. Hence, the balanced mixing of local and non-local exchange and correlation effects as it is achieved by hybrid functionals mimics SIC-DFT and can be considered as an economic way to include some SIC into standard DFT. However, the investigation shows also that the SIC-DFT description of molecules is unreliable because the standard functionals used were optimized for DFT including the SIE.

Functional response and population dynamics for fighting predator, based on activity distribution.

PubMed

Garay, József; Varga, Zoltán; Gámez, Manuel; Cabello, Tomás

2015-03-07

The classical Holling type II functional response, describing the per capita predation as a function of prey density, was modified by Beddington and de Angelis to include interference of predators that increases with predator density and decreases the number of killed prey. In the present paper we further generalize the Beddington-de Angelis functional response, considering that all predator activities (searching and handling prey, fight and recovery) have time duration, the probabilities of predator activities depend on the encounter probabilities, and hence on the prey and predator abundance, too. Under these conditions, the aim of the study is to introduce a functional response for fighting the predator and to analyse the corresponding dynamics, when predator-predator-prey encounters also occur. From this general approach, the Holling type functional responses can also be obtained as particular cases. In terms of the activity distribution, we give biologically interpretable sufficient conditions for stable coexistence. We consider two-individual (predator-prey) and three-individual (predator-predator-prey) encounters. In the three-individual encounter model there is a relatively higher fighting rate and a lower killing rate. Using numerical simulation, we surprisingly found that when the intrinsic prey growth rate and the conversion rate are small enough, the equilibrium predator abundance is higher in the three-individual encounter case. The above means that, when the equilibrium abundance of the predator is small, coexistence appears first in the three-individual encounter model. Copyright © 2014 Elsevier Ltd. All rights reserved.

FDE-vdW: A van der Waals inclusive subsystem density-functional theory.

PubMed

Kevorkyants, Ruslan; Eshuis, Henk; Pavanello, Michele

2014-07-28

We present a formally exact van der Waals inclusive electronic structure theory, called FDE-vdW, based on the Frozen Density Embedding formulation of subsystem Density-Functional Theory. In subsystem DFT, the energy functional is composed of subsystem additive and non-additive terms. We show that an appropriate definition of the long-range correlation energy is given by the value of the non-additive correlation functional. This functional is evaluated using the fluctuation-dissipation theorem aided by a formally exact decomposition of the response functions into subsystem contributions. FDE-vdW is derived in detail and several approximate schemes are proposed, which lead to practical implementations of the method. We show that FDE-vdW is Casimir-Polder consistent, i.e., it reduces to the generalized Casimir-Polder formula for asymptotic inter-subsystems separations. Pilot calculations of binding energies of 13 weakly bound complexes singled out from the S22 set show a dramatic improvement upon semilocal subsystem DFT, provided that an appropriate exchange functional is employed. The convergence of FDE-vdW with basis set size is discussed, as well as its dependence on the choice of associated density functional approximant.

FDE-vdW: A van der Waals inclusive subsystem density-functional theory

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

Kevorkyants, Ruslan; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu; Eshuis, Henk

2014-07-28

We present a formally exact van der Waals inclusive electronic structure theory, called FDE-vdW, based on the Frozen Density Embedding formulation of subsystem Density-Functional Theory. In subsystem DFT, the energy functional is composed of subsystem additive and non-additive terms. We show that an appropriate definition of the long-range correlation energy is given by the value of the non-additive correlation functional. This functional is evaluated using the fluctuation–dissipation theorem aided by a formally exact decomposition of the response functions into subsystem contributions. FDE-vdW is derived in detail and several approximate schemes are proposed, which lead to practical implementations of the method.more » We show that FDE-vdW is Casimir-Polder consistent, i.e., it reduces to the generalized Casimir-Polder formula for asymptotic inter-subsystems separations. Pilot calculations of binding energies of 13 weakly bound complexes singled out from the S22 set show a dramatic improvement upon semilocal subsystem DFT, provided that an appropriate exchange functional is employed. The convergence of FDE-vdW with basis set size is discussed, as well as its dependence on the choice of associated density functional approximant.« less

Nonlinear viscoelastic response of highly filled elastomers under multiaxial finite deformation

NASA Technical Reports Server (NTRS)

Peng, Steven T. J.; Landel, Robert F.

1990-01-01

A biaxial tester was used to obtain precise biaxial stress responses of highly filled, high strain capability elastomers. Stress-relaxation experiments show that the time-dependent part of the relaxation response can be reasonably approximated by a function which is strain and biaxiality independent. Thus, isochronal data from the stress-relaxation curves can be used to determine the stored energy density function. The complex behavior of the elastomers under biaxial deformation may be caused by dewetting.

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

PubMed

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

2013-01-01

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

Shapes matter: examining the optical response evolution in stretched aluminium nanoparticles via time-dependent density functional theory.

PubMed

Mokkath, Junais Habeeb

2017-12-20

Using first-principles time-dependent density functional theory calculations, we investigate the shape-anisotropy effects on the optical response of a spherical aluminium nanoparticle subjected to a stretching process in different directions. Progressively increased stretching in one direction resulted in prolate spheroid (nanorice) geometries and produced a couple of well-distinguishable dominant peaks together with some satellite peaks in the UV-visible region of the electromagnetic spectrum. On the other hand, progressively increased stretching in two directions caused multiple peaks to appear in the UV-visible region of the electromagnetic spectrum. We believe that our findings can be beneficial for the emerging and potentially far-reaching field of aluminum plasmonics.

Energy-density field approach for low- and medium-frequency vibroacoustic analysis of complex structures using a statistical computational model

NASA Astrophysics Data System (ADS)

Kassem, M.; Soize, C.; Gagliardini, L.

2009-06-01

In this paper, an energy-density field approach applied to the vibroacoustic analysis of complex industrial structures in the low- and medium-frequency ranges is presented. This approach uses a statistical computational model. The analyzed system consists of an automotive vehicle structure coupled with its internal acoustic cavity. The objective of this paper is to make use of the statistical properties of the frequency response functions of the vibroacoustic system observed from previous experimental and numerical work. The frequency response functions are expressed in terms of a dimensionless matrix which is estimated using the proposed energy approach. Using this dimensionless matrix, a simplified vibroacoustic model is proposed.

Characteristics of cesium iodide for use as a particle discriminator for high energy cosmic rays

NASA Technical Reports Server (NTRS)

Crannell, C. J.; Kurz, R. J.; Viehmann, W.

1973-01-01

The possible use of CsI to discriminate between high energy cosmic ray electrons and interacting protons has been investigated. The pulse-shape properties as a function of ionization density, temperature, and spectral response are presented for thallium-activated CsI and as a function of ionization density for sodium-activated CsI. The results are based on previously published data and on corroborative measurements from the present work. Experimental results on the response of CsI to electron-induced electromagnetic cascades and to interacting hadrons are described. Bibliographies of publications dealing with the properties of CsI and with pulse-shape discrimination techniques are presented.

Tree mortality across biomes is promoted by drought intensity, lower wood density and higher specific leaf area

USGS Publications Warehouse

Greenwood, Sarah; Ruiz-Benito, Paloma; Martinez-Vilalta, Jordi; Lloret, Francisco; Kitzberger, Thomas; Allen, Craig D.; Fensham, Rod; Laughlin, Daniel C.; Kattge, Jens; Bönisch, Gerhard; Kraft, Nathan J. B.; Jump, Alistair S.

2017-01-01

Drought events are increasing globally, and reports of consequent forest mortality are widespread. However, due to a lack of a quantitative global synthesis, it is still not clear whether drought-induced mortality rates differ among global biomes and whether functional traits influence the risk of drought-induced mortality. To address these uncertainties, we performed a global meta-analysis of 58 studies of drought-induced forest mortality. Mortality rates were modelled as a function of drought, temperature, biomes, phylogenetic and functional groups and functional traits. We identified a consistent global-scale response, where mortality increased with drought severity [log mortality (trees trees−1 year−1) increased 0.46 (95% CI = 0.2–0.7) with one SPEI unit drought intensity]. We found no significant differences in the magnitude of the response depending on forest biomes or between angiosperms and gymnosperms or evergreen and deciduous tree species. Functional traits explained some of the variation in drought responses between species (i.e. increased from 30 to 37% when wood density and specific leaf area were included). Tree species with denser wood and lower specific leaf area showed lower mortality responses. Our results illustrate the value of functional traits for understanding patterns of drought-induced tree mortality and suggest that mortality could become increasingly widespread in the future.

Tree mortality across biomes is promoted by drought intensity, lower wood density and higher specific leaf area.

PubMed

Greenwood, Sarah; Ruiz-Benito, Paloma; Martínez-Vilalta, Jordi; Lloret, Francisco; Kitzberger, Thomas; Allen, Craig D; Fensham, Rod; Laughlin, Daniel C; Kattge, Jens; Bönisch, Gerhard; Kraft, Nathan J B; Jump, Alistair S

2017-04-01

Drought events are increasing globally, and reports of consequent forest mortality are widespread. However, due to a lack of a quantitative global synthesis, it is still not clear whether drought-induced mortality rates differ among global biomes and whether functional traits influence the risk of drought-induced mortality. To address these uncertainties, we performed a global meta-analysis of 58 studies of drought-induced forest mortality. Mortality rates were modelled as a function of drought, temperature, biomes, phylogenetic and functional groups and functional traits. We identified a consistent global-scale response, where mortality increased with drought severity [log mortality (trees trees -1  year -1 ) increased 0.46 (95% CI = 0.2-0.7) with one SPEI unit drought intensity]. We found no significant differences in the magnitude of the response depending on forest biomes or between angiosperms and gymnosperms or evergreen and deciduous tree species. Functional traits explained some of the variation in drought responses between species (i.e. increased from 30 to 37% when wood density and specific leaf area were included). Tree species with denser wood and lower specific leaf area showed lower mortality responses. Our results illustrate the value of functional traits for understanding patterns of drought-induced tree mortality and suggest that mortality could become increasingly widespread in the future. © 2017 John Wiley & Sons Ltd/CNRS.

Evaluating the B-cell density with various activation functions using White Noise Path Integral Approach

NASA Astrophysics Data System (ADS)

Aban, C. J. G.; Bacolod, R. O.; Confesor, M. N. P.

2015-06-01

A The White Noise Path Integral Approach is used in evaluating the B-cell density or the number of B-cell per unit volume for a basic type of immune system response based on the modeling done by Perelson and Wiegel. From the scaling principles of Perelson [1], the B- cell density is obtained where antigens and antibodies mutates and activation function f(|S-SA|) is defined describing the interaction between a specific antigen and a B-cell. If the activation function f(|S-SA|) is held constant, the major form of the B-cell density evaluated using white noise analysis is similar to the form of the B-cell density obtained by Perelson and Wiegel using a differential approach.A piecewise linear functionis also used to describe the activation f(|S-SA|). If f(|S-SA|) is zero, the density decreases exponentially. If f(|S-SA|) = S-SA-SB, the B- cell density increases exponentially until it reaches a certain maximum value. For f(|S-SA|) = 2SA-SB-S, the behavior of B-cell density is oscillating and remains to be in small values.

Assessing Hubbard-corrected AM05+ U and PBEsol+ U density functionals for strongly correlated oxides CeO 2 and Ce 2O 3

DOE PAGES

Weck, Philippe F.; Kim, Eunja

2016-09-12

The structure–property relationships of bulk CeO 2 and Ce 2O 3 have been investigated using AM05 and PBEsol exchange–correlation functionals within the frameworks of Hubbard-corrected density functional theory (DFT+ U) and density functional perturbation theory (DFPT+ U). Compared with conventional PBE+ U, RPBE+ U, PW91+ U and LDA+ U functionals, AM05+ U and PBEsol+ U describe experimental crystalline parameters and properties of CeO 2 and Ce 2O 3 with superior accuracy, especially when + U is chosen close to its value derived by the linear-response approach. Lastly, the present findings call for a reexamination of some of the problematic oxidemore » materials featuring strong f- and d-electron correlation using AM05+ U and PBEsol+ U.« less

Assessing Hubbard-corrected AM05+ U and PBEsol+ U density functionals for strongly correlated oxides CeO 2 and Ce 2O 3

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

Weck, Philippe F.; Kim, Eunja

The structure–property relationships of bulk CeO 2 and Ce 2O 3 have been investigated using AM05 and PBEsol exchange–correlation functionals within the frameworks of Hubbard-corrected density functional theory (DFT+ U) and density functional perturbation theory (DFPT+ U). Compared with conventional PBE+ U, RPBE+ U, PW91+ U and LDA+ U functionals, AM05+ U and PBEsol+ U describe experimental crystalline parameters and properties of CeO 2 and Ce 2O 3 with superior accuracy, especially when + U is chosen close to its value derived by the linear-response approach. Lastly, the present findings call for a reexamination of some of the problematic oxidemore » materials featuring strong f- and d-electron correlation using AM05+ U and PBEsol+ U.« less

Time domain simulation of the response of geometrically nonlinear panels subjected to random loading

NASA Technical Reports Server (NTRS)

Moyer, E. Thomas, Jr.

1988-01-01

The response of composite panels subjected to random pressure loads large enough to cause geometrically nonlinear responses is studied. A time domain simulation is employed to solve the equations of motion. An adaptive time stepping algorithm is employed to minimize intermittent transients. A modified algorithm for the prediction of response spectral density is presented which predicts smooth spectral peaks for discrete time histories. Results are presented for a number of input pressure levels and damping coefficients. Response distributions are calculated and compared with the analytical solution of the Fokker-Planck equations. RMS response is reported as a function of input pressure level and damping coefficient. Spectral densities are calculated for a number of examples.

Plasmonic resonances of nanoparticles from large-scale quantum mechanical simulations

NASA Astrophysics Data System (ADS)

Zhang, Xu; Xiang, Hongping; Zhang, Mingliang; Lu, Gang

2017-09-01

Plasmonic resonance of metallic nanoparticles results from coherent motion of its conduction electrons, driven by incident light. For the nanoparticles less than 10 nm in diameter, localized surface plasmonic resonances become sensitive to the quantum nature of the conduction electrons. Unfortunately, quantum mechanical simulations based on time-dependent Kohn-Sham density functional theory are computationally too expensive to tackle metal particles larger than 2 nm. Herein, we introduce the recently developed time-dependent orbital-free density functional theory (TD-OFDFT) approach which enables large-scale quantum mechanical simulations of plasmonic responses of metallic nanostructures. Using TD-OFDFT, we have performed quantum mechanical simulations to understand size-dependent plasmonic response of Na nanoparticles and plasmonic responses in Na nanoparticle dimers and trimers. An outlook of future development of the TD-OFDFT method is also presented.

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.

Effect of altered reproductive function and lowered testosterone levels on bone density in male endurance athletes.

PubMed

Bennell, K L; Brukner, P D; Malcolm, S A

1996-09-01

It is apparent that bone density in male athletes can be reduced without a concomitant decrease in testosterone, suggesting that bone density and testosterone concentrations in the normal range are not closely related in male athletes. Further research is necessary to monitor concurrent changes in bone density and testosterone over a period of time in exercising males. In any case, the effect of exercise on the male reproductive system does not appear as extreme as that which can occur in female athletes, and any impact on bone density is not nearly as evident. These results imply that factors apart from testosterone concentrations must be responsible for the observed osteopenia in some male athletes. Many factors have the potential to adversely affect bone density, independently of alterations in reproductive function. These include low calcium intake, energy deficit, weight loss, psychological stress, and low body fat, all of which may be associated with intense endurance training. Future research investigating skeletal health in male athletes should include a thorough assessment of reproductive function in addition to these other factors.

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

PubMed

Abrams, Peter A

2009-09-01

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

Experimental evolution reveals differences between phenotypic and evolutionary responses to population density.

PubMed

McNamara, K B; Simmons, L W

2017-09-01

Group living can select for increased immunity, given the heightened risk of parasite transmission. Yet, it also may select for increased male reproductive investment, given the elevated risk of female multiple mating. Trade-offs between immunity and reproduction are well documented. Phenotypically, population density mediates both reproductive investment and immune function in the Indian meal moth, Plodia interpunctella. However, the evolutionary response of populations to these traits is unknown. We created two replicated populations of P. interpunctella, reared and mated for 14 generations under high or low population densities. These population densities cause plastic responses in immunity and reproduction: at higher numbers, both sexes invest more in one index of immunity [phenoloxidase (PO) activity] and males invest more in sperm. Interestingly, our data revealed divergence in PO and reproduction in a different direction to previously reported phenotypic responses. Males evolving at low population densities transferred more sperm, and both males and females displayed higher PO than individuals at high population densities. These positively correlated responses to selection suggest no apparent evolutionary trade-off between immunity and reproduction. We speculate that the reduced PO activity and sperm investment when evolving under high population density may be due to the reduced population fitness predicted under increased sexual conflict and/or to trade-offs between pre- and post-copulatory traits. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Prey and predator emigration responses in the acarine system Tetranychus urticae-Phytoseiulus persimilis.

PubMed

Bernstein, C

1984-01-01

Some of the processes that influence the emigration of prey and predatory mites from bean plants were investigated experimentally. The emigration of the prey depends on the damage they cause to the plants and on predator density. The predator's emigration rate is a decreasing function of prey density, and does not change (or it slightly decreases) when prey and predator numbers are increased maintaining the same prey/predator ratio. The probability of emigration of the predators is independent of their own density when prey are absent and density dependent when prey density is kep constant. Forty three per cent of the variability in the predator's instantaneous rate of emigration in the different experiments is accounted for by a two parameter negative exponential function of capture rate (number of prey eaten per predator and per unit of time).

Cell density dependence of Microcystis aeruginosa responses to copper algaecide concentrations: Implications for microcystin-LR release.

PubMed

Kinley, Ciera M; Iwinski, Kyla J; Hendrikse, Maas; Geer, Tyler D; Rodgers, John H

2017-11-01

Along with mechanistic models, predictions of exposure-response relationships for copper are often derived from laboratory toxicity experiments with standardized experimental exposures and conditions. For predictions of copper toxicity to algae, cell density is a critical factor often overlooked. For pulse exposures of copper-based algaecides in aquatic systems, cell density can significantly influence copper sorbed by the algal population, and consequent responses. A cyanobacterium, Microcystis aeruginosa, was exposed to a copper-based algaecide over a range of cell densities to model the density-dependence of exposures, and effects on microcystin-LR (MC-LR) release. Copper exposure concentrations were arrayed to result in a gradient of MC-LR release, and masses of copper sorbed to algal populations were measured following exposures. While copper exposure concentrations eliciting comparable MC-LR release ranged an order of magnitude (24-h EC50s 0.03-0.3mg Cu/L) among cell densities of 10 6 through 10 7 cells/mL, copper doses (mg Cu/mg algae) were similar (24-h EC50s 0.005-0.006mg Cu/mg algae). Comparisons of MC-LR release as a function of copper exposure concentrations and doses provided a metric of the density dependence of algal responses in the context of copper-based algaecide applications. Combined with estimates of other site-specific factors (e.g. water characteristics) and fate processes (e.g. dilution and dispersion, sorption to organic matter and sediments), measuring exposure-response relationships for specific cell densities can refine predictions for in situ exposures and algal responses. These measurements can in turn decrease the likelihood of amending unnecessary copper concentrations to aquatic systems, and minimize risks for non-target aquatic organisms. Copyright © 2017 Elsevier Inc. All rights reserved.

Experimental Investigation of Ultrafast Hydration Structure and Dynamics at Sub-Angstrom Lengthscales

ERIC Educational Resources Information Center

Coridan, Robert Henry

2009-01-01

This thesis outlines how meV-resolution inelastic x-ray scattering and causality-enforcing mathematics can be used to measure the dynamical density-density linear response function for liquid water with Angstrom spatial resolution and 50fs temporal resolution. The results are compared to high-resolution spectroscopic and scattering experiments and…

Single and double photoemission and generalizations

NASA Astrophysics Data System (ADS)

Pavlyukh, Yaroslav

2016-03-01

A unified diagrammatic treatment of single and double electron photoemission currents is presented. The irreducible lesser density-density response function is the starting point of these derivations. Diagrams for higher order processes in which several electrons are observed in coincidence can likewise be obtained. For physically relevant situations, in which the photoemission cross-section can be written as the Fermi Golden rule, the diagrams from the nonequilibrium Green's function approach can be put in direct correspondence with the diagrams of the scattering theory.

Serenity: A subsystem quantum chemistry program.

PubMed

Unsleber, Jan P; Dresselhaus, Thomas; Klahr, Kevin; Schnieders, David; Böckers, Michael; Barton, Dennis; Neugebauer, Johannes

2018-05-15

We present the new quantum chemistry program Serenity. It implements a wide variety of functionalities with a focus on subsystem methodology. The modular code structure in combination with publicly available external tools and particular design concepts ensures extensibility and robustness with a focus on the needs of a subsystem program. Several important features of the program are exemplified with sample calculations with subsystem density-functional theory, potential reconstruction techniques, a projection-based embedding approach and combinations thereof with geometry optimization, semi-numerical frequency calculations and linear-response time-dependent density-functional theory. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Invited Paper - Density functional theory: coverage of dynamic and non-dynamic electron correlation effects

NASA Astrophysics Data System (ADS)

Cremer, Dieter

The electron correlation effects covered by density functional theory (DFT) can be assessed qualitatively by comparing DFT densities ρ(r) with suitable reference densities obtained with wavefunction theory (WFT) methods that cover typical electron correlation effects. The analysis of difference densities ρ(DFT)-ρ(WFT) reveals that LDA and GGA exchange (X) functionals mimic non-dynamic correlation effects in an unspecified way. It is shown that these long range correlation effects are caused by the self-interaction error (SIE) of standard X functionals. Self-interaction corrected (SIC) DFT exchange gives, similar to exact exchange, for the bonding region a delocalized exchange hole, and does not cover any correlation effects. Hence, the exchange SIE is responsible for the fact that DFT densities often resemble MP4 or MP2 densities. The correlation functional changes X-only DFT densities in a manner observed when higher order coupling effects between lower order N-electron correlation effects are included. Hybrid functionals lead to changes in the density similar to those caused by SICDFT, which simply reflects the fact that hybrid functionals have been developed to cover part of the SIE and its long range correlation effects in a balanced manner. In the case of spin-unrestricted DFT (UDFT), non-dynamic electron correlation effects enter the calculation both via the X functional and via the wavefunction, which may cause a double-counting of correlation effects. The use of UDFT in the form of permuted orbital and broken-symmetry DFT (PO-UDFT, BS-UDFT) can lead to reasonable descriptions of multireference systems provided certain conditions are fulfilled. More reliable, however, is a combination of DFT and WFT methods, which makes the routine description of multireference systems possible. The development of such methods implies a separation of dynamic and non-dynamic correlation effects. Strategies for accomplishing this goal are discussed in general and tested in practice for CAS (complete active space)-DFT.

Electromagnetic scaling functions within the Green's function Monte Carlo approach

DOE PAGES

Rocco, N.; Alvarez-Ruso, L.; Lovato, A.; ...

2017-07-24

We have studied the scaling properties of the electromagnetic response functions of 4He and 12C nuclei computed by the Green's function Monte Carlo approach, retaining only the one-body current contribution. Longitudinal and transverse scaling functions have been obtained in the relativistic and nonrelativistic cases and compared to experiment for various kinematics. The characteristic asymmetric shape of the scaling function exhibited by data emerges in the calculations in spite of the nonrelativistic nature of the model. The results are mostly consistent with scaling of zeroth, first, and second kinds. Our analysis reveals a direct correspondence between the scaling and the nucleon-densitymore » response functions. In conclusion, the scaling function obtained from the proton-density response displays scaling of the first kind, even more evidently than the longitudinal and transverse scaling functions« less

Electromagnetic scaling functions within the Green's function Monte Carlo approach

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

Rocco, N.; Alvarez-Ruso, L.; Lovato, A.

We have studied the scaling properties of the electromagnetic response functions of 4He and 12C nuclei computed by the Green's function Monte Carlo approach, retaining only the one-body current contribution. Longitudinal and transverse scaling functions have been obtained in the relativistic and nonrelativistic cases and compared to experiment for various kinematics. The characteristic asymmetric shape of the scaling function exhibited by data emerges in the calculations in spite of the nonrelativistic nature of the model. The results are mostly consistent with scaling of zeroth, first, and second kinds. Our analysis reveals a direct correspondence between the scaling and the nucleon-densitymore » response functions. In conclusion, the scaling function obtained from the proton-density response displays scaling of the first kind, even more evidently than the longitudinal and transverse scaling functions« less

Many-Body Perturbation Theory (MBPT) and Time-Dependent Density-Functional Theory (TD-DFT): MBPT Insights About What Is Missing In, and Corrections To, the TD-DFT Adiabatic Approximation.

PubMed

Casida, Mark E; Huix-Rotllant, Miquel

2016-01-01

In their famous paper, Kohn and Sham formulated a formally exact density-functional theory (DFT) for the ground-state energy and density of a system of N interacting electrons, albeit limited at the time by certain troubling representability questions. As no practical exact form of the exchange-correlation (xc) energy functional was known, the xc-functional had to be approximated, ideally by a local or semilocal functional. Nowadays, however, the realization that Nature is not always so nearsighted has driven us up Perdew's Jacob's ladder to find increasingly nonlocal density/wavefunction hybrid functionals. Time-dependent (TD-) DFT is a younger development which allows DFT concepts to be used to describe the temporal evolution of the density in the presence of a perturbing field. Linear response (LR) theory then allows spectra and other information about excited states to be extracted from TD-DFT. Once again the exact TD-DFT xc-functional must be approximated in practical calculations and this has historically been done using the TD-DFT adiabatic approximation (AA) which is to TD-DFT very similar to what the local density approximation (LDA) is to conventional ground-state DFT. Although some of the recent advances in TD-DFT focus on what can be done within the AA, others explore ways around the AA. After giving an overview of DFT, TD-DFT, and LR-TD-DFT, this chapter focuses on many-body corrections to LR-TD-DFT as one way to build hybrid density-functional/wavefunction methodology for incorporating aspects of nonlocality in time not present in the AA.

Efficient Algorithms for Estimating the Absorption Spectrum within Linear Response TDDFT

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

Brabec, Jiri; Lin, Lin; Shao, Meiyue

We present two iterative algorithms for approximating the absorption spectrum of molecules within linear response of time-dependent density functional theory (TDDFT) framework. These methods do not attempt to compute eigenvalues or eigenvectors of the linear response matrix. They are designed to approximate the absorption spectrum as a function directly. They take advantage of the special structure of the linear response matrix. Neither method requires the linear response matrix to be constructed explicitly. They only require a procedure that performs the multiplication of the linear response matrix with a vector. These methods can also be easily modified to efficiently estimate themore » density of states (DOS) of the linear response matrix without computing the eigenvalues of this matrix. We show by computational experiments that the methods proposed in this paper can be much more efficient than methods that are based on the exact diagonalization of the linear response matrix. We show that they can also be more efficient than real-time TDDFT simulations. We compare the pros and cons of these methods in terms of their accuracy as well as their computational and storage cost.« less

Forward and inverse functional variations in rotationally inelastic scattering

NASA Astrophysics Data System (ADS)

Guzman, Robert; Rabitz, Herschel

1986-09-01

This paper considers the response of various rotational energy transfer processes to functional variations about an assumed model intermolecular potential. Attention is focused on the scattering of an atom and a linear rigid rotor. The collision dynamics are approximated by employing both the infinite order sudden (IOS) and exponential distorted wave (EDW) methods to describe Ar-N2 and He-H2, respectively. The following cross sections are considered: state-to-state differential and integral, final state summed differential and integral, and effective diffusion and viscosity cross sections. Attention is first given to the forward sensitivity densities δ0/δV(R,r) where 0 denotes any of the aforementioned cross sections, R is the intermolecular distance, and r is the internal coordinates. These forward sensitivity densities (functional derivatives) offer a quantitative measure of the importance of different regions of the potential surface to a chosen cross section. Via knowledge of the forward sensitivities and a particular variation δV(R,r) the concomitant response δ0 is generated. It was found that locally a variation in the potential can give rise to a large response in the cross sections as measured by these forward densities. In contrast, a unit percent change in the overall potential produced a 1%-10% change in the cross sections studied indicating that the large + and - responses to local variations tend to cancel. In addition, inverse sensitivity densities δV(R,r)/δ0 are obtained. These inverse densities are of interest since they are the exact solution to the infinitesimal inverse scattering problem. Although the inverse sensitivity densities do not in themselves form an inversion algorithm, they do offer a quantitative measure of the importance of performing particular measurements for the ultimate purpose of inversion. Using a set of state-to-state integral cross sections we found that the resultant responses from the infinitesimal inversion were typically small such that ‖δV(R,r)‖≪‖V(R,r)‖. From the viewpoint of an actual inversion, these results indicate that only through an extensive effort will significant knowledge of the potential be gained from the cross sections. All of these calculations serve to illustrate the methodology, and other observables as well as dynamical schemes could be explored as desired.

Density and delay of punishment of free-operant avoidance1

PubMed Central

Baron, Alan; Kaufman, Arnold; Fazzini, Dan

1969-01-01

In two experiments, the free-operant shock-avoidance behavior of rats was punished by electric shock. Two aspects of the schedule of response-produced shock were varied: the frequency of punishment over time (punishment density) and the temporal interval between the punished response and the punishment (punishment delay). The general finding was that response-produced shock suppressed avoidance responding under most of the density-delay combinations studied, and suppression increased as a function of increases in density and decreases in delay. Rate increases of small magnitude also were observed, usually as an initial reaction to the lesser densities and longer delays. Response suppression, while decreasing the number of punishment shocks received, also increased the number of avoidance shocks, so that the total number of shocks received usually was greater than the minimal number possible. The results were discussed from the standpoint of similarities between the effects of punishing positively and negatively reinforced behavior. The finding that subjects did not minimize the total number of shocks suggested that when avoidance behavior is punished, responding is controlled more by the local consequences of responding than by overall shock frequencies during the course of the session. PMID:16811408

A theoretical study for electronic and transport properties of covalent functionalized MoS2 monolayer

NASA Astrophysics Data System (ADS)

Gao, Lijuan; Yang, Zhao-Di; Zhang, Guiling

2017-06-01

The geometries, electronic and electron transport properties of a series of functionalized MoS2 monolayers were investigated using density-functional theory (DFT) and the non-equilibrium Green's function (NEGF) methods. n-Propyl, n-trisilicyl, phenyl, p-nitrophenyl and p-methoxyphenyl are chosen as electron-donating groups. The results show covalent functionalization with electron-donating groups could make a transformation from typical semiconducting to metallic properties for appearance of midgap level across the Fermi level (Ef). The calculations of transport properties for two-probe devices indicate that conductivities of functionalized systems are obviously enhanced relative to pristine MoS2 monolayer. Grafted groups contribute to the major transport path and play an important role in enhancing conductivity. The NDR effect is found. The influence of grafted density is also studied. Larger grafted density leads to wider bandwidth of midgap level, larger current response of I-V curves and larger current difference between peak and valley.

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

Effects of spatial grouping on the functional response of predators

USGS Publications Warehouse

Cosner, C.; DeAngelis, D.L.; Ault, J.S.; Olson, D.B.

1999-01-01

A unified mechanistic approach is given for the derivation of various forms of functional response in predator-prey models. The derivation is based on the principle-of-mass action but with the crucial refinement that the nature of the spatial distribution of predators and/or opportunities for predation are taken into account in an implicit way. If the predators are assumed to have a homogeneous spatial distribution, then the derived functional response is prey-dependent. If the predators are assumed to form a dense colony or school in a single (possibly moving) location, or if the region where predators can encounter prey is assumed to be of limited size, then the functional response depends on both predator and prey densities in a manner that reflects feeding interference between predators. Depending on the specific assumptions, the resulting functional response may be of Beddington-DeAngelis type, of Hassell-Varley type, or ratio-dependent.

K- and L-edge X-ray absorption spectrum calculations of closed-shell carbon, silicon, germanium, and sulfur compounds using damped four-component density functional response theory.

PubMed

Fransson, Thomas; Burdakova, Daria; Norman, Patrick

2016-05-21

X-ray absorption spectra of carbon, silicon, germanium, and sulfur compounds have been investigated by means of damped four-component density functional response theory. It is demonstrated that a reliable description of relativistic effects is obtained at both K- and L-edges. Notably, an excellent agreement with experimental results is obtained for L2,3-spectra-with spin-orbit effects well accounted for-also in cases when the experimental intensity ratio deviates from the statistical one of 2 : 1. The theoretical results are consistent with calculations using standard response theory as well as recently reported real-time propagation methods in time-dependent density functional theory, and the virtues of different approaches are discussed. As compared to silane and silicon tetrachloride, an anomalous error in the absolute energy is reported for the L2,3-spectrum of silicon tetrafluoride, amounting to an additional spectral shift of ∼1 eV. This anomaly is also observed for other exchange-correlation functionals, but it is seen neither at other silicon edges nor at the carbon K-edge of fluorine derivatives of ethene. Considering the series of molecules SiH4-XFX with X = 1, 2, 3, 4, a gradual divergence from interpolated experimental ionization potentials is observed at the level of Kohn-Sham density functional theory (DFT), and to a smaller extent with the use of Hartree-Fock. This anomalous error is thus attributed partly to difficulties in correctly emulating the electronic structure effects imposed by the very electronegative fluorines, and partly due to inconsistencies in the spurious electron self-repulsion in DFT. Substitution with one, or possibly two, fluorine atoms is estimated to yield small enough errors to allow for reliable interpretations and predictions of L2,3-spectra of more complex and extended silicon-based systems.

Dynamic kinetic energy potential for orbital-free density functional theory.

PubMed

Neuhauser, Daniel; Pistinner, Shlomo; Coomar, Arunima; Zhang, Xu; Lu, Gang

2011-04-14

A dynamic kinetic energy potential (DKEP) is developed for time-dependent orbital-free (TDOF) density function theory applications. This potential is constructed to affect only the dynamical (ω ≠ 0) response of an orbital-free electronic system. It aims at making the orbital-free simulation respond in the same way as that of a noninteracting homogenous electron gas (HEG), as required by a correct kinetic energy, therefore enabling extension of the success of orbital-free density functional theory in the static case (e.g., for embedding and description of processes in bulk materials) to dynamic processes. The potential is constructed by expansions of terms, each of which necessitates only simple time evolution (concurrent with the TDOF evolution) and a spatial convolution at each time-step. With 14 such terms a good fit is obtained to the response of the HEG at a large range of frequencies, wavevectors, and densities. The method is demonstrated for simple jellium spheres, approximating Na(9)(+) and Na(65)(+) clusters. It is applicable both to small and large (even ultralarge) excitations and the results converge (i.e., do not blow up) as a function of time. An extension to iterative frequency-resolved extraction is briefly outlined, as well as possibly numerically simpler expansions. The approach could also be extended to fit, instead of the HEG susceptibility, either an experimental susceptibility or a theoretically derived one for a non-HEG system. The DKEP potential should be a powerful tool for embedding a dynamical system described by a more accurate method (such as time-dependent density functional theory, TDDFT) in a large background described by TDOF with a DKEP potential. The type of expansions used and envisioned should be useful for other approaches, such as memory functionals in TDDFT. Finally, an appendix details the formal connection between TDOF and TDDFT.

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.

A general framework for numerical simulation of improvised explosive device (IED)-detection scenarios using density functional theory (DFT) and terahertz (THz) spectra.

PubMed

Shabaev, Andrew; Lambrakos, Samuel G; Bernstein, Noam; Jacobs, Verne L; Finkenstadt, Daniel

2011-04-01

We have developed a general framework for numerical simulation of various types of scenarios that can occur for the detection of improvised explosive devices (IEDs) through the use of excitation using incident electromagnetic waves. A central component model of this framework is an S-matrix representation of a multilayered composite material system. Each layer of the system is characterized by an average thickness and an effective electric permittivity function. The outputs of this component are the reflectivity and the transmissivity as functions of frequency and angle of the incident electromagnetic wave. The input of the component is a parameterized analytic-function representation of the electric permittivity as a function of frequency, which is provided by another component model of the framework. The permittivity function is constructed by fitting response spectra calculated using density functional theory (DFT) and parameter adjustment according to any additional information that may be available, e.g., experimentally measured spectra or theory-based assumptions concerning spectral features. A prototype simulation is described that considers response characteristics for THz excitation of the high explosive β-HMX. This prototype simulation includes a description of a procedure for calculating response spectra using DFT as input to the Smatrix model. For this purpose, the DFT software NRLMOL was adopted. © 2011 Society for Applied Spectroscopy

Derivation of the RPA (Random Phase Approximation) Equation of ATDDFT (Adiabatic Time Dependent Density Functional Ground State Response Theory) from an Excited State Variational Approach Based on the Ground State Functional.

PubMed

Ziegler, Tom; Krykunov, Mykhaylo; Autschbach, Jochen

2014-09-09

The random phase approximation (RPA) equation of adiabatic time dependent density functional ground state response theory (ATDDFT) has been used extensively in studies of excited states. It extracts information about excited states from frequency dependent ground state response properties and avoids, thus, in an elegant way, direct Kohn-Sham calculations on excited states in accordance with the status of DFT as a ground state theory. Thus, excitation energies can be found as resonance poles of frequency dependent ground state polarizability from the eigenvalues of the RPA equation. ATDDFT is approximate in that it makes use of a frequency independent energy kernel derived from the ground state functional. It is shown in this study that one can derive the RPA equation of ATDDFT from a purely variational approach in which stationary states above the ground state are located using our constricted variational DFT (CV-DFT) method and the ground state functional. Thus, locating stationary states above the ground state due to one-electron excitations with a ground state functional is completely equivalent to solving the RPA equation of TDDFT employing the same functional. The present study is an extension of a previous work in which we demonstrated the equivalence between ATDDFT and CV-DFT within the Tamm-Dancoff approximation.

Functional Response of Aphidoletes aphidimyza Rondani (Diptera: Cecidomyiidae) to Aphis gossypii Glover (Hemiptera: Aphididae): Effects of Vermicompost and Host Plant Cultivar.

PubMed

Mottaghinia, L; Hassanpour, M; Razmjou, J; Hosseini, M; Chamani, E

2016-02-01

Interactions between natural enemies and herbivores may be affected by application of fertilizers and different cultivars. We investigated the functional response of the predatory gall midge, Aphidoletes aphidimyza Rondani (Diptera: Cecidomyiidae) larvae to the nymphs of the melon aphid, Aphis gossypii Glover (Hemiptera: Aphididae), reared on two commonly grown cucumber cultivars in Iran (Khasib and Karim) treated with different vermicompost/soil ratios (0:100, 10:90, 20:80, and 30:70%). Based on logistic regression analysis, A. aphidimyza revealed a type II functional response to the aphid in all treatments. Attack rates and handling times of A. aphidimyza larvae on different vermicompost/soil ratios ranged from 0.076 to 0.140 h(-1) and 0.969 to 1.164 h on Khasib and from 0.092 to 0.123 h(-1) and 0.905 to 1.229 h on Karim, respectively. Furthermore, increasing the density of the melon aphid on both cultivars amended with vermicompost/soil ratios resulted in increased prey consumption by the predator. Density of trichomes increased when plants received higher concentrations of vermicompost. So, trichomes may be responsible for different attack rates and handling times of A. aphidimyza on both cultivars.

Critical assessment of density functional theory for computing vibrational (hyper)polarizabilities

NASA Astrophysics Data System (ADS)

Zaleśny, R.; Bulik, I. W.; Mikołajczyk, M.; Bartkowiak, W.; Luis, J. M.; Kirtman, B.; Avramopoulos, A.; Papadopoulos, M. G.

2012-12-01

Despite undisputed success of the density functional theory (DFT) in various branches of chemistry and physics, an application of the DFT for reliable predictions of nonlinear optical properties of molecules has been questioned a decade ago. As it was shown by Champagne, et al. [1, 2, 3] most conventional DFT schemes were unable to qualitatively predict the response of conjugated oligomers to a static electric field. Long-range corrected (LRC) functionals, like LC-BLYP or CAM-B3LYP, have been proposed to alleviate this deficiency. The reliability of LRC functionals for evaluating molecular (hyper)polarizabilities is studied for various groups of organic systems, with a special focus on vibrational corrections to the electric properties.

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

NASA Astrophysics Data System (ADS)

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

2015-02-01

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

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

PubMed

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

2015-02-28

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

Characterization of the thermal conductivity for Advanced Toughened Uni-piece Fibrous Insulations

NASA Technical Reports Server (NTRS)

Stewart, David A.; Leiser, Daniel B.

1993-01-01

Advanced Toughened Uni-piece Fibrous Insulations (TUFI) is discussed in terms of their thermal response to an arc-jet air stream. A modification of the existing Ames thermal conductivity program to predict the thermal response of these functionally gradient materials is described in the paper. The modified program was used to evaluate the effect of density, surface porosity, and density gradient through the TUFI materials on the thermal response of these insulations. Predictions using a finite-difference code and calculated thermal conductivity values from the modified program were compared with in-depth temperature measurements taken from TUFI insulations during short exposures to arc-jet hypersonic air streams.

Dynamics of a Two-Dimensional System of Quantum Dipoles

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

Mazzanti, F.; Astrakharchik, G. E.; Boronat, J.

2009-03-20

A detailed microscopic analysis of the dynamic structure function S(k,{omega}) of a two-dimensional Bose system of dipoles polarized along the direction perpendicular to the plane is presented and discussed. Starting from ground-state quantities obtained using a quantum diffusion Monte Carlo algorithm, the density-density response is evaluated in the context of the correlated basis functions (CBF) theory. CBF predicts a sharp peak and a multiexcitation component at higher energies produced by the decay of excitations. We discuss the structure of the phonon-roton peak and show that the Feynman and Bogoliubov predictions depart from the CBF result already at low densities. Wemore » finally discuss the emergence of a roton in the spectrum, but find the roton energy not low enough to make the system unstable under density fluctuations up to the highest density considered that is close to the freezing point.« less

Stomatal density and metabolic determinants mediate salt stress adaptation and water use efficiency in basil (Ocimum basilicum L.).

PubMed

Barbieri, Giancarlo; Vallone, Simona; Orsini, Francesco; Paradiso, Roberta; De Pascale, Stefania; Negre-Zakharov, Florence; Maggio, Albino

2012-11-15

Increasing salinity tolerance and water-use efficiency in crop plants are two major challenges that agriculture must face in the next decades. Many physiological mechanisms and molecular components mediating crop response to environmental stresses have been identified. However, the functional inter-links between stress adaptation responses have not been completely understood. Using two basil cultivars (Napoletano and Genovese) with contrasting ability to respond to salt stress, here we demonstrate that reduced stomatal density, high ascorbate level and polyphenol oxidase (PPO) activity coordinately contribute to improve basil adaptation and water use efficiency (WUE) in saline environment. The constitutively reduced stomatal density was associated with a "delayed" accumulation of stress molecules (and growth inhibiting signals) such as abscisic acid (ABA) and proline, in the more tolerant Genovese. Leaf volatile profiling also revealed cultivar-specific patterns, which may suggest a role for the volatile phenylpropanoid eugenol and monoterpenes in conferring stress tolerance via antioxidant and signalling functions. Copyright © 2012 Elsevier GmbH. All rights reserved.

Sound waves and flexural mode dynamics in two-dimensional crystals

NASA Astrophysics Data System (ADS)

Michel, K. H.; Scuracchio, P.; Peeters, F. M.

2017-09-01

Starting from a Hamiltonian with anharmonic coupling between in-plane acoustic displacements and out-of-plane (flexural) modes, we derived coupled equations of motion for in-plane displacements correlations and flexural mode density fluctuations. Linear response theory and time-dependent thermal Green's functions techniques are applied in order to obtain different response functions. As external perturbations we allow for stresses and thermal heat sources. The displacement correlations are described by a Dyson equation where the flexural density distribution enters as an additional perturbation. The flexural density distribution satisfies a kinetic equation where the in-plane lattice displacements act as a perturbation. In the hydrodynamic limit this system of coupled equations is at the basis of a unified description of elastic and thermal phenomena, such as isothermal versus adiabatic sound motion and thermal conductivity versus second sound. The general theory is formulated in view of application to graphene, two-dimensional h-BN, and 2H-transition metal dichalcogenides and oxides.

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.

The adaptation of generalist predators' diet in a multi-prey context: insights from new functional responses.

PubMed

Baudrot, Virgile; Perasso, Antoine; Fritsch, Clémentine; Giraudoux, Patrick; Raoul, Francis

2016-07-01

The ability for a generalist consumer to adapt its foraging strategy (the multi-species functional response, MSFR) is a milestone in ecology as it contributes to the structure of food webs. The trophic interaction between a generalist predator, as the red fox or the barn owl, and its prey community, mainly composed of small mammals, has been empirically and theoretically widely studied. However, the extent to which these predators adapt their diet according to both multi-annual changes in multiple prey species availability (frequency dependence) and the variation of the total prey density (density dependence) is unexplored.We provide a new general model of MSFR disentangling changes in prey preference according to variation of prey frequency (switching) and of total prey density (we propose the new concept of "rank switching"). We apply these models to two large data sets of red fox and barn owl foraging. We show that both frequency-dependent and density-dependent switching are critical properties of these two systems, suggesting that barn owl and red fox have an accurate image of the prey community in terms of frequency and absolute density. Moreover, we show that negative switching, which can lead to prey instability, is a strong property of the two systems. © 2016 by the Ecological Society of America.

Electronic Excitations in Solution: The Interplay between State Specific Approaches and a Time-Dependent Density Functional Theory Description.

PubMed

Guido, Ciro A; Jacquemin, Denis; Adamo, Carlo; Mennucci, Benedetta

2015-12-08

We critically analyze the performances of continuum solvation models when coupled to time-dependent density functional theory (TD-DFT) to predict solvent effects on both absorption and emission energies of chromophores in solution. Different polarization schemes of the polarizable continuum model (PCM), such as linear response (LR) and three different state specific (SS) approaches, are considered and compared. We show the necessity of introducing a SS model in cases where large electron density rearrangements are involved in the excitations, such as charge-transfer transitions in both twisted and quadrupolar compounds, and underline the very delicate interplay between the selected polarization method and the chosen exchange-correlation functional. This interplay originates in the different descriptions of the transition and ground/excited state multipolar moments by the different functionals. As a result, the choice of both the DFT functional and the solvent polarization scheme has to be consistent with the nature of the studied electronic excitation.

Galaxy power-spectrum responses and redshift-space super-sample effect

NASA Astrophysics Data System (ADS)

Li, Yin; Schmittfull, Marcel; Seljak, Uroš

2018-02-01

As a major source of cosmological information, galaxy clustering is susceptible to long-wavelength density and tidal fluctuations. These long modes modulate the growth and expansion rate of local structures, shifting them in both amplitude and scale. These effects are often named the growth and dilation effects, respectively. In particular the dilation shifts the baryon acoustic oscillation (BAO) peak and breaks the assumption of the Alcock-Paczynski (AP) test. This cannot be removed with reconstruction techniques because the effect originates from long modes outside the survey. In redshift space, the long modes generate a large-scale radial peculiar velocity that affects the redshift-space distortion (RSD) signal. We compute the redshift-space response functions of the galaxy power spectrum to long density and tidal modes at leading order in perturbation theory, including both the growth and dilation terms. We validate these response functions against measurements from simulated galaxy mock catalogs. As one application, long density and tidal modes beyond the scale of a survey correlate various observables leading to an excess error known as the super-sample covariance, and thus weaken their constraining power. We quantify the super-sample effect on BAO, AP, and RSD measurements, and study its impact on current and future surveys.

Augmented potential, energy densities, and virial relations in the weak- and strong-interaction limits of DFT

NASA Astrophysics Data System (ADS)

Vuckovic, Stefan; Levy, Mel; Gori-Giorgi, Paola

2017-12-01

The augmented potential introduced by Levy and Zahariev [Phys. Rev. Lett. 113, 113002 (2014)] is shifted with respect to the standard exchange-correlation potential of the Kohn-Sham density functional theory by a density-dependent constant that makes the total energy become equal to the sum of the occupied orbital energies. In this work, we analyze several features of this approach, focusing on the limit of infinite coupling strength and studying the shift and the corresponding energy density at different correlation regimes. We present and discuss coordinate scaling properties of the augmented potential, study its connection to the response potential, and use the shift to analyze the classical jellium and uniform gas models. We also study other definitions of the energy densities in relation to the functional construction by local interpolations along the adiabatic connection. Our findings indicate that the energy density that is defined in terms of the electrostatic potential of the exchange-correlation hole is particularly well suited for this purpose.

Test-Anchored Vibration Response Predictions for an Acoustically Energized Curved Orthogrid Panel with Mounted Components

NASA Technical Reports Server (NTRS)

Frady, Gregory P.; Duvall, Lowery D.; Fulcher, Clay W. G.; Laverde, Bruce T.; Hunt, Ronald A.

2011-01-01

rich body of vibroacoustic test data was recently generated at Marshall Space Flight Center for component-loaded curved orthogrid panels typical of launch vehicle skin structures. The test data were used to anchor computational predictions of a variety of spatially distributed responses including acceleration, strain and component interface force. Transfer functions relating the responses to the input pressure field were generated from finite element based modal solutions and test-derived damping estimates. A diffuse acoustic field model was applied to correlate the measured input sound pressures across the energized panel. This application quantifies the ability to quickly and accurately predict a variety of responses to acoustically energized skin panels with mounted components. Favorable comparisons between the measured and predicted responses were established. The validated models were used to examine vibration response sensitivities to relevant modeling parameters such as pressure patch density, mesh density, weight of the mounted component and model form. Convergence metrics include spectral densities and cumulative root-mean squared (RMS) functions for acceleration, velocity, displacement, strain and interface force. Minimum frequencies for response convergence were established as well as recommendations for modeling techniques, particularly in the early stages of a component design when accurate structural vibration requirements are needed relatively quickly. The results were compared with long-established guidelines for modeling accuracy of component-loaded panels. A theoretical basis for the Response/Pressure Transfer Function (RPTF) approach provides insight into trends observed in the response predictions and confirmed in the test data. The software developed for the RPTF method allows easy replacement of the diffuse acoustic field with other pressure fields such as a turbulent boundary layer (TBL) model suitable for vehicle ascent. Structural responses using a TBL model were demonstrated, and wind tunnel tests have been proposed to anchor the predictions and provide new insight into modeling approaches for this environment. Finally, design load factors were developed from the measured and predicted responses and compared with those derived from traditional techniques such as historical Mass Acceleration Curves and Barrett scaling methods for acreage and component-loaded panels.

Extended polarization in 3rd order SCC-DFTB from chemical potential equilization

PubMed Central

Kaminski, Steve; Giese, Timothy J.; Gaus, Michael; York, Darrin M.; Elstner, Marcus

2012-01-01

In this work we augment the approximate density functional method SCC-DFTB (DFTB3) with the chemical potential equilization (CPE) approach in order to improve the performance for molecular electronic polarizabilities. The CPE method, originally implemented for NDDO type methods by Giese and York, has been shown to emend minimal basis methods wrt response properties significantly, and has been applied to SCC-DFTB recently. CPE allows to overcome this inherent limitation of minimal basis methods by supplying an additional response density. The systematic underestimation is thereby corrected quantitatively without the need to extend the atomic orbital basis, i.e. without increasing the overall computational cost significantly. Especially the dependency of polarizability as a function of molecular charge state was significantly improved from the CPE extension of DFTB3. The empirical parameters introduced by the CPE approach were optimized for 172 organic molecules in order to match the results from density functional methods (DFT) methods using large basis sets. However, the first order derivatives of molecular polarizabilities, as e.g. required to compute Raman activities, are not improved by the current CPE implementation, i.e. Raman spectra are not improved. PMID:22894819

NMR shieldings from density functional perturbation theory: GIPAW versus all-electron calculations

NASA Astrophysics Data System (ADS)

de Wijs, G. A.; Laskowski, R.; Blaha, P.; Havenith, R. W. A.; Kresse, G.; Marsman, M.

2017-02-01

We present a benchmark of the density functional linear response calculation of NMR shieldings within the gauge-including projector-augmented-wave method against all-electron augmented-plane-wave+local-orbital and uncontracted Gaussian basis set results for NMR shieldings in molecular and solid state systems. In general, excellent agreement between the aforementioned methods is obtained. Scalar relativistic effects are shown to be quite large for nuclei in molecules in the deshielded limit. The small component makes up a substantial part of the relativistic corrections.

NMR shieldings from density functional perturbation theory: GIPAW versus all-electron calculations.

PubMed

de Wijs, G A; Laskowski, R; Blaha, P; Havenith, R W A; Kresse, G; Marsman, M

2017-02-14

We present a benchmark of the density functional linear response calculation of NMR shieldings within the gauge-including projector-augmented-wave method against all-electron augmented-plane-wave+local-orbital and uncontracted Gaussian basis set results for NMR shieldings in molecular and solid state systems. In general, excellent agreement between the aforementioned methods is obtained. Scalar relativistic effects are shown to be quite large for nuclei in molecules in the deshielded limit. The small component makes up a substantial part of the relativistic corrections.

Statistics of some atmospheric turbulence records relevant to aircraft response calculations

NASA Technical Reports Server (NTRS)

Mark, W. D.; Fischer, R. W.

1981-01-01

Methods for characterizing atmospheric turbulence are described. The methods illustrated include maximum likelihood estimation of the integral scale and intensity of records obeying the von Karman transverse power spectral form, constrained least-squares estimation of the parameters of a parametric representation of autocorrelation functions, estimation of the power spectra density of the instantaneous variance of a record with temporally fluctuating variance, and estimation of the probability density functions of various turbulence components. Descriptions of the computer programs used in the computations are given, and a full listing of these programs is included.

Local functional connectivity density is closely associated with the response of electroconvulsive therapy in major depressive disorder.

PubMed

Wang, Jiaojian; Wei, Qiang; Yuan, Xinru; Jiang, Xiaoyan; Xu, Jinping; Zhou, Xiaoqin; Tian, Yanghua; Wang, Kai

2018-01-01

Electroconvulsive therapy (ECT) has been demonstrated to be an effective treatment of major depressive disorder (MDD). However, the neuroanatomical basis of response to ECT is still largely unknown. In present study, we used functional connectivity density (FCD) and resting-state functional connectivity (RSFC) to identify the relationship between the changes of resting-state activities and ECT responses in 23 MDD patients before and after ECT. In addition, the identified neural indices as classification characteristics were entered into multivariate pattern analysis using linear support vector machine (SVM) to classify 23 MDD patients before ECT from 25 gender, age and years of education matched healthy controls. We found that the changes of local FCD (lFCD), not long-range FCD, of the left pre-/postcentral gyrus (Pre-/postCG), left superior temporal gyrus (STG), and right STG were significantly correlated with the changes of Hamilton Rating Scale for Depression (HRSD) scores in MDD patients before and after ECT. The subsequent functional connectivity analysis revealed significantly decreased functional connectivity between right STG and right intraparietal sulcus (IPS) in MDD after ECT in spite of no correlation with HRSD scores. Finally, SVM-based classification achieved an accuracy of 72.92% with a sensitivity of 73.91% and a specificity of 72% by leave-one-out cross-validation. Our findings indicated that Pre-/postCG and bilateral STG play an important role in response of ECT in MDD patients, and the lFCD in these areas may serve as a biomarker for predicting ECT response. Copyright © 2017 Elsevier B.V. All rights reserved.

Consequences of Ignoring Guessing when Estimating the Latent Density in Item Response Theory

ERIC Educational Resources Information Center

Woods, Carol M.

2008-01-01

In Ramsay-curve item response theory (RC-IRT), the latent variable distribution is estimated simultaneously with the item parameters. In extant Monte Carlo evaluations of RC-IRT, the item response function (IRF) used to fit the data is the same one used to generate the data. The present simulation study examines RC-IRT when the IRF is imperfectly…

Vibration responses of h-BN sheet to charge doping and external strain

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

Yang, Wei; Yang, Yu; Zheng, Fawei

2013-12-07

Based on density functional theory and density functional perturbation theory calculations, we systematically investigate the vibration responses of h-BN sheet to charge doping and external strains. It is found that under hole doping, the phonon frequencies of the ZO and TO branches at different wave vector q shift linearly with different slopes. Under electron doping, although the phonon frequencies shift irregularly, the shifting values are different at different phonon wave vectors. Interestingly, we find that external strain can restrain the irregular vibration responses of h-BN sheet to electron doping. The critical factor is revealed to be the relative position ofmore » the nearly free electron and boron p{sub z} states of h-BN sheet. Under external strains, the vibration responses of h-BN sheet are also found to be highly dependent on the phonon branches. Different vibration modes at different q points are revealed to be responsible for the vibration responses of h-BN sheet to charge doping and external strain. Our results point out a new way to detect the doping or strain status of h-BN sheet by measuring the vibration frequencies at different wave vector.« less

Non-linear non-local molecular electrodynamics with nano-optical fields.

PubMed

Chernyak, Vladimir Y; Saurabh, Prasoon; Mukamel, Shaul

2015-10-28

The interaction of optical fields sculpted on the nano-scale with matter may not be described by the dipole approximation since the fields may vary appreciably across the molecular length scale. Rather than incrementally adding higher multipoles, it is advantageous and more physically transparent to describe the optical process using non-local response functions that intrinsically include all multipoles. We present a semi-classical approach for calculating non-local response functions based on the minimal coupling Hamiltonian. The first, second, and third order response functions are expressed in terms of correlation functions of the charge and the current densities. This approach is based on the gauge invariant current rather than the polarization, and on the vector potential rather than the electric and magnetic fields.

The influence of sublethal deposits of agricultural mineral oil on the functional and numerical responses of Phytoseiulus persimilis (Acari: Phytoseiidae) to its prey, Tetranychus urticae (Acari: Tetranychidae).

PubMed

Xue, Yingen; Meats, Alan; Beattie, G Andrew C; Spooner-Hart, Robert; Herron, Grant A

2009-08-01

Occasional pesticide application in integrated pest management to at least part of a crop requires that any biological control agents must re-invade previously sprayed areas in order that resurgent pests can be constrained. The ability of the phytoseiid predatory mite Phytoseiulus persimilis to feed on adult two-spotted spider mite (TSSM) Tetranychus urticae on excised leaf discs in both control conditions and in a treatment with a sub lethal residue of agricultural mineral oil (AMO) was assessed. The predator exhibited a Type II functional response with the asymptote significantly higher in the AMO conditions due to the fact that the prey grew slower and reached a smaller size in this treatment. In terms of prey volume eaten, the satiation level of the predator was unchanged by the AMO deposits. The numbers of eggs produced by adult P. persimilis females at densities of 4, 8 and 16 TSSM adult females/disc in the control were significantly higher than those in the AMO treatment, but were similar for the higher density levels, 32 and 64 prey per disc. Thus the functional response in terms of volume of prey eaten explained the numerical response in terms of predator eggs produced. The presence of AMO deposits when the prey were at high density had no effect on predator efficiency (volume eaten) but resulted in a lower intake than that in control conditions when there was a greater distance between prey.

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.

Test-Anchored Vibration Response Predictions for an Acoustically Energized Curved Orthogrid Panel with Mounted Components

NASA Technical Reports Server (NTRS)

Frady, Gregory P.; Duvall, Lowery D.; Fulcher, Clay W. G.; Laverde, Bruce T.; Hunt, Ronald A.

2011-01-01

A rich body of vibroacoustic test data was recently generated at Marshall Space Flight Center for a curved orthogrid panel typical of launch vehicle skin structures. Several test article configurations were produced by adding component equipment of differing weights to the flight-like vehicle panel. The test data were used to anchor computational predictions of a variety of spatially distributed responses including acceleration, strain and component interface force. Transfer functions relating the responses to the input pressure field were generated from finite element based modal solutions and test-derived damping estimates. A diffuse acoustic field model was employed to describe the assumed correlation of phased input sound pressures across the energized panel. This application demonstrates the ability to quickly and accurately predict a variety of responses to acoustically energized skin panels with mounted components. Favorable comparisons between the measured and predicted responses were established. The validated models were used to examine vibration response sensitivities to relevant modeling parameters such as pressure patch density, mesh density, weight of the mounted component and model form. Convergence metrics include spectral densities and cumulative root-mean squared (RMS) functions for acceleration, velocity, displacement, strain and interface force. Minimum frequencies for response convergence were established as well as recommendations for modeling techniques, particularly in the early stages of a component design when accurate structural vibration requirements are needed relatively quickly. The results were compared with long-established guidelines for modeling accuracy of component-loaded panels. A theoretical basis for the Response/Pressure Transfer Function (RPTF) approach provides insight into trends observed in the response predictions and confirmed in the test data. The software modules developed for the RPTF method can be easily adapted for quick replacement of the diffuse acoustic field with other pressure field models; for example a turbulent boundary layer (TBL) model suitable for vehicle ascent. Wind tunnel tests have been proposed to anchor the predictions and provide new insight into modeling approaches for this type of environment. Finally, component vibration environments for design were developed from the measured and predicted responses and compared with those derived from traditional techniques such as Barrett scaling methods for unloaded and component-loaded panels.

Lipopolysaccharide effects on the proliferation of NRK52E cells via alternations in gap-junction function.

PubMed

Hei, Ziqing; Zhang, Ailan; Wei, Jing; Gan, Xiaoliang; Wang, Yanling; Luo, Gangjian; Li, Xiaoyun

2012-07-01

Gap junctions regulate proper kidney function by facilitating intercellular communication, vascular conduction, and tubular purinergic signaling. However, no clear relationship has been described between gap-junction function and acute kidney injury induced by the endotoxin lipopolysaccharide (LPS). Normal rat kidney epithelial cells (NRK52E cells) were seeded at high and low densities to promote or impede gap-junction formation, respectively, and establish distinctive levels of intercellular communication in culture. Cells were then challenged with LPS at various concentrations (10-1,000 ng/mL). LPS-induced formation and function of gap junctions were assessed by measuring changes in cell proliferation and colony-forming rates, fluorescent dye transmission to adjacent cells, expression levels of connexin43, and repositioning of confluent cells in response to the gap junction inhibitor oleamide or agonist retinoic acid. The cell proliferation rate and colony-forming rate of high- and low-density NRK52E cells were decreased upon LPS challenge, in a dose-dependent manner. The colony-forming rate of confluent high-density cells was significantly lower than that of low-density cells. Oleamide treatment raised the LPS-induced colony-forming rate of high-density cells, whereas retinoic acid decreased the rate. Neither oleamide nor retinoic acid significantly affected the LPS-induced colony-forming rate of low-density cells. Fluorescence transmission of high-density cells was reduced by LPS challenge, in a dose-dependent manner, but inclusion of retinoic acid increased the LPS-induced transmission of fluorescence. LPS challenge of either high- or low-density NRK52E cells resulted in down-regulated connexin43 expression. Gap-junction function plays an important role in concentration-dependent cytotoxic effect of LPS on normal rat kidney cells in vitro.

Diffuse Waves and Energy Densities Near Boundaries

NASA Astrophysics Data System (ADS)

Sanchez-Sesma, F. J.; Rodriguez-Castellanos, A.; Campillo, M.; Perton, M.; Luzon, F.; Perez-Ruiz, J. A.

2007-12-01

Green function can be retrieved from averaging cross correlations of motions within a diffuse field. In fact, it has been shown that for an elastic inhomogeneous, anisotropic medium under equipartitioned, isotropic illumination, the average cross correlations are proportional to the imaginary part of Green function. For instance coda waves are due to multiple scattering and their intensities follow diffusive regimes. Coda waves and the noise sample the medium and effectively carry information along their paths. In this work we explore the consequences of assuming both source and receiver at the same point. From the observable side, the autocorrelation is proportional to the energy density at a given point. On the other hand, the imaginary part of the Green function at the source itself is finite because the singularity of Green function is restricted to the real part. The energy density at a point is proportional with the trace of the imaginary part of Green function tensor at the source itself. The Green function availability may allow establishing the theoretical energy density of a seismic diffuse field generated by a background equipartitioned excitation. We study an elastic layer with free surface and overlaying a half space and compute the imaginary part of the Green function for various depths. We show that the resulting spectrum is indeed closely related to the layer dynamic response and the corresponding resonant frequencies are revealed. One implication of present findings lies in the fact that spatial variations may be useful in detecting the presence of a target by its signature in the distribution of diffuse energy. These results may be useful in assessing the seismic response of a given site if strong ground motions are scarce. It suffices having a reasonable illumination from micro earthquakes and noise. We consider that the imaginary part of Green function at the source is a spectral signature of the site. The relative importance of the peaks of this energy spectrum, ruling out non linear effects, may influence the seismic response for future earthquakes. Partial supports from DGAPA-UNAM, Project IN114706, Mexico; from Proyect MCyT CGL2005-05500-C02/BTE, Spain; from project DyETI of INSU-CNRS, France, and from the Instituto Mexicano del Petróleo are greatly appreciated.

Gauge invariance of excitonic linear and nonlinear optical response

NASA Astrophysics Data System (ADS)

Taghizadeh, Alireza; Pedersen, T. G.

2018-05-01

We study the equivalence of four different approaches to calculate the excitonic linear and nonlinear optical response of multiband semiconductors. These four methods derive from two choices of gauge, i.e., length and velocity gauges, and two ways of computing the current density, i.e., direct evaluation and evaluation via the time-derivative of the polarization density. The linear and quadratic response functions are obtained for all methods by employing a perturbative density-matrix approach within the mean-field approximation. The equivalence of all four methods is shown rigorously, when a correct interaction Hamiltonian is employed for the velocity gauge approaches. The correct interaction is written as a series of commutators containing the unperturbed Hamiltonian and position operators, which becomes equivalent to the conventional velocity gauge interaction in the limit of infinite Coulomb screening and infinitely many bands. As a case study, the theory is applied to hexagonal boron nitride monolayers, and the linear and nonlinear optical response found in different approaches are compared.

Exercise-mediated changes in high-density lipoprotein: impact on form and function.

PubMed

Blazek, Alisa; Rutsky, Jessica; Osei, Kwame; Maiseyeu, Andrei; Rajagopalan, Sanjay

2013-09-01

The goal of this systematic review was to assess the current understanding of the effects of exercise intervention on high-density lipoprotein (HDL) cholesterol (HDL-C) and changes in HDL function as well as modification of these effects by genomic factors. The reviewed studies demonstrate that exercise has modest effects on HDL-C with limited data suggesting an effect on HDL function. Genetic polymorphisms in proteins associated with HDL metabolism play a role in modifying the HDL-C response to exercise and possibly its function. Exercise as an intervention for patients at risk for cardiovascular events can lead to small improvements in HDL-C and potential changes in HDL function. There is an important modifier effect of genetics in determining these changes. Copyright © 2013 Mosby, Inc. All rights reserved.

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

Escartín, J. M.; CNRS, UMR5152, F-31062 Toulouse Cedex; Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, J.J. Thomson Avenue, Cambridge CB3 0HE

Time-Dependent Density-Functional Theory (TDDFT) is a well-established theoretical approach to describe and understand irradiation processes in clusters and molecules. However, within the so-called adiabatic local density approximation (ALDA) to the exchange-correlation (xc) potential, TDDFT can show insufficiencies, particularly in violently dynamical processes. This is because within ALDA the xc potential is instantaneous and is a local functional of the density, which means that this approximation neglects memory effects and long-range effects. A way to go beyond ALDA is to use Time-Dependent Current-Density-Functional Theory (TDCDFT), in which the basic quantity is the current density rather than the density as in TDDFT.more » This has been shown to offer an adequate account of dissipation in the linear domain when the Vignale-Kohn (VK) functional is used. Here, we go beyond the linear regime and we explore this formulation in the time domain. In this case, the equations become very involved making the computation out of reach; we hence propose an approximation to the VK functional which allows us to calculate the dynamics in real time and at the same time to keep most of the physics described by the VK functional. We apply this formulation to the calculation of the time-dependent dipole moment of Ca, Mg and Na{sub 2}. Our results show trends similar to what was previously observed in model systems or within linear response. In the non-linear domain, our results show that relaxation times do not decrease with increasing deposited excitation energy, which sets some limitations to the practical use of TDCDFT in such a domain of excitations.« less

The specific purpose Monte Carlo code McENL for simulating the response of epithermal neutron lifetime well logging tools

NASA Astrophysics Data System (ADS)

Prettyman, T. H.; Gardner, R. P.; Verghese, K.

1993-08-01

A new specific purpose Monte Carlo code called McENL for modeling the time response of epithermal neutron lifetime tools is described. The weight windows technique, employing splitting and Russian roulette, is used with an automated importance function based on the solution of an adjoint diffusion model to improve the code efficiency. Complete composition and density correlated sampling is also included in the code, and can be used to study the effect on tool response of small variations in the formation, borehole, or logging tool composition and density. An illustration of the latter application is given for the density of a thermal neutron filter. McENL was benchmarked against test-pit data for the Mobil pulsed neutron porosity tool and was found to be very accurate. Results of the experimental validation and details of code performance are presented.

Rich Global Dynamics in a Prey-Predator Model with Allee Effect and Density Dependent Death Rate of Predator

NASA Astrophysics Data System (ADS)

Sen, Moitri; Banerjee, Malay

In this work we have considered a prey-predator model with strong Allee effect in the prey growth function, Holling type-II functional response and density dependent death rate for predators. It presents a comprehensive study of the complete global dynamics for the considered system. Especially to see the effect of the density dependent death rate of predator on the system behavior, we have presented the two parametric bifurcation diagrams taking it as one of the bifurcation parameters. In course of that we have explored all possible local and global bifurcations that the system could undergo, namely the existence of transcritical bifurcation, saddle node bifurcation, cusp bifurcation, Hopf-bifurcation, Bogdanov-Takens bifurcation and Bautin bifurcation respectively.

Linear response coupled cluster theory with the polarizable continuum model within the singles approximation for the solvent response.

PubMed

Caricato, Marco

2018-04-07

We report the theory and the implementation of the linear response function of the coupled cluster (CC) with the single and double excitations method combined with the polarizable continuum model of solvation, where the correlation solvent response is approximated with the perturbation theory with energy and singles density (PTES) scheme. The singles name is derived from retaining only the contribution of the CC single excitation amplitudes to the correlation density. We compare the PTES working equations with those of the full-density (PTED) method. We then test the PTES scheme on the evaluation of excitation energies and transition dipoles of solvated molecules, as well as of the isotropic polarizability and specific rotation. Our results show a negligible difference between the PTED and PTES schemes, while the latter affords a significantly reduced computational cost. This scheme is general and can be applied to any solvation model that includes mutual solute-solvent polarization, including explicit models. Therefore, the PTES scheme is a competitive approach to compute response properties of solvated systems using CC methods.

Linear response coupled cluster theory with the polarizable continuum model within the singles approximation for the solvent response

NASA Astrophysics Data System (ADS)

Caricato, Marco

2018-04-01

We report the theory and the implementation of the linear response function of the coupled cluster (CC) with the single and double excitations method combined with the polarizable continuum model of solvation, where the correlation solvent response is approximated with the perturbation theory with energy and singles density (PTES) scheme. The singles name is derived from retaining only the contribution of the CC single excitation amplitudes to the correlation density. We compare the PTES working equations with those of the full-density (PTED) method. We then test the PTES scheme on the evaluation of excitation energies and transition dipoles of solvated molecules, as well as of the isotropic polarizability and specific rotation. Our results show a negligible difference between the PTED and PTES schemes, while the latter affords a significantly reduced computational cost. This scheme is general and can be applied to any solvation model that includes mutual solute-solvent polarization, including explicit models. Therefore, the PTES scheme is a competitive approach to compute response properties of solvated systems using CC methods.

Revised Thomas-Fermi approximation for singular potentials

NASA Astrophysics Data System (ADS)

Dufty, James W.; Trickey, S. B.

2016-08-01

Approximations for the many-fermion free-energy density functional that include the Thomas-Fermi (TF) form for the noninteracting part lead to singular densities for singular external potentials (e.g., attractive Coulomb). This limitation of the TF approximation is addressed here by a formal map of the exact Euler equation for the density onto an equivalent TF form characterized by a modified Kohn-Sham potential. It is shown to be a "regularized" version of the Kohn-Sham potential, tempered by convolution with a finite-temperature response function. The resulting density is nonsingular, with the equilibrium properties obtained from the total free-energy functional evaluated at this density. This new representation is formally exact. Approximate expressions for the regularized potential are given to leading order in a nonlocality parameter, and the limiting behavior at high and low temperatures is described. The noninteracting part of the free energy in this approximation is the usual Thomas-Fermi functional. These results generalize and extend to finite temperatures the ground-state regularization by R. G. Parr and S. Ghosh [Proc. Natl. Acad. Sci. U.S.A. 83, 3577 (1986), 10.1073/pnas.83.11.3577] and by L. R. Pratt, G. G. Hoffman, and R. A. Harris [J. Chem. Phys. 88, 1818 (1988), 10.1063/1.454105] and formally systematize the finite-temperature regularization given by the latter authors.

Optimization of intermittent microwave–convective drying using response surface methodology

PubMed Central

Aghilinategh, Nahid; Rafiee, Shahin; Hosseinpur, Soleiman; Omid, Mahmoud; Mohtasebi, Seyed Saeid

2015-01-01

In this study, response surface methodology was used for optimization of intermittent microwave–convective air drying (IMWC) parameters with employing desirability function. Optimization factors were air temperature (40–80°C), air velocity (1–2 m/sec), pulse ratio) PR ((2–6), and microwave power (200–600 W) while responses were rehydration ratio, bulk density, total phenol content (TPC), color change, and energy consumption. Minimum color change, bulk density, energy consumption, maximum rehydration ratio, and TPC were assumed as criteria for optimizing drying conditions of apple slices in IMWC. The optimum values of process variables were 1.78 m/sec air velocity, 40°C air temperature, PR 4.48, and 600 W microwave power that characterized by maximum desirability function (0.792) using Design expert 8.0. The air temperature and microwave power had significant effect on total responses, but the role of air velocity can be ignored. Generally, the results indicated that it was possible to obtain a higher desirability value if the microwave power and temperature, respectively, increase and decrease. PMID:26286706

Complex-energy approach to sum rules within nuclear density functional theory

DOE PAGES

Hinohara, Nobuo; Kortelainen, Markus; Nazarewicz, Witold; ...

2015-04-27

The linear response of the nucleus to an external field contains unique information about the effective interaction, correlations governing the behavior of the many-body system, and properties of its excited states. To characterize the response, it is useful to use its energy-weighted moments, or sum rules. By comparing computed sum rules with experimental values, the information content of the response can be utilized in the optimization process of the nuclear Hamiltonian or nuclear energy density functional (EDF). But the additional information comes at a price: compared to the ground state, computation of excited states is more demanding. To establish anmore » efficient framework to compute energy-weighted sum rules of the response that is adaptable to the optimization of the nuclear EDF and large-scale surveys of collective strength, we have developed a new technique within the complex-energy finite-amplitude method (FAM) based on the quasiparticle random- phase approximation. The proposed sum-rule technique based on the complex-energy FAM is a tool of choice when optimizing effective interactions or energy functionals. The method is very efficient and well-adaptable to parallel computing. As a result, the FAM formulation is especially useful when standard theorems based on commutation relations involving the nuclear Hamiltonian and external field cannot be used.« less

Structure determination and characterization of two rare-earth molybdenum borate compounds: LnMoBO(6) (Ln = La, Ce).

PubMed

Zhao, Dan; Cheng, Wen-Dan; Zhang, Hao; Hang, Shu-Ping; Fang, Ming

2008-07-28

The structural, optical, and electronic properties of two rare-earth molybdenum borate compounds, LnMoBO(6) (Ln = La, Ce), have been investigated by means of single-crystal X-ray diffraction, elemental analyses, and spectral measurements, as well as calculations of energy band structures, density of states, and optical response functions by the density functional method. The title compounds, which crystallize in monoclinic space group P2(1)/c, possess a similar network of interconnected [Ce(2)(MoO(4))(2)](2+) chains and [BO(2)](-) wavy chains. Novel 1D molybdenum oxide chains are contained in their three-dimensional (3D) networks. The calculated results of crystal energy band structure by the density functional theory (DFT) method show that the solid-state compound LaMoBO(6) is a semiconductor with indirect band gaps.

Dielectric function for doped graphene layer with barium titanate

NASA Astrophysics Data System (ADS)

Martinez Ramos, Manuel; Garces Garcia, Eric; Magana, Fernado; Vazquez Fonseca, Gerardo Jorge

2015-03-01

The aim of our study is to calculate the dielectric function for a system formed with a graphene layer doped with barium titanate. Density functional theory, within the local density approximation, plane-waves and pseudopotentials scheme as implemented in Quantum Espresso suite of programs was used. We considered 128 carbon atoms with a barium titanate cluster of 11 molecules as unit cell with periodic conditions. The geometry optimization is achieved. Optimization of structural configuration is performed by relaxation of all atomic positions to minimize their total energies. Band structure, density of states and linear optical response (the imaginary part of dielectric tensor) were calculated. We thank Dirección General de Asuntos del Personal Académico de la Universidad Nacional Autónoma de México, partial financial support by Grant IN-106514 and we also thank Miztli Super-Computing center the technical assistance.

Optimization of constrained density functional theory

NASA Astrophysics Data System (ADS)

O'Regan, David D.; Teobaldi, Gilberto

2016-07-01

Constrained density functional theory (cDFT) is a versatile electronic structure method that enables ground-state calculations to be performed subject to physical constraints. It thereby broadens their applicability and utility. Automated Lagrange multiplier optimization is necessary for multiple constraints to be applied efficiently in cDFT, for it to be used in tandem with geometry optimization, or with molecular dynamics. In order to facilitate this, we comprehensively develop the connection between cDFT energy derivatives and response functions, providing a rigorous assessment of the uniqueness and character of cDFT stationary points while accounting for electronic interactions and screening. In particular, we provide a nonperturbative proof that stable stationary points of linear density constraints occur only at energy maxima with respect to their Lagrange multipliers. We show that multiple solutions, hysteresis, and energy discontinuities may occur in cDFT. Expressions are derived, in terms of convenient by-products of cDFT optimization, for quantities such as the dielectric function and a condition number quantifying ill definition in multiple constraint cDFT.

Molecular properties via a subsystem density functional theory formulation: a common framework for electronic embedding.

PubMed

Höfener, Sebastian; Gomes, André Severo Pereira; Visscher, Lucas

2012-01-28

In this article, we present a consistent derivation of a density functional theory (DFT) based embedding method which encompasses wave-function theory-in-DFT (WFT-in-DFT) and the DFT-based subsystem formulation of response theory (DFT-in-DFT) by Neugebauer [J. Neugebauer, J. Chem. Phys. 131, 084104 (2009)] as special cases. This formulation, which is based on the time-averaged quasi-energy formalism, makes use of the variation Lagrangian techniques to allow the use of non-variational (in particular: coupled cluster) wave-function-based methods. We show how, in the time-independent limit, we naturally obtain expressions for the ground-state DFT-in-DFT and WFT-in-DFT embedding via a local potential. We furthermore provide working equations for the special case in which coupled cluster theory is used to obtain the density and excitation energies of the active subsystem. A sample application is given to demonstrate the method. © 2012 American Institute of Physics

The adsorption of NO, NH3, N2 on carbon surface: a density functional theory study.

PubMed

Wang, Jiayong; Yang, Mo; Deng, Debing; Qiu, Shuxia

2017-08-11

To explore the adsorption mechanism of NO, NH 3 , N 2 on a carbon surface, and the effect of basic and acidic functional groups, density functional theory was employed to investigate the interactions between these molecules and carbon surfaces. Molecular electrostatic potential, Mulliken population analyses, reduced density gradient, and Mayer bond order analyses were used to clarify the adsorption mechanism. The results indicate that van der Waals interactions are responsible for N 2 physisorption, and N 2 is the least likely to adsorb on a carbon surface. Modification of carbon materials to decorate basic or acidic functional groups could enhance the NH 3 physisorption because of hydrogen bonding or electrostatic interactions, however, NO physisorption on a carbon surface is poor. Zig-zag sites are more reactive than armchair sites when these gas molecules absorb on the edge sites of carbon surface. Graphical abstract NH 3 , N 2 , NO adsortion on carbon surface.

Ratiometric sensing of fluoride and acetate anions based on a BODIPY-azaindole platform and its application to living cell imaging.

PubMed

Mahapatra, Ajit Kumar; Maji, Rajkishor; Maiti, Kalipada; Adhikari, Susanta Sekhar; Das Mukhopadhyay, Chitrangada; Mandal, Debasish

2014-01-07

A new BODIPY-azaindole based fluorescent sensor 1 was designed and synthesized as a new colorimetric and ratiometric fluorescent chemosensor for fluoride. The binding and sensing abilities of sensor 1 towards various anions were studied by absorption, emission and (1)H NMR titration spectroscopies. The spectral responses of 1 to fluoride in acetonitrile-water were studied: an approximately 69 nm red shift in absorption and ratiometric fluorescent response was observed. The striking light yellow to deep brown color change in ambient light and green to blue emission color change are thought to be due to the deprotonation of the indole moiety of the azaindole fluorophore. From the changes in the absorption, fluorescence, and (1)H NMR titration spectra, proton-transfer mechanisms were deduced. Density function theory and time-dependent density function theory calculations were conducted to rationalize the optical response of the sensor. Results were supported by confocal fluorescence imaging and MTT assay of live cells.

A newly developed highly selective ratiometric fluoride ion sensor: spectroscopic, NMR and density functional studies.

PubMed

Mallick, Arabinda; Roy, Ujjal Kanti; Haldar, Basudeb; Pratihar, Sanjay

2012-03-07

A new easy-to-synthesize chemosensor, 3,3'-bis(indolyl)-4-chlorophenylmethane (hereafter S), was designed, synthesized and employed as a selective optical chemosensor for fluoride ions.(1)H NMR and density functional studies on the system have been carried out to determine the nature of the interaction between S and X(-) (X = inorganic anions) responsible for the significant fluoride-induced changes in the absorption properties of S. The experimental results reveal that abstraction of an acidic proton of S by the fluoride ion, leading to the formation of anionic species, is responsible for the spectral changes. These changes allow signaling for the fluoride ion to detect and estimate the concentration of fluoride ion present even at the submicromolar level, accurate up to 2 μM. Calculations of the transition energies of S, S(-), and S···F(-) (hydrogen bonded complex) show that only S(-) is responsible for the long-wavelength absorption band in the presence of F(-).

Propagation of second sound in a superfluid Fermi gas in the unitary limit

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

Arahata, Emiko; Nikuni, Tetsuro

2009-10-15

We study sound propagation in a uniform superfluid gas of Fermi atoms in the unitary limit. The existence of normal and superfluid components leads to appearance of two sound modes in the collisional regime, referred to as first and second sounds. The second sound is of particular interest as it is a clear signal of a superfluid component. Using Landau's two-fluid hydrodynamic theory, we calculate hydrodynamic sound velocities and these weights in the density response function. The latter is used to calculate the response to a sudden modification of the external potential generating pulse propagation. The amplitude of a pulsemore » which is proportional to the weight in the response function is calculated, the basis of the approach of Nozieres and Schmitt-Rink for the BCS-BEC. We show that, in a superfluid Fermi gas at unitarity, the second-sound pulse is excited with an appreciate amplitude by density perturbations.« less

Probabilistic Modeling of High-Temperature Material Properties of a 5-Harness 0/90 Sylramic Fiber/ CVI-SiC/ MI-SiC Woven Composite

NASA Technical Reports Server (NTRS)

Nagpal, Vinod K.; Tong, Michael; Murthy, P. L. N.; Mital, Subodh

1998-01-01

An integrated probabilistic approach has been developed to assess composites for high temperature applications. This approach was used to determine thermal and mechanical properties and their probabilistic distributions of a 5-harness 0/90 Sylramic fiber/CVI-SiC/Mi-SiC woven Ceramic Matrix Composite (CMC) at high temperatures. The purpose of developing this approach was to generate quantitative probabilistic information on this CMC to help complete the evaluation for its potential application for HSCT combustor liner. This approach quantified the influences of uncertainties inherent in constituent properties called primitive variables on selected key response variables of the CMC at 2200 F. The quantitative information is presented in the form of Cumulative Density Functions (CDFs). Probability Density Functions (PDFS) and primitive variable sensitivities on response. Results indicate that the scatters in response variables were reduced by 30-50% when the uncertainties in the primitive variables, which showed the most influence, were reduced by 50%.

Effect of physisorbed molecules and an external external fields on the metallic Shockley surface state of Cu(111): A density functional theory study

NASA Astrophysics Data System (ADS)

Berland, Kristian; Einstein, T. L.; Hyldgaard, Per

2012-02-01

To manipulate the Cu(111) partially-filled Shockley surface state, we study its response to an external fieldootnotetextKB, TLE, PH; arXiv 1109:6706 E and physisorbed PAHs and quinone molecules. We use density-functional theory calculations with periodic-boundary conditions. The van der Waals density functional version vdW-DF2 accounts for the molecular adsorption. The issue that the Kohn-Sham wave functions couple to both sides of the Cu slab is handled with a decoupling scheme based on a rotation in Hilbert space. A convergence study reveals that to obtain a proper Shockley surface state, 6 Cu layers is sufficient, while 15 is optimal. We use 6 layers for the response to the molecules and 15 to external field. We find that the surface state displays isotropic dispersion (up to order k^6), free-electron like until the Fermi wave vector but with a significant quartic component beyond. The shift in band minimum and effective mass depend linearly on E, with a smaller fractional change in the latter. Charge transfer occurs beyond the outermost copper atoms, and most of the screening is due to bulk electrons. We find that the molecular physisorption increases the band minimum, with the effect the of a quinone being much stronger than the corresponding PAH.

Dielectric Response at THz Frequencies of Fe Water Complexes and Their Interaction with O3 Calculated by Density Functional Theory

DTIC Science & Technology

2012-10-24

geometric arrangement of the atoms in a chemical system , at the maximal peak of the energy surface separating reactants from products . In the...Sonnenberg, M. Hada, M. Ehara, K. Toyota , R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda , O. Kitao, H. Nakai, T. Vreven, J. A. Montgomery... using DFT. The calculation of ground state resonance structure is for the construction of parameterized dielectric response functions for excitation

Quadratic response functions in the relativistic four-component Kohn-Sham approximation

NASA Astrophysics Data System (ADS)

Henriksson, Johan; Saue, Trond; Norman, Patrick

2008-01-01

A formulation and implementation of the quadratic response function in the adiabatic four-component Kohn-Sham approximation is presented. The noninteracting reference state is time-reversal symmetric and formed from Kramers pair spinors, and the energy density is gradient corrected. Example calculations are presented for the optical properties of disubstituted halobenzenes in their meta and ortho conformations. It is demonstrated that correlation and relativistic effects are not additive, and it is shown that relativity alone reduces the μβ¯-response signal by 62% and 75% for meta- and ortho-bromobenzene, respectively, and enhances the same response by 17% and 21% for meta- and ortho-iodobenzene, respectively. Of the employed functionals, CAM-B3LYP shows the best performance and gives hyperpolarizabilities β distinctly different from B3LYP.

Changes in the free amino acid composition of Capsicum annuum (pepper) leaves in response to Myzus persicae (green peach aphid) infestation. A comparison with water stress.

PubMed

Florencio-Ortiz, Victoria; Sellés-Marchart, Susana; Zubcoff-Vallejo, José; Jander, Georg; Casas, José L

2018-01-01

Amino acids play a central role in aphid-plant interactions. They are essential components of plant primary metabolism, function as precursors for the synthesis of defense-related specialized metabolites, and are major growth-limiting nutrients for aphids. To quantify changes in the free amino acid content of pepper (Capsicum annuum L.) leaves in response to green peach aphid (Myzus persicae Sulzer) feeding, plants were infested with a low (20 aphids/plant) or a high (200 aphids/plant) aphid density in time-course experiments ranging from 3 hours to 7 days. A parallel experiment was conducted with pepper plants that had been subjected to water stress. Factor Analysis of Mixed Data revealed a significant interaction of time x density in the free amino acid response of aphid-infested leaves. At low aphid density, M. persicae did not trigger a strong response in pepper leaves. Conversely, at high density, a large increase in total free amino acid content was observed and specific amino acids peaked at different times post-infestation. Comparing aphid-infested with water-stressed plants, most of the observed differences were quantitative. In particular, proline and hydroxyproline accumulated dramatically in response to water stress, but not in response to aphid infestation. Some additional differences and commonalities between the two stress treatments are discussed.

Lattice dynamics of Ru2FeX (X = Si, Ge) Full Heusler alloys

NASA Astrophysics Data System (ADS)

Rizwan, M.; Afaq, A.; Aneeza, A.

2018-05-01

In present work, the lattice dynamics of Ru2FeX (X = Si, Ge) full Heusler alloys are investigated using density functional theory (DFT) within generalized gradient approximation (GGA) in a plane wave basis, with norm-conserving pseudopotentials. Phonon dispersion curves and phonon density of states are obtained using first-principles linear response approach of density functional perturbation theory (DFPT) as implemented in Quantum ESPRESSO code. Phonon dispersion curves indicates for both Heusler alloys that there is no imaginary phonon in whole Brillouin zone, confirming dynamical stability of these alloys in L21 type structure. There is a considerable overlapping between acoustic and optical phonon modes predicting no phonon band gap exists in dispersion curves of alloys. The same result is shown by phonon density of states curves for both Heusler alloys. Reststrahlen band for Ru2FeSi is found smaller than Ru2FeGe.

Time-dependent density functional theory description of total photoabsorption cross sections

NASA Astrophysics Data System (ADS)

Tenorio, Bruno Nunes Cabral; Nascimento, Marco Antonio Chaer; Rocha, Alexandre Braga

2018-02-01

The time-dependent version of the density functional theory (TDDFT) has been used to calculate the total photoabsorption cross section of a number of molecules, namely, benzene, pyridine, furan, pyrrole, thiophene, phenol, naphthalene, and anthracene. The discrete electronic pseudo-spectra, obtained in a L2 basis set calculation were used in an analytic continuation procedure to obtain the photoabsorption cross sections. The ammonia molecule was chosen as a model system to compare the results obtained with TDDFT to those obtained with the linear response coupled cluster approach in order to make a link with our previous work and establish benchmarks.

Molecular docking and spectroscopic investigations aided by density functional theory of Parkinson's drug 2-(3,4-dihydroxyphenyl)ethylamine

NASA Astrophysics Data System (ADS)

Sherlin, Y. Sheeba; Vijayakumar, T.; Roy, S. D. D.; Jayakumar, V. S.

2018-05-01

Molecular geometry of Parkinson's drug 2-(3,4-Dihydroxyphenyl)ethylamine hydrochloride (Dopamine, DA) has been evaluated and compared with experimental XRD data. Molecular docking and vibrational spectral analysis of DA have been carried out using FT-Raman and FT-IR spectra aided by Density Functional Theory at B3LYP/6-311++G(d,p). The present investigation deals with the analysis of structural and spectral features responsible for drug activities, nature of hydrogen bonding interactions of the molecule and the correlation of Parkinson's nature with its molecular structural features.

Grand canonical electronic density-functional theory: Algorithms and applications to electrochemistry

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

Sundararaman, Ravishankar; Goddard, III, William A.; Arias, Tomas A.

First-principles calculations combining density-functional theory and continuum solvation models enable realistic theoretical modeling and design of electrochemical systems. When a reaction proceeds in such systems, the number of electrons in the portion of the system treated quantum mechanically changes continuously, with a balancing charge appearing in the continuum electrolyte. A grand-canonical ensemble of electrons at a chemical potential set by the electrode potential is therefore the ideal description of such systems that directly mimics the experimental condition. We present two distinct algorithms: a self-consistent field method and a direct variational free energy minimization method using auxiliary Hamiltonians (GC-AuxH), to solvemore » the Kohn-Sham equations of electronic density-functional theory directly in the grand canonical ensemble at fixed potential. Both methods substantially improve performance compared to a sequence of conventional fixed-number calculations targeting the desired potential, with the GC-AuxH method additionally exhibiting reliable and smooth exponential convergence of the grand free energy. Lastly, we apply grand-canonical density-functional theory to the under-potential deposition of copper on platinum from chloride-containing electrolytes and show that chloride desorption, not partial copper monolayer formation, is responsible for the second voltammetric peak.« less

Grand canonical electronic density-functional theory: Algorithms and applications to electrochemistry.

PubMed

Sundararaman, Ravishankar; Goddard, William A; Arias, Tomas A

2017-03-21

First-principles calculations combining density-functional theory and continuum solvation models enable realistic theoretical modeling and design of electrochemical systems. When a reaction proceeds in such systems, the number of electrons in the portion of the system treated quantum mechanically changes continuously, with a balancing charge appearing in the continuum electrolyte. A grand-canonical ensemble of electrons at a chemical potential set by the electrode potential is therefore the ideal description of such systems that directly mimics the experimental condition. We present two distinct algorithms: a self-consistent field method and a direct variational free energy minimization method using auxiliary Hamiltonians (GC-AuxH), to solve the Kohn-Sham equations of electronic density-functional theory directly in the grand canonical ensemble at fixed potential. Both methods substantially improve performance compared to a sequence of conventional fixed-number calculations targeting the desired potential, with the GC-AuxH method additionally exhibiting reliable and smooth exponential convergence of the grand free energy. Finally, we apply grand-canonical density-functional theory to the under-potential deposition of copper on platinum from chloride-containing electrolytes and show that chloride desorption, not partial copper monolayer formation, is responsible for the second voltammetric peak.

Self-Consistent Optimization of Excited States within Density-Functional Tight-Binding.

PubMed

Kowalczyk, Tim; Le, Khoa; Irle, Stephan

2016-01-12

We present an implementation of energies and gradients for the ΔDFTB method, an analogue of Δ-self-consistent-field density functional theory (ΔSCF) within density-functional tight-binding, for the lowest singlet excited state of closed-shell molecules. Benchmarks of ΔDFTB excitation energies, optimized geometries, Stokes shifts, and vibrational frequencies reveal that ΔDFTB provides a qualitatively correct description of changes in molecular geometries and vibrational frequencies due to excited-state relaxation. The accuracy of ΔDFTB Stokes shifts is comparable to that of ΔSCF-DFT, and ΔDFTB performs similarly to ΔSCF with the PBE functional for vertical excitation energies of larger chromophores where the need for efficient excited-state methods is most urgent. We provide some justification for the use of an excited-state reference density in the DFTB expansion of the electronic energy and demonstrate that ΔDFTB preserves many of the properties of its parent ΔSCF approach. This implementation fills an important gap in the extended framework of DFTB, where access to excited states has been limited to the time-dependent linear-response approach, and affords access to rapid exploration of a valuable class of excited-state potential energy surfaces.

Grand canonical electronic density-functional theory: Algorithms and applications to electrochemistry

DOE PAGES

Sundararaman, Ravishankar; Goddard, III, William A.; Arias, Tomas A.

2017-03-16

First-principles calculations combining density-functional theory and continuum solvation models enable realistic theoretical modeling and design of electrochemical systems. When a reaction proceeds in such systems, the number of electrons in the portion of the system treated quantum mechanically changes continuously, with a balancing charge appearing in the continuum electrolyte. A grand-canonical ensemble of electrons at a chemical potential set by the electrode potential is therefore the ideal description of such systems that directly mimics the experimental condition. We present two distinct algorithms: a self-consistent field method and a direct variational free energy minimization method using auxiliary Hamiltonians (GC-AuxH), to solvemore » the Kohn-Sham equations of electronic density-functional theory directly in the grand canonical ensemble at fixed potential. Both methods substantially improve performance compared to a sequence of conventional fixed-number calculations targeting the desired potential, with the GC-AuxH method additionally exhibiting reliable and smooth exponential convergence of the grand free energy. Lastly, we apply grand-canonical density-functional theory to the under-potential deposition of copper on platinum from chloride-containing electrolytes and show that chloride desorption, not partial copper monolayer formation, is responsible for the second voltammetric peak.« less

Central serotonin modulates neural responses to virtual violent actions in emotion regulation networks.

PubMed

Wolf, Dhana; Klasen, Martin; Eisner, Patrick; Zepf, Florian D; Zvyagintsev, Mikhail; Palomero-Gallagher, Nicola; Weber, René; Eisert, Albrecht; Mathiak, Klaus

2018-06-08

Disruptions in the cortico-limbic emotion regulation networks have been linked to depression, anxiety, impulsivity, and aggression. Altered transmission of the central nervous serotonin (5-HT) contributes to dysfunctions in the cognitive control of emotions. To date, studies relating to pharmaco-fMRI challenging of the 5-HT system have focused on emotion processing for facial expressions. We investigated effects of a single-dose selective 5-HT reuptake inhibitor (escitalopram) on emotion regulation during virtual violence. For this purpose, 38 male participants played a violent video game during fMRI scanning. The SSRI reduced neural responses to violent actions in right-hemispheric inferior frontal gyrus and medial prefrontal cortex encompassing the anterior cingulate cortex (ACC), but not to non-violent actions. Within the ACC, the drug effect differentiated areas with high inhibitory 5-HT1A receptor density (subgenual s25) from those with a lower density (pregenual p32, p24). This finding links functional responses during virtual violent actions with 5-HT neurotransmission in emotion regulation networks, underpinning the ecological validity of the 5-HT model in aggressive behavior. Available 5-HT receptor density data suggest that this SSRI effect is only observable when inhibitory and excitatory 5-HT receptors are balanced. The observed early functional changes may impact patient groups receiving SSRI treatment.

Effects of thinning on drought vulnerability and climate response in north temperate forest ecosystems

USGS Publications Warehouse

D’Amato, Anthony W.; Bradford, John B.; Fraver, Shawn; Palik, Brian J.

2013-01-01

Reducing tree densities through silvicultural thinning has been widely advocated as a strategy for enhancing resistance and resilience to drought, yet few empirical evaluations of this approach exist. We examined detailed dendrochronological data from a long-term (>50 yrs) replicated thinning experiment to determine if density reductions conferred greater resistance and/or resilience to droughts, assessed by the magnitude of stand-level growth reductions. Our results suggest that thinning generally enhanced drought resistance and resilience; however, this relationship showed a pronounced reversal over time in stands maintained at lower tree densities. Specifically, lower-density stands exhibited greater resistance and resilience at younger ages (49 years), yet exhibited lower resistance and resilience at older ages (76 years), relative to higher-density stands. We attribute this reversal to significantly greater tree sizes attained within the lower-density stands through stand development, which in turn increased tree-level water demand during the later droughts. Results from response-function analyses indicate that thinning altered growth-climate relationships, such that higher-density stands were more sensitive to growing-season precipitation relative to lower-density stands. These results confirm the potential of density management to moderate drought impacts on growth, and they highlight the importance of accounting for stand structure when predicting climate-change impacts to forest systems.

Effects of thinning on drought vulnerability and climate response in north temperate forest ecosystems.

PubMed

D'Amato, Anthony W; Bradford, John B; Fraver, Shawn; Palik, Brian J

2013-12-01

Reducing tree densities through silvicultural thinning has been widely advocated as a strategy for enhancing resistance and resilience to drought, yet few empirical evaluations of this approach exist. We examined detailed dendrochronological data from a long-term (> 50 years) replicated thinning experiment to determine if density reductions conferred greater resistance and/or resilience to droughts, assessed by the magnitude of stand-level growth reductions. Our results suggest that thinning generally enhanced drought resistance and resilience; however, this relationship showed a pronounced reversal over time in stands maintained at lower tree densities. Specifically, lower-density stands exhibited greater resistance and resilience at younger ages (49 years), yet exhibited lower resistance and resilience at older ages (76 years), relative to higher-density stands. We attribute this reversal to significantly greater tree sizes attained within the lower-density stands through stand development, which in turn increased tree-level water demand during the later droughts. Results from response-function analyses indicate that thinning altered growth-climate relationships, such that higher-density stands were more sensitive to growing-season precipitation relative to lower-density stands. These results confirm the potential of density management to moderate drought impacts on growth, and they highlight the importance of accounting for stand structure when predicting climate-change impacts to forests.

Multifocal electroretinography changes at the 1-year follow-up in a cohort of diabetic macular edema patients treated with ranibizumab.

PubMed

Baget-Bernaldiz, Marc; Romero-Aroca, Pedro; Bautista-Perez, Angel; Mercado, Joaquin

2017-10-01

To determine the changes in the multifocal electroretinogram (mfERG) at 1 year in a clinical series of diabetic macular edema (DME) patients treated with ranibizumab (RNBZ) using a pro re nata protocol. We analyzed a clinical series of 35 eyes of 35 patients with DME at baseline and after treating them with RNBZ over 1 year, in order to determine the change in the macular function, which was assessed by means of the response density and the implicit time of the first-order kernel (FOK) P1 wave of the mfERG at the foveola (R1), fovea (R2) and parafovea (R3). These electrophysiological parameters were studied taking into account different independent variables, such as DME type, degree of diabetic retinopathy (DR), level of preservation of both the ellipsoid zone (IS/OS) and the external limiting membrane (ELM) and changes in central retinal thickness (CRT) and total macular volume (TMV). We also studied the relationship between the response density and the best-corrected visual acuity (BCVA). Eyes with cystic and spongiform DME showed better response density with respect to the serous type (p < 0.001) at baseline. Similarly, eyes with high IS/OS and ELM preservation rates showed higher initial response density compared to the others (p < 0.001). Eyes with moderate DR had better response density compared to those with severe and proliferative DR (p = 0.001). At the beginning of the study, those eyes with proliferative and severe DR showed longer implicit times with respect to those with moderate DR (p = 0.04). The response density significantly increased in eyes that anatomically restored the IS/OS and the ELM after being treated with RNBZ (both p < 0.001). Similarly, eyes with spongiform DME further improved the response density with respect to those with cystic and serous DME (p < 0.001). On the contrary, eyes with hard exudates showed less improvement in their response density at the end of the study (p < 0.001). We observed a significant relationship between BCVA and the response density achieved at the end of the study (p = 0.012). Eyes with severe and proliferative DR significantly shortened implicit time compared to those with moderate DR (p = 0.04). The multifocal electroretinogram allowed us to differentiate groups of eyes with DME according to their electrophysiological profile, both initially and after being treated with RNBZ. Ranibizumab increased the response density in all DME types included in the study, with a maximum response in those eyes with spongiform type. Once treated with RNBZ, the macular electrophysiological activity improved in eyes that had a well-preserved ellipsoid zone and ELM. The presence of hard exudates was a limitation to the response density achieved at the foveola.

Calculation of spin-densities within the context of density functional theory. The crucial role of the correlation functional

NASA Astrophysics Data System (ADS)

Filatov, Michael; Cremer, Dieter

2005-09-01

It is demonstrated that the LYP correlation functional is not suited to be used for the calculation of electron spin resonance hyperfine structure (HFS) constants, nuclear magnetic resonance spin-spin coupling constants, magnetic, shieldings and other properties that require a balanced account of opposite- and equal-spin correlation, especially in the core region. In the case of the HFS constants of alkali atoms, LYP exaggerates opposite-spin correlation effects thus invoking too strong in-out correlation effects, an exaggerated spin-polarization pattern in the core shells of the atoms, and, consequently, too large HFS constants. Any correlation functional that provides a balanced account of opposite- and equal-spin correlation leads to improved HFS constants, which is proven by comparing results obtained with the LYP and the PW91 correlation functional. It is suggested that specific response properties are calculated with the PW91 rather than the LYP correlation functional.

Band structure and phonon properties of lithium fluoride at high pressure

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

Panchal, J. M., E-mail: amitjignesh@yahoo.co.in; Department of Physics, University School of Sciences, Gujarat University, Ahmedabad 380009, Gujarat; Joshi, Mitesh

2016-05-23

High pressure structural and electronic properties of Lithium Fluoride (LiF) have been studied by employing an ab-initio pseudopotential method and a linear response scheme within the density functional theory (DFT) in conjunction with quasi harmonic Debye model. The band structure and electronic density of states conforms that the LiF is stable and is having insulator behavior at ambient as well as at high pressure up to 1 Mbar. Conclusions based on Band structure, phonon dispersion and phonon density of states are outlined.

Response of space shuttle insulation panels to acoustic noise pressure

NASA Technical Reports Server (NTRS)

Vaicaitis, R.

1976-01-01

The response of reusable space shuttle insulation panels to random acoustic pressure fields are studied. The basic analytical approach in formulating the governing equations of motion uses a Rayleigh-Ritz technique. The input pressure field is modeled as a stationary Gaussian random process for which the cross-spectral density function is known empirically from experimental measurements. The response calculations are performed in both frequency and time domain.

Renal microvascular disease determines the responses to revascularization in experimental renovascular disease.

PubMed

Chade, Alejandro R; Kelsen, Silvia

2010-08-01

Percutaneous transluminal renal angioplasty (PTRA) is the most frequent therapeutic approach to resolving renal artery stenosis (RAS). However, renal function recovers in only 30% of the cases. The causes of these poor outcomes are still unknown. We hypothesized that preserving the renal microcirculation distal to RAS will improve the responses to PTRA. RAS was induced in 28 pigs. In 14, vascular endothelial growth factor (VEGF)-165 0.05 microg/kg was infused intrarenally (RAS+VEGF). Single-kidney function was assessed in all pigs in vivo using ultrafast CT after 6 weeks. Observation of half of the RAS and RAS+VEGF pigs was completed. The other half underwent PTRA and repeated VEGF, and CT studies were repeated 4 weeks later. Pigs were then euthanized, the stenotic kidney removed, renal microvascular (MV) architecture reconstructed ex vivo using 3D micro-CT, and renal fibrosis quantified. The degree of RAS and hypertension were similar in RAS and RAS+VEGF. Renal function and MV density were decreased in RAS but improved in RAS+VEGF. PTRA largely resolved RAS, but the improvements of hypertension and renal function were greater in RAS+VEGF+PTRA than in RAS+PTRA, accompanied by a 34% increase in MV density and decreased fibrosis. Preservation of the MV architecture and function in the stenotic kidney improved the responses to PTRA, indicating that renal MV integrity plays a role in determining the responses to PTRA. This study indicates that damage and early loss of renal MV is an important determinant of the progression of renal injury in RAS and instigates often irreversible damage.

RENAL MICROVASCULAR DISEASE DETERMINES THE RESPONSES TO REVASCULARIZATION IN EXPERIMENTAL RENOVASCULAR DISEASE

PubMed Central

Chade, Alejandro R.; Kelsen, Silvia

2011-01-01

Background Percutaneous trasluminal renal angioplasty (PTRA) is the most frequent therapeutic approach to resolve renal artery stenosis (RAS). However, renal function recovers in only 30% of the cases. The causes of these poor outcomes are still unknown. We hypothesize that preserving the renal microcirculation distal to RAS will improve the responses to PTRA. Methods and Results RAS was induced in 28 pigs. In 14, vascular endothelial growth factor (VEGF)-165 was infused intra-renally (RAS+VEGF, 0.05 µg/kg). Single-kidney function was assessed in all pigs in vivo using ultra-fast CT after 6 weeks. Half of the RAS/RAS+VEGF completed their observation, and the other half underwent PTRA, VEGF was repeated, and CT studies repeated 4 weeks later. Pigs were then euthanized, the stenotic kidney removed, renal microvascular (MV) architecture reconstructed ex-vivo using 3D micro-CT, and renal fibrosis quantified. Degree of RAS and hypertension were similar in RAS and RAS+VEGF. Renal function and MV density were decreased in RAS but improved in RAS+VEGF. PTRA largely resolved RAS, but the improvements of hypertension and renal function were greater in RAS+VEGF+PTRA than in RAS+PTRA, accompanied by a 34% increase in MV density and decreased fibrosis. Conclusion Preservation of the MV architecture and function in the stenotic kidney improved the responses to PTRA, indicating that renal MV integrity plays a role in determining the responses to PTRA. This study indicates that damage and early loss of renal MV is an important determinant of the progression of renal injury in RAS and instigates often irreversible damage. PMID:20587789

The study of electrical conduction mechanisms. [dielectric response of lunar fines

NASA Technical Reports Server (NTRS)

Morrison, H. F.

1974-01-01

The dielectric response of lunar fines 74241,2 is presented in the audio-frequency range and under lunarlike conditions. Results suggest that volatiles are released during storage and transport of the lunar sample. Apparently, subsequent absorption of volatiles on the sample surface alter its dielectric response. The assumed volatile influence disappear after evacuation. A comparison of the dielectric properties of lunar and terrestrial materials as a function of density, temperature, and frequency indicates that if the lunar simulator analyzed were completely devoid of atmospheric moisture it would present dielectric losses smaller than those of the lunar sample. It is concluded that density prevails over temperature as the controlling factor of dielectric permittivity in the lunar regolith and that dielectric losses vary slowly with depth.

Exchange potential from the common energy denominator approximation for the Kohn-Sham Green's function: Application to (hyper)polarizabilities of molecular chains

NASA Astrophysics Data System (ADS)

Grüning, M.; Gritsenko, O. V.; Baerends, E. J.

2002-04-01

An approximate Kohn-Sham (KS) exchange potential vxσCEDA is developed, based on the common energy denominator approximation (CEDA) for the static orbital Green's function, which preserves the essential structure of the density response function. vxσCEDA is an explicit functional of the occupied KS orbitals, which has the Slater vSσ and response vrespσCEDA potentials as its components. The latter exhibits the characteristic step structure with "diagonal" contributions from the orbital densities |ψiσ|2, as well as "off-diagonal" ones from the occupied-occupied orbital products ψiσψj(≠1)σ*. Comparison of the results of atomic and molecular ground-state CEDA calculations with those of the Krieger-Li-Iafrate (KLI), exact exchange (EXX), and Hartree-Fock (HF) methods show, that both KLI and CEDA potentials can be considered as very good analytical "closure approximations" to the exact KS exchange potential. The total CEDA and KLI energies nearly coincide with the EXX ones and the corresponding orbital energies ɛiσ are rather close to each other for the light atoms and small molecules considered. The CEDA, KLI, EXX-ɛiσ values provide the qualitatively correct order of ionizations and they give an estimate of VIPs comparable to that of the HF Koopmans' theorem. However, the additional off-diagonal orbital structure of vxσCEDA appears to be essential for the calculated response properties of molecular chains. KLI already considerably improves the calculated (hyper)polarizabilities of the prototype hydrogen chains Hn over local density approximation (LDA) and standard generalized gradient approximations (GGAs), while the CEDA results are definitely an improvement over the KLI ones. The reasons of this success are the specific orbital structures of the CEDA and KLI response potentials, which produce in an external field an ultranonlocal field-counteracting exchange potential.

Neonatal hemodynamic response to visual cortex activity: high-density near-infrared spectroscopy study

NASA Astrophysics Data System (ADS)

Liao, Steve M.; Gregg, Nick M.; White, Brian R.; Zeff, Benjamin W.; Bjerkaas, Katelin A.; Inder, Terrie E.; Culver, Joseph P.

2010-03-01

The neurodevelopmental outcome of neonatal intensive care unit (NICU) infants is a major clinical concern with many infants displaying neurobehavioral deficits in childhood. Functional neuroimaging may provide early recognition of neural deficits in high-risk infants. Near-infrared spectroscopy (NIRS) has the advantage of providing functional neuroimaging in infants at the bedside. However, limitations in traditional NIRS have included contamination from superficial vascular dynamics in the scalp. Furthermore, controversy exists over the nature of normal vascular, responses in infants. To address these issues, we extend the use of novel high-density NIRS arrays with multiple source-detector distances and a superficial signal regression technique to infants. Evaluations of healthy term-born infants within the first three days of life are performed without sedation using a visual stimulus. We find that the regression technique significantly improves brain activation signal quality. Furthermore, in six out of eight infants, both oxy- and total hemoglobin increases while deoxyhemoglobin decreases, suggesting that, at term, the neurovascular coupling in the visual cortex is similar to that found in healthy adults. These results demonstrate the feasibility of using high-density NIRS arrays in infants to improve signal quality through superficial signal regression, and provide a foundation for further development of high-density NIRS as a clinical tool.

Optical response tuning in nanorod-on-semicontinous film systems: A computational study

NASA Astrophysics Data System (ADS)

Mokkath, Junais Habeeb

2018-01-01

Strongly confined and intense optical fields within the plasmonic metal nanocavities show outstanding potential for a wide range of functionalities in nanophotonics. Using time dependent density functional theory calculations, we investigate the optical response evolution as a function of the gap separation distances in nanorod-on-film systems comprised of a nanorod (NR) made of Al or Na on top of an Al film. Huge optical field modulations emerged in the chemically distinct Na NR - Al film system in comparison to the Al NR - Al film system, indicating the vital role of metals involved. We further study the optical response modifications by placing a conducting molecule in the gap region, finding strong spectral modulations via through-molecule electron tunneling.

Conceptual DFT: the chemical relevance of higher response functions.

PubMed

Geerlings, P; De Proft, F

2008-06-07

In recent years conceptual density functional theory offered a perspective for the interpretation/prediction of experimental/theoretical reactivity data on the basis of a series of response functions to perturbations in the number of electrons and/or external potential. This approach has enabled the sharp definition and computation, from first principles, of a series of well-known but sometimes vaguely defined chemical concepts such as electronegativity and hardness. In this contribution, a short overview of the shortcomings of the simplest, first order response functions is illustrated leading to a description of chemical bonding in a covalent interaction in terms of interacting atoms or groups, governed by electrostatics with the tendency to polarize bonds on the basis of electronegativity differences. The second order approach, well known until now, introduces the hardness/softness and Fukui function concepts related to polarizability and frontier MO theory, respectively. The introduction of polarizability/softness is also considered in a historical perspective in which polarizability was, with some exceptions, mainly put forward in non covalent interactions. A particular series of response functions, arising when the changes in the external potential are solely provoked by changes in nuclear configurations (the "R-analogues") are also systematically considered. The main part of the contribution is devoted to third order response functions which, at first sight, may be expected not to yield chemically significant information, as turns out to be for the hyperhardness. A counterexample is the dual descriptor and its R analogue, the initial hardness response, which turns out to yield a firm basis to regain the Woodward-Hoffmann rules for pericyclic reactions based on a density-only basis, i.e. without involving the phase, sign, symmetry of the wavefunction. Even the second order nonlinear response functions are shown possibly to bear interesting information, e.g. on the local and global polarizability. Its derivatives may govern the influence of charge on the polarizability, the R-analogues being the nuclear Fukui function and the quadratic and cubic force constants. Although some of the higher order derivatives may be difficult to evaluate a comparison with the energy expansion used in spectroscopy in terms of nuclear displacements, nuclear magnetic moments, electric and magnetic fields leads to the conjecture that, certainly cross terms may contain new, intricate information for understanding chemical reactivity.

Image-based 3D modeling study of the influence of vessel density and blood hemoglobin concentration on tumor oxygenation and response to irradiation.

PubMed

Lagerlöf, Jakob H; Kindblom, Jon; Cortez, Eliane; Pietras, Kristian; Bernhardt, Peter

2013-02-01

Hypoxia is one of the most important factors influencing clinical outcome after radiotherapy. Improved knowledge of factors affecting the levels and distribution of oxygen within a tumor is needed. The authors constructed a theoretical 3D model based on histological images to analyze the influence of vessel density and hemoglobin (Hb) concentration on the response to irradiation. The pancreases of a Rip-Tag2 mouse, a model of malignant insulinoma, were excised, cryosectioned, immunostained, and photographed. Vessels were identified by image thresholding and a 3D vessel matrix assembled. The matrix was reduced to functional vessel segments and enlarged by replication. The steady-state oxygen tension field of the tumor was calculated by iteratively employing Green's function method for diffusion and the Michaelis-Menten model for consumption. The impact of vessel density on the radiation response was studied by removing a number of randomly selected vessels. The impact of Hb concentration was studied by independently changing vessel oxygen partial pressure (pO(2)). For each oxygen distribution, the oxygen enhancement ratio (OER) was calculated and the mean absorbed dose at which the tumor control probability (TCP) was 0.99 (D(99)) was determined using the linear-quadratic cell survival model (LQ model). Decreased pO(2) shifted the oxygen distribution to lower values, whereas decreased vessel density caused the distribution to widen and shift to lower values. Combined scenarios caused lower-shifted distributions, emphasising log-normal characteristics. Vessel reduction combined with increased blood pO(2) caused the distribution to widen due to a lack of vessels. The most pronounced radiation effect of increased pO(2) occurred with tumor tissue with 50% of the maximum vessel density used in the simulations. A 51% decrease in D(99), from 123 to 60 Gy, was found between the lowest and highest pO(2) concentrations. Our results indicate that an intermediate vascular density region exists where enhanced blood oxygen concentration may be beneficial for radiation response. The results also suggest that it is possible to distinguish between diffusion-limited and anemic hypoxia from the characteristics of the pO(2) distribution.

Unconstrained Recovery Characterization of Shape-Memory Polymer Networks for Cardiovascular Applications

PubMed Central

Yakacki, Christopher M.; Shandas, Robin; Lanning, Craig; Rech, Bryan; Eckstein, Alex; Gall, Ken

2009-01-01

Shape-memory materials have been proposed in biomedical device design due to their ability to facilitate minimally invasive surgery and recover to a predetermined shape in-vivo. Use of the shape-memory effect in polymers is proposed for cardiovascular stent interventions to reduce the catheter size for delivery and offer highly controlled and tailored deployment at body temperature. Shape-memory polymer networks were synthesized via photopolymerization of tert-butyl acrylate and poly (ethylene glycol) dimethacrylate to provide precise control over the thermomechanical response of the system. The free recovery response of the polymer stents at body temperature was studied as a function of glass transition temperature (Tg), crosslink density, geometrical perforation, and deformation temperature, all of which can be independently controlled. Room temperature storage of the stents was shown to be highly dependent on Tg and crosslink density. The pressurized response of the stents is also demonstrated to depend on crosslink density. This polymer system exhibits a wide range of shape-memory and thermomechanical responses to adapt and meet specific needs of minimally invasive cardiovascular devices. PMID:17296222

The deformation and failure response of closed-cell PMDI foams subjected to dynamic impact loading

DOE PAGES

Koohbor, Behrad; Mallon, Silas; Kidane, Addis; ...

2015-04-07

The present work aims to investigate the bulk deformation and failure response of closed-cell Polymeric Methylene Diphenyl Diisocyanate (PMDI) foams subjected to dynamic impact loading. First, foam specimens of different initial densities are examined and characterized in quasi-static loading conditions, where the deformation behavior of the samples is quantified in terms of the compressive elastic modulus and effective plastic Poisson's ratio. Then, the deformation response of the foam specimens subjected to direct impact loading is examined by taking into account the effects of material compressibility and inertia stresses developed during deformation, using high speed imaging in conjunction with 3D digitalmore » image correlation. The stress-strain response and the energy absorption as a function of strain rate and initial density are presented and the bulk failure mechanisms are discussed. As a result, it is observed that the initial density of the foam and the applied strain rates have a substantial influence on the strength, bulk failure mechanism and the energy dissipation characteristics of the foam specimens.« less

A Hybrid Density Functional Theory/Molecular Mechanics Approach for Linear Response Properties in Heterogeneous Environments.

PubMed

Rinkevicius, Zilvinas; Li, Xin; Sandberg, Jaime A R; Mikkelsen, Kurt V; Ågren, Hans

2014-03-11

We introduce a density functional theory/molecular mechanical approach for computation of linear response properties of molecules in heterogeneous environments, such as metal surfaces or nanoparticles embedded in solvents. The heterogeneous embedding environment, consisting from metallic and nonmetallic parts, is described by combined force fields, where conventional force fields are used for the nonmetallic part and capacitance-polarization-based force fields are used for the metallic part. The presented approach enables studies of properties and spectra of systems embedded in or placed at arbitrary shaped metallic surfaces, clusters, or nanoparticles. The capability and performance of the proposed approach is illustrated by sample calculations of optical absorption spectra of thymidine absorbed on gold surfaces in an aqueous environment, where we study how different organizations of the gold surface and how the combined, nonadditive effect of the two environments is reflected in the optical absorption spectrum.

Bose Condensation at He-4 Interfaces

NASA Technical Reports Server (NTRS)

Draeger, E. W.; Ceperley, D. M.

2003-01-01

Path Integral Monte Carlo was used to calculate the Bose-Einstein condensate fraction at the surface of a helium film at T = 0:77 K, as a function of density. Moving from the center of the slab to the surface, the condensate fraction was found to initially increase with decreasing density to a maximum value of 0.9, before decreasing. Long wavelength density correlations were observed in the static structure factor at the surface of the slab. A surface dispersion relation was calculated from imaginary-time density-density correlations. Similar calculations of the superfluid density throughout He-4 droplets doped with linear impurities (HCN)(sub n) are presented. After deriving a local estimator for the superfluid density distribution, we find a decreased superfluid response in the first solvation layer. This effective normal fluid exhibits temperature dependence similar to that of a two-dimensional helium system.

Bonding and magnetic response properties of several toroid structures. Insights of the role of Ni2S2 as a building block from relativistic density functional theory calculations.

PubMed

Muñoz-Castro, Alvaro

2011-10-06

Relativistic density functional calculations were carried out on several nickel toroid mercaptides of the general formula [Ni(μ-SR)(2)](n), with the aim to characterize and analyze their stability and magnetic response properties, in order to gain more insights into their stabilization and size-dependent behavior. The Ni-ligand interaction has been studied by means projected density of states and energy decomposition analysis, which denotes its stabilizing character. The graphical representation of the response to an external magnetic field is applied for the very first time taking into account the spin-orbit term. This map allows one to clearly characterize the magnetic behavior inside and in the closeness of the toroid structure showing the prescence of paratropic ring currents inside the Ni(n) ring, and by contrast, diatropic currents confined in each Ni(2)S(2) motif denoting an aromatic behavior (in terms of magnetic criteria). The calculated data suggests that the Ni(2)S(2) moiety can be regarded as a stable constructing block, which can afford several toroid structures of different nuclearities in agreement with that reported in the experimental literature. In addition, the effects of the relativistic treatment over the magnetic response properties on these lighter compounds are denoted by comparing nonrelativistic, scalar relativistic, and scalar plus spin-orbit relativistic treatments, showing their acting, although nonpronunced, role.

Amorphous to amorphous transition in particle rafts

NASA Astrophysics Data System (ADS)

Varshney, Atul; Sane, A.; Ghosh, Shankar; Bhattacharya, S.

2012-09-01

Space-filling assemblies of athermal hydrophobic particles floating at an air-water interface, called particle rafts, are shown to undergo an unusual phase transition between two amorphous states, i.e., a low density “less-rigid” state and a high density “more-rigid” state, as a function of particulate number density (Φ). The former is shown to be a capillary bridged solid and the latter is shown to be a frictionally coupled one. Simultaneous studies involving direct imaging as well as measuring its mechanical response to longitudinal and shear stresses show that the transition is marked by a subtle structural anomaly and a weakening of the shear response. The structural anomaly is identified from the variation of the mean coordination number, mean area of the Voronoi cells, and spatial profile of the displacement field with Φ. The weakened shear response is related to local plastic instabilities caused by the depinning of the contact line of the underlying fluid on the rough surfaces of the particles.

Carrington 2? Estimated response of the magnetosphere to a major outburst'

NASA Astrophysics Data System (ADS)

Bala, R.; Reiff, P. H.; Russell, C. T.

2013-12-01

On July 23, 2012, a major CME outburst on the far side of the Sun was observed by STEREO A [Russell et al, 2013]. Because of its intensity and by the fact that it included a significant flux of SEP's, it has been hailed as "Carrington 2" by some, warning that, had that CME been heading towards the Earth, it might have caused a major space weather event. We then used our neural network algorithm to use the solar wind and IMF parameters measured in situ by STEREO A to infer what the geoeffectiveness of that storm might have been. We presently show three of our neural network models on our realtime prediction site: http://mms.rice.edu/realtime/forecast.html. The three models use different base functions, trained by a solar cycle worth of solar wind input and geomagnetic response data. One model uses the "Boyle Index" (BI) as the base transfer function (which includes Bz and velocity but not density). The "Ram" function includes the Boyle Index plus a pressure term. The "Newell" function uses the Newell formula which does include density. Statistically, each of them is good for either a one-hour or three-hour prediction to better than one unit in Kp. (Another talk will show the relative success of each as a realtime predictor). STEREO density data were not available for this event, so we chose as a density proxy the density from a similar event in April 2001. Running this "C2" event through our neural network predictors showed that, in fact, this would have been an exceptional (but perhaps not devastating) event. The BI prediction resulted in a Kp of 8+, a Dst of less than -300 nT, but an AE index of only 1000 nT. Using the "Ram" code, the Kp prediction increased to almost 9+, with Dst again below -300 nT and AE of 1200 nT. Results of a range of possible assumptions about the density structure will be shown.

Species loss, delayed numerical responses, and functional compensation in an antbird guild.

PubMed

Touchton, Janeene M; Smith, James N M

2011-05-01

When a community loses species through fragmentation, its total food consumption may drop. Compensatory responses of remaining species, whereby survivors assume roles of extinct competitors, may reduce the impact of species loss through numerical or functional responses. We measured compensatory responses in two remaining antbird species on Barro Colorado Island, Panama, four decades after the loss of their dominant competitor, the Ocellated Antbird, Phaenostictus mcleannani. We compared current abundances and behavior of these two species on Barro Colorado to those reported before the island lost Ocellated Antbirds, and to those in a nearby mainland population where all three species still exist as a space-for-time substitution. The smaller, more subordinate Spotted Antbird, Hylophylax naevioides, responded far more strongly than the larger Bicolored Antbird, Gymnopithys leucaspis, which is functionally more like the Ocellated Antbird. Islandwide density of Spotted Antbirds has more than doubled since the loss of Ocellated Antbirds. Moreover, Spotted Antbirds now spend so much more of their time following ant swarms that their metabolic biomass at these swarms has more than tripled since Ocellated Antbirds disappeared. These responses in Spotted Antbirds were apparently delayed by >20 years. Bicolored Antbirds have not increased substantially in islandwide density or metabolic biomass at ant swarms. We hypothesize that behavioral flexibility, as shown by Spotted Antbirds on Barro Colorado Island, is a major factor governing the extent to which fragmented ecosystems can buffer the impacts of species loss.

Low-energy isovector and isoscalar dipole response in neutron-rich nuclei

NASA Astrophysics Data System (ADS)

Vretenar, D.; Niu, Y. F.; Paar, N.; Meng, J.

2012-04-01

The self-consistent random-phase approximation, based on the framework of relativistic energy density functionals, is employed in the study of isovector and isoscalar dipole response in 68Ni,132Sn, and 208Pb. The evolution of pygmy dipole states (PDSs) in the region of low excitation energies is analyzed as a function of the density dependence of the symmetry energy for a set of relativistic effective interactions. The occurrence of PDSs is predicted in the response to both the isovector and the isoscalar dipole operators, and its strength is enhanced with the increase in the symmetry energy at saturation and the slope of the symmetry energy. In both channels, the PDS exhausts a relatively small fraction of the energy-weighted sum rule but a much larger percentage of the inverse energy-weighted sum rule. For the isovector dipole operator, the reduced transition probability B(E1) of the PDSs is generally small because of pronounced cancellation of neutron and proton partial contributions. The isoscalar-reduced transition amplitude is predominantly determined by neutron particle-hole configurations, most of which add coherently, and this results in a collective response of the PDSs to the isoscalar dipole operator.

Impact of Pilot Delay and Non-Responsiveness on the Safety Performance of Airborne Separation

NASA Technical Reports Server (NTRS)

Consiglio, Maria; Hoadley, Sherwood; Wing, David; Baxley, Brian; Allen, Bonnie Danette

2008-01-01

Assessing the safety effects of prediction errors and uncertainty on automationsupported functions in the Next Generation Air Transportation System concept of operations is of foremost importance, particularly safety critical functions such as separation that involve human decision-making. Both ground-based and airborne, the automation of separation functions must be designed to account for, and mitigate the impact of, information uncertainty and varying human response. This paper describes an experiment that addresses the potential impact of operator delay when interacting with separation support systems. In this study, we evaluated an airborne separation capability operated by a simulated pilot. The experimental runs are part of the Safety Performance of Airborne Separation (SPAS) experiment suite that examines the safety implications of prediction errors and system uncertainties on airborne separation assistance systems. Pilot actions required by the airborne separation automation to resolve traffic conflicts were delayed within a wide range, varying from five to 240 seconds while a percentage of randomly selected pilots were programmed to completely miss the conflict alerts and therefore take no action. Results indicate that the strategicAirborne Separation Assistance System (ASAS) functions exercised in the experiment can sustain pilot response delays of up to 90 seconds and more, depending on the traffic density. However, when pilots or operators fail to respond to conflict alerts the safety effects are substantial, particularly at higher traffic densities.

Amide I vibrational circular dichroism of dipeptide: Conformation dependence and fragment analysis

NASA Astrophysics Data System (ADS)

Choi, Jun-Ho; Cho, Minhaeng

2004-03-01

The amide I vibrational circular dichroic response of alanine dipeptide analog (ADA) was theoretically investigated and the density functional theory calculation and fragment analysis results are presented. A variety of vibrational spectroscopic properties, local and normal mode frequencies, coupling constant, dipole, and rotational strengths, are calculated by varying two dihedral angles determining the three-dimensional ADA conformation. Considering two monopeptide fragments separately, we show that the amide I vibrational circular dichroism of the ADA can be quantitatively predicted. For several representative conformations of the model ADA, vibrational circular dichroism spectra are calculated by using both the density functional theory calculation and fragment analysis methods.

Prediction of Excitation Energies for Conjugated Oligomers and Polymers from Time-Dependent Density Functional Theory

PubMed Central

Tao, Jianmin; Tretiak, Sergei; Zhu, Jian-Xin

2010-01-01

With technological advances, light-emitting conjugated oligomers and polymers have become competitive candidates in the commercial market of light-emitting diodes for display and other technologies, due to the ultralow cost, light weight, and flexibility. Prediction of excitation energies of these systems plays a crucial role in the understanding of their optical properties and device design. In this review article, we discuss the calculation of excitation energies with time-dependent density functional theory, which is one of the most successful methods in the investigation of the dynamical response of molecular systems to external perturbation, owing to its high computational efficiency.

Vibrational Spectra and Density functional calculation of Organic Nonlinear Optic Crystal p-Amino Acetanilide

NASA Astrophysics Data System (ADS)

Saja, D.; Joe, I. Hubert; Jayakumar, V. S.

2006-01-01

The NIR-FT Raman, FT-IR spectral analysis of potential NLO material P-Amino Acetanilide is carried out by density functional computations. The optimized geometry shows that NH2 and NHCOCH3 groups substituted in para position of phenyl ring are non-planar which predicts maximum conjugation of molecule with donor and acceptor groups. Vibrational analysis reveals that simultaneous IR and Raman activation of the phenyl ring modes also provide evidence for the charge transfer interaction between the donors and the acceptor can make the molecule highly polarized and the intra molecular charge transfer interaction must be responsible for the NLO properties of PAA.

Individual Component Map of Rotatory Strength (ICM-RS) and Rotatory Strength Density (RSD) plots as analysis tools of circular dicroism spectra of complex systems.

PubMed

Chang, Le; Baseggio, Oscar; Sementa, Luca; Cheng, Daojian; Fronzoni, Giovanna; Toffoli, Daniele; Aprà, Edoardo; Stener, Mauro; Fortunelli, Alessandro

2018-06-13

We introduce Individual Component Maps of Rotatory Strength (ICM-RS) and Rotatory Strength Density (RSD) plots as analysis tools of chiro-optical linear response spectra deriving from time-dependent density functional theory (TDDFT) simulations. ICM-RS and RSD allow one to visualize the origin of chiro-optical response in momentum or real space, including signed contributions and therefore highlighting cancellation terms that are ubiquitous in chirality phenomena, and should be especially useful in analyzing the spectra of complex systems. As test cases, we use ICM-RS and RSD to analyze circular dichroism spectra of selected (Ag-Au)30(SR)18 monolayer-protected metal nanoclusters, showing the potential of the proposed tools to derive insight and understanding, and eventually rational design, in chiro-optical studies of complex systems.

Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method.

PubMed

Sinha, Debalina; Pavanello, Michele

2015-08-28

The correlation energy of interaction is an elusive and sought-after interaction between molecular systems. By partitioning the response function of the system into subsystem contributions, the Frozen Density Embedding (FDE)-vdW method provides a computationally amenable nonlocal correlation functional based on the adiabatic connection fluctuation dissipation theorem applied to subsystem density functional theory. In reproducing potential energy surfaces of weakly interacting dimers, we show that FDE-vdW, either employing semilocal or exact nonadditive kinetic energy functionals, is in quantitative agreement with high-accuracy coupled cluster calculations (overall mean unsigned error of 0.5 kcal/mol). When employing the exact kinetic energy (which we term the Kohn-Sham (KS)-vdW method), the binding energies are generally closer to the benchmark, and the energy surfaces are also smoother.

Exact kinetic energy enables accurate evaluation of weak interactions by the FDE-vdW method

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

Sinha, Debalina; Pavanello, Michele, E-mail: m.pavanello@rutgers.edu

2015-08-28

The correlation energy of interaction is an elusive and sought-after interaction between molecular systems. By partitioning the response function of the system into subsystem contributions, the Frozen Density Embedding (FDE)-vdW method provides a computationally amenable nonlocal correlation functional based on the adiabatic connection fluctuation dissipation theorem applied to subsystem density functional theory. In reproducing potential energy surfaces of weakly interacting dimers, we show that FDE-vdW, either employing semilocal or exact nonadditive kinetic energy functionals, is in quantitative agreement with high-accuracy coupled cluster calculations (overall mean unsigned error of 0.5 kcal/mol). When employing the exact kinetic energy (which we term themore » Kohn-Sham (KS)-vdW method), the binding energies are generally closer to the benchmark, and the energy surfaces are also smoother.« less

Discontinuous functional for linear-response time-dependent density-functional theory: The exact-exchange kernel and approximate forms

NASA Astrophysics Data System (ADS)

Hellgren, Maria; Gross, E. K. U.

2013-11-01

We present a detailed study of the exact-exchange (EXX) kernel of time-dependent density-functional theory with an emphasis on its discontinuity at integer particle numbers. It was recently found that this exact property leads to sharp peaks and step features in the kernel that diverge in the dissociation limit of diatomic systems [Hellgren and Gross, Phys. Rev. APLRAAN1050-294710.1103/PhysRevA.85.022514 85, 022514 (2012)]. To further analyze the discontinuity of the kernel, we here make use of two different approximations to the EXX kernel: the Petersilka Gossmann Gross (PGG) approximation and a common energy denominator approximation (CEDA). It is demonstrated that whereas the PGG approximation neglects the discontinuity, the CEDA includes it explicitly. By studying model molecular systems it is shown that the so-called field-counteracting effect in the density-functional description of molecular chains can be viewed in terms of the discontinuity of the static kernel. The role of the frequency dependence is also investigated, highlighting its importance for long-range charge-transfer excitations as well as inner-shell excitations.

Nonharmonicity in vibrated granular solids

NASA Astrophysics Data System (ADS)

Schreck, Carl

2012-02-01

We have shown that granular packings composed of frictionless particles with repulsive contact interactions are strongly nonharmonic. When infinitesimally perturbed along linear response eigenmodes of the static packing, energy leaks from the original mode of vibration to a continuum of frequencies due solely to contact breaking even when the system is under significant compression. Further, vibrated packings possess well-defined equilibrium positions that are different than those of the unperturbed packing. The vibrational density of states obtained using the displacement matrix and velocity autocorrelation function methods exhibit an increase in the number of low-frequency modes over that obtained from linear response of the static packing. The form of the density of states in vibrated granular packings is reminiscent of the low-frequency behavior of the vibrational density of states in fluid systems. We also investigate the effects of inter-particle friction, dissipation, particle shape, and degree of positional order on the density of states and thermal transport properties in driven granular packings.

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.

Acute Ischemia Induced by High-Density Culture Increases Cytokine Expression and Diminishes the Function and Viability of Highly Purified Human Islets of Langerhans.

PubMed

Smith, Kate E; Kelly, Amy C; Min, Catherine G; Weber, Craig S; McCarthy, Fiona M; Steyn, Leah V; Badarinarayana, Vasudeo; Stanton, J Brett; Kitzmann, Jennifer P; Strop, Peter; Gruessner, Angelika C; Lynch, Ronald M; Limesand, Sean W; Papas, Klearchos K

2017-11-01

Encapsulation devices have the potential to enable cell-based insulin replacement therapies (such as human islet or stem cell-derived β cell transplantation) without immunosuppression. However, reasonably sized encapsulation devices promote ischemia due to high β cell densities creating prohibitively large diffusional distances for nutrients. It is hypothesized that even acute ischemic exposure will compromise the therapeutic potential of cell-based insulin replacement. In this study, the acute effects of high-density ischemia were investigated in human islets to develop a detailed profile of early ischemia induced changes and targets for intervention. Human islets were exposed in a pairwise model simulating high-density encapsulation to normoxic or ischemic culture for 12 hours, after which viability and function were measured. RNA sequencing was conducted to assess transcriptome-wide changes in gene expression. Islet viability after acute ischemic exposure was reduced compared to normoxic culture conditions (P < 0.01). Insulin secretion was also diminished, with ischemic β cells losing their insulin secretory response to stimulatory glucose levels (P < 0.01). RNA sequencing revealed 657 differentially expressed genes following ischemia, with many that are associated with increased inflammatory and hypoxia-response signaling and decreased nutrient transport and metabolism. In order for cell-based insulin replacement to be applied as a treatment for type 1 diabetes, oxygen and nutrient delivery to β cells will need to be maintained. We demonstrate that even brief ischemic exposure such as would be experienced in encapsulation devices damages islet viability and β cell function and leads to increased inflammatory signaling.

Speed-of-light limitations in passive linear media

NASA Astrophysics Data System (ADS)

Welters, Aaron; Avniel, Yehuda; Johnson, Steven G.

2014-08-01

We prove that well-known speed-of-light restrictions on electromagnetic energy velocity can be extended to a new level of generality, encompassing even nonlocal chiral media in periodic geometries, while at the same time weakening the underlying assumptions to only passivity and linearity of the medium (either with a transparency window or with dissipation). As was also shown by other authors under more limiting assumptions, passivity alone is sufficient to guarantee causality and positivity of the energy density (with no thermodynamic assumptions). Our proof is general enough to include a very broad range of material properties, including anisotropy, bianisotropy (chirality), nonlocality, dispersion, periodicity, and even delta functions or similar generalized functions. We also show that the "dynamical energy density" used by some previous authors in dissipative media reduces to the standard Brillouin formula for dispersive energy density in a transparency window. The results in this paper are proved by exploiting deep results from linear-response theory, harmonic analysis, and functional analysis that had previously not been brought together in the context of electrodynamics.

Final Technical Report [Scalable methods for electronic excitations and optical responses of nanostructures: mathematics to algorithms to observables

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

Saad, Yousef

2014-03-19

The master project under which this work is funded had as its main objective to develop computational methods for modeling electronic excited-state and optical properties of various nanostructures. The specific goals of the computer science group were primarily to develop effective numerical algorithms in Density Functional Theory (DFT) and Time Dependent Density Functional Theory (TDDFT). There were essentially four distinct stated objectives. The first objective was to study and develop effective numerical algorithms for solving large eigenvalue problems such as those that arise in Density Functional Theory (DFT) methods. The second objective was to explore so-called linear scaling methods ormore » Methods that avoid diagonalization. The third was to develop effective approaches for Time-Dependent DFT (TDDFT). Our fourth and final objective was to examine effective solution strategies for other problems in electronic excitations, such as the GW/Bethe-Salpeter method, and quantum transport problems.« less

Electric Field Induced Spectra of H sub 2 and D sub 2

NASA Technical Reports Server (NTRS)

Boyd, William Joseph

1974-01-01

The frequencies of four Q-branch lines of H2 and five Q-branch lines of D2 were measured as a function of density, and their shifts were observed to be in the linear region. The individual slopes and extrapolated zero density frequency of each line was determined. Hydrogen was measured for polarizability using the integrated intensity of the Q1(0) and S1(1), H2 absorption line. A highly automated technique for determining the response function of the spectrometer using digitally recorded data is presented. For the Q1(0) and Q1(1) lines of H2 the halfwidths were measured as a function of electric field intensity at constant pressure, and again at several densities and compared to previously measured widths. Technical and operational details of equipment built for this experiment, and for the five-meter Littrow spectrometer used, are described. Modifications of the spectrometer optics to accept the Stark cell are discussed.

Adaptive frozen orbital treatment for the fragment molecular orbital method combined with density-functional tight-binding

NASA Astrophysics Data System (ADS)

Nishimoto, Yoshio; Fedorov, Dmitri G.

2018-02-01

The exactly analytic gradient is derived and implemented for the fragment molecular orbital (FMO) method combined with density-functional tight-binding (DFTB) using adaptive frozen orbitals. The response contributions which arise from freezing detached molecular orbitals on the border between fragments are computed by solving Z-vector equations. The accuracy of the energy, its gradient, and optimized structures is verified on a set of representative inorganic materials and polypeptides. FMO-DFTB is applied to optimize the structure of a silicon nano-wire, and the results are compared to those of density functional theory and experiment. FMO accelerates the DFTB calculation of a boron nitride nano-ring with 7872 atoms by a factor of 406. Molecular dynamics simulations using FMO-DFTB applied to a 10.7 μm chain of boron nitride nano-rings, consisting of about 1.2 × 106 atoms, reveal the rippling and twisting of nano-rings at room temperature.

Multicomponent Time-Dependent Density Functional Theory: Proton and Electron Excitation Energies.

PubMed

Yang, Yang; Culpitt, Tanner; Hammes-Schiffer, Sharon

2018-04-05

The quantum mechanical treatment of both electrons and protons in the calculation of excited state properties is critical for describing nonadiabatic processes such as photoinduced proton-coupled electron transfer. Multicomponent density functional theory enables the consistent quantum mechanical treatment of more than one type of particle and has been implemented previously for studying ground state molecular properties within the nuclear-electronic orbital (NEO) framework, where all electrons and specified protons are treated quantum mechanically. To enable the study of excited state molecular properties, herein the linear response multicomponent time-dependent density functional theory (TDDFT) is derived and implemented within the NEO framework. Initial applications to FHF - and HCN illustrate that NEO-TDDFT provides accurate proton and electron excitation energies within a single calculation. As its computational cost is similar to that of conventional electronic TDDFT, the NEO-TDDFT approach is promising for diverse applications, particularly nonadiabatic proton transfer reactions, which may exhibit mixed electron-proton vibronic excitations.

Unique magnetic and thermoelectric properties of chemically functionalized narrow carbon polymers.

PubMed

Zberecki, K; Wierzbicki, M; Swirkowicz, R; Barnaś, J

2017-02-01

We analyze magnetic, transport and thermoelectric properties of narrow carbon polymers, which are chemically functionalized with nitroxide groups. Numerical calculations of the electronic band structure and the corresponding transmission function are based on density functional theory. Transport and thermoelectric parameters are calculated in the linear response regime, with particular interest in charge and spin thermopowers (charge and spin Seebeck effects). Such nanoribbons are shown to have thermoelectric properties described by large thermoelectric efficiency, which makes these materials promising from the application point of view.

Use of Subsonic Kernel Function in an Influence-Coefficient Method of Aeroelastic Analysis and some Comparisons with Experiment

NASA Technical Reports Server (NTRS)

Sewall, John L.; Herr, Robert W.; Watkins, Charles E.

1960-01-01

This paper illustrates the development and application of an influence-coefficient method of analysis for calculating the response of a flexible wing in an airstream to an oscillating disturbing force and for treating such aeroelastic instabilities as flutter and divergence. Aerodynamic coefficients are derived on the basis of lifting - surface theory for subsonic compressible flow by use of the method presented in NASA Technical Report R-48. Application of the analysis is made to a uniform cantilever wing- tip tank configuration for which responses to a sinusoidal disturbing force and flutter speeds were measured over a range of subsonic Mach numbers and densities. Calculated responses and flutter speeds based on flexibility influence coefficients measured at nine stations are in good agreement with experiment, provided the aerodynamic load is distributed over the wing so that local centers of pressure very nearly coincide with these nine influence stations. The use of experimental values of bending and torsional structural damping coefficients in the analysis generally improved the agreement between calculated and experimental responses. Some calculations were made to study the effects on density on responses near the flutter conditions, and linear response trends were obtained over a wide range of densities.

Investigation of the shear response and geometrically necessary dislocation densities in shear localization in high-purity titanium

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

Zhu, Chaoyi; Livescu, Veronica; Harrington, Tyler

The influence of microstructural anisotropy on shear response of high-purity titanium was studied using the compact forced-simple-shear specimen (CFSS) loaded under quasi-static loading conditions. Post-mortem characterization reveals significant difference in shear response of different directions in the same material due to material crystallographic texture anisotropy. Shear bands are narrower in specimens in which the shear zone is aligned along the direction with a strong {0001} basal texture. Twinning was identified as an active mechanism to accommodate strains in the shear region in both orientations. This paper confirms the applicability of the CFSS design for the investigation of differences in themore » shear response of materials as a function of process-induced crystallographic texture. A detailed, systematic approach to quantifying shear band evolution by evaluating geometrically necessary dislocations (GND) associated with crystallographic anisotropy is presented. Finally, the results show that: i) line average GND density profiles, for Ti samples that possess a uniform equiaxed-grain structure, but with strong crystallographic anisotropy, exhibit significant differences in GND density close to the shear band center; ii) GND profiles decrease steadily away from the shear band as the plastic strain diminishes, in agreement with Ashby's theory of work hardening, where the higher GND density in the through-thickness (TT) orientation is a result of restricted < a > type slip in the shear band compared with in-plane (IP) samples; iii) the anisotropy in deformation response is derived from initial crystallographic texture of the materials, where GND density of < a > GNDs are higher adjacent to the shear band in the through-thickness sample oriented away from easy slip, but the density of < c+a > type GNDs are very similar in these two samples; and iv) the increase in grain average GND density was determined to have strong correlation to an increase in the Euler Φ angle of the grain average orientation, indicating an increased misorientation angle evolution.« less

Investigation of the shear response and geometrically necessary dislocation densities in shear localization in high-purity titanium

DOE PAGES

Zhu, Chaoyi; Livescu, Veronica; Harrington, Tyler; ...

2017-03-31

The influence of microstructural anisotropy on shear response of high-purity titanium was studied using the compact forced-simple-shear specimen (CFSS) loaded under quasi-static loading conditions. Post-mortem characterization reveals significant difference in shear response of different directions in the same material due to material crystallographic texture anisotropy. Shear bands are narrower in specimens in which the shear zone is aligned along the direction with a strong {0001} basal texture. Twinning was identified as an active mechanism to accommodate strains in the shear region in both orientations. This paper confirms the applicability of the CFSS design for the investigation of differences in themore » shear response of materials as a function of process-induced crystallographic texture. A detailed, systematic approach to quantifying shear band evolution by evaluating geometrically necessary dislocations (GND) associated with crystallographic anisotropy is presented. Finally, the results show that: i) line average GND density profiles, for Ti samples that possess a uniform equiaxed-grain structure, but with strong crystallographic anisotropy, exhibit significant differences in GND density close to the shear band center; ii) GND profiles decrease steadily away from the shear band as the plastic strain diminishes, in agreement with Ashby's theory of work hardening, where the higher GND density in the through-thickness (TT) orientation is a result of restricted < a > type slip in the shear band compared with in-plane (IP) samples; iii) the anisotropy in deformation response is derived from initial crystallographic texture of the materials, where GND density of < a > GNDs are higher adjacent to the shear band in the through-thickness sample oriented away from easy slip, but the density of < c+a > type GNDs are very similar in these two samples; and iv) the increase in grain average GND density was determined to have strong correlation to an increase in the Euler Φ angle of the grain average orientation, indicating an increased misorientation angle evolution.« less

Seagrass canopy photosynthetic response is a function of canopy density and light environment: a model for Amphibolis griffithii.

PubMed

Hedley, John D; McMahon, Kathryn; Fearns, Peter

2014-01-01

A three-dimensional computer model of canopies of the seagrass Amphibolis griffithii was used to investigate the consequences of variations in canopy structure and benthic light environment on leaf-level photosynthetic saturation state. The model was constructed using empirical data of plant morphometrics from a previously conducted shading experiment and validated well to in-situ data on light attenuation in canopies of different densities. Using published values of the leaf-level saturating irradiance for photosynthesis, results show that the interaction of canopy density and canopy-scale photosynthetic response is complex and non-linear, due to the combination of self-shading and the non-linearity of photosynthesis versus irradiance (P-I) curves near saturating irradiance. Therefore studies of light limitation in seagrasses should consider variation in canopy structure and density. Based on empirical work, we propose a number of possible measures for canopy scale photosynthetic response that can be plotted to yield isoclines in the space of canopy density and light environment. These plots can be used to interpret the significance of canopy changes induced as a response to decreases in the benthic light environment: in some cases canopy thinning can lead to an equivalent leaf level light environment, in others physiological changes may also be required but these alone may be inadequate for canopy survival. By providing insight to these processes the methods developed here could be a valuable management tool for seagrass conservation during dredging or other coastal developments.

Seagrass Canopy Photosynthetic Response Is a Function of Canopy Density and Light Environment: A Model for Amphibolis griffithii

PubMed Central

Hedley, John D.; McMahon, Kathryn; Fearns, Peter

2014-01-01

A three-dimensional computer model of canopies of the seagrass Amphibolis griffithii was used to investigate the consequences of variations in canopy structure and benthic light environment on leaf-level photosynthetic saturation state. The model was constructed using empirical data of plant morphometrics from a previously conducted shading experiment and validated well to in-situ data on light attenuation in canopies of different densities. Using published values of the leaf-level saturating irradiance for photosynthesis, results show that the interaction of canopy density and canopy-scale photosynthetic response is complex and non-linear, due to the combination of self-shading and the non-linearity of photosynthesis versus irradiance (P-I) curves near saturating irradiance. Therefore studies of light limitation in seagrasses should consider variation in canopy structure and density. Based on empirical work, we propose a number of possible measures for canopy scale photosynthetic response that can be plotted to yield isoclines in the space of canopy density and light environment. These plots can be used to interpret the significance of canopy changes induced as a response to decreases in the benthic light environment: in some cases canopy thinning can lead to an equivalent leaf level light environment, in others physiological changes may also be required but these alone may be inadequate for canopy survival. By providing insight to these processes the methods developed here could be a valuable management tool for seagrass conservation during dredging or other coastal developments. PMID:25347849

Characterization of the Earwig, Doru lineare, as a Predator of Larvae of the Fall Armyworm, Spodoptera frugiperda: A Functional Response Study

PubMed Central

Sueldo, Mabel Romero; Bruzzone, Octavio A.; Virla, Eduardo G.

2010-01-01

Spodoptera frugiperda Smith (Lepidoptera: Noctuidae) is considered as the most important pest of maize in almost all tropical America. In Argentina, the earwig Doru lineare Eschscholtz (Dermaptera: Forficulidae) has been observed preying on S. frugiperda egg masses in corn crops, but no data about its potential role as a biocontrol agent of this pest have been provided. The predation efficiency of D. lineare on newly emerged S. frugiperda larva was evaluated through a laboratory functional response study. D. lineare showed type II functional response to S. frugiperda larval density, and disc equation estimations of searching efficiency and handling time were (a) = 0.374 and (t) = 182.9 s, respectively. Earwig satiation occurred at 39.4 S. frugiperda larvae. PMID:20575739

Hidden multiparticle excitation in a weakly interacting Bose-Einstein condensate

NASA Astrophysics Data System (ADS)

Watabe, Shohei

2018-03-01

We investigate multiparticle excitation effect on a collective density excitation as well as a single-particle excitation in a weakly interacting Bose-Einstein condensate (BEC). We find that although the weakly interacting BEC offers weak multiparticle excitation spectrum at low temperatures, this multiparticle excitation effect may not remain hidden, but emerges as bimodality in the density response function through the single-particle excitation. Identification of spectra in the BEC between the single-particle excitation and the density excitation is also assessed at nonzero temperatures, which has been known to be unique nature in the BEC at absolute zero temperature.

Study of electronic structure and Compton profiles of transition metal diborides

NASA Astrophysics Data System (ADS)

Bhatt, Samir; Heda, N. L.; Kumar, Kishor; Ahuja, B. L.

2017-08-01

We report Compton profiles (CPs) of transition metal diborides (MB2; M= Ti and Zr) using a 740 GBq 137Cs Compton spectrometer measured at an intermediate resolution of 0.34 a.u. To validate the experimental momentum densities, we have employed the linear combination of atomic orbitals (LCAO) method to compute the theoretical CPs along with the energy bands, density of states (DOS) and Mulliken's population response. The LCAO computations have been performed in the frame work of density functional theory (DFT) and hybridization of Hartree-Fock and DFT (namely B3LYP and PBE0). For both the diborides, the CPs based on revised Perdew-Burke-Ernzerhof exchange and correlation functions (DFT-PBESol) lead to a better agreement with the experimental momentum densities than other reported approximations. Energy bands, DOS and real space analysis of CPs confirm a metallic-like character of both the borides. Further, a comparison of DFT-PBESol and experimental data on equal-valence-electron-density scale shows more ionicity in ZrB2 than that in TiB2, which is also supported by the Mulliken's population based charge transfer data.

Time delay between the SYMH and the solar wind energy input during intense storms determined by response function analysis

NASA Astrophysics Data System (ADS)

Cao, X.; Du, A.

2014-12-01

We statistically studied the response time of the SYMH to the solar wind energy input ɛ by using the RFA approach. The average response time was 64 minutes. There was no clear trend among these events concerning to the minimum SYMH and storm type. It seems that the response time of magnetosphere to the solar wind energy input is independent on the storm intensity and the solar wind condition. The response function shows one peak even when the solar wind energy input and the SYMH have multi-peak. The response time exhibits as the intrinsic property of the magnetosphere that stands for the typical formation time of the ring current. This may be controlled by magnetospheric temperature, average number density, the oxygen abundance et al.

Calculation of nuclear spin-spin coupling constants using frozen density embedding

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

Götz, Andreas W., E-mail: agoetz@sdsc.edu; Autschbach, Jochen; Visscher, Lucas, E-mail: visscher@chem.vu.nl

2014-03-14

We present a method for a subsystem-based calculation of indirect nuclear spin-spin coupling tensors within the framework of current-spin-density-functional theory. Our approach is based on the frozen-density embedding scheme within density-functional theory and extends a previously reported subsystem-based approach for the calculation of nuclear magnetic resonance shielding tensors to magnetic fields which couple not only to orbital but also spin degrees of freedom. This leads to a formulation in which the electron density, the induced paramagnetic current, and the induced spin-magnetization density are calculated separately for the individual subsystems. This is particularly useful for the inclusion of environmental effects inmore » the calculation of nuclear spin-spin coupling constants. Neglecting the induced paramagnetic current and spin-magnetization density in the environment due to the magnetic moments of the coupled nuclei leads to a very efficient method in which the computationally expensive response calculation has to be performed only for the subsystem of interest. We show that this approach leads to very good results for the calculation of solvent-induced shifts of nuclear spin-spin coupling constants in hydrogen-bonded systems. Also for systems with stronger interactions, frozen-density embedding performs remarkably well, given the approximate nature of currently available functionals for the non-additive kinetic energy. As an example we show results for methylmercury halides which exhibit an exceptionally large shift of the one-bond coupling constants between {sup 199}Hg and {sup 13}C upon coordination of dimethylsulfoxide solvent molecules.« less

Self-consistent DFT +U method for real-space time-dependent density functional theory calculations

NASA Astrophysics Data System (ADS)

Tancogne-Dejean, Nicolas; Oliveira, Micael J. T.; Rubio, Angel

2017-12-01

We implemented various DFT+U schemes, including the Agapito, Curtarolo, and Buongiorno Nardelli functional (ACBN0) self-consistent density-functional version of the DFT +U method [Phys. Rev. X 5, 011006 (2015), 10.1103/PhysRevX.5.011006] within the massively parallel real-space time-dependent density functional theory (TDDFT) code octopus. We further extended the method to the case of the calculation of response functions with real-time TDDFT+U and to the description of noncollinear spin systems. The implementation is tested by investigating the ground-state and optical properties of various transition-metal oxides, bulk topological insulators, and molecules. Our results are found to be in good agreement with previously published results for both the electronic band structure and structural properties. The self-consistent calculated values of U and J are also in good agreement with the values commonly used in the literature. We found that the time-dependent extension of the self-consistent DFT+U method yields improved optical properties when compared to the empirical TDDFT+U scheme. This work thus opens a different theoretical framework to address the nonequilibrium properties of correlated systems.

Predatory potential of Euseius alatus (Phytoseiidae) on different life stages of Oligonychus ilicis (Tetranychidae) on coffee leaves under laboratory conditions.

PubMed

de Toledo, M A; Reis, P R; da Silveira, E C; de P Marafeli, P; de Souza-Pimentel, G C

2013-04-01

This study evaluated the predatory capacity of Euseius alatus (DeLeon) as a biological control agent of the pest mite Oligonychus ilicis (McGregor) on coffee leaves under laboratory conditions, using arenas containing 25 O. ilicis per coffee (Coffea arabica) leaf to one specimen of each stage of the predator mite. The functional response and oviposition rate of adult females of E. alatus were evaluated on coffee leaf arenas and offered from 1 to 125 immature stages of O. ilicis per arena. The number of preys killed and the number of eggs laid by the predator were evaluated every 24 h during 8 days. The preys consumed were daily replaced. Male and female adults of E. alatus were the most efficient in killing all developmental stages of O. ilicis. Larvae and nymphs of O. ilicis were the most consumed by all stages of the predatory mite. The functional response and oviposition rates of E. alatus increased as the prey density increased, with a positive and highly significant correlation. Regression analysis suggested a type II functional response, with a maximum predation of 22 O. ilicis/arena and a maximum oviposition rate of 1.7 eggs/day at a density of 70 O. ilicis/arena.

Electrophysiological heterogeneity of pacemaker cells in the rabbit intercaval region, including the SA node: insights from recording multiple ion currents in each cell.

PubMed

Monfredi, Oliver; Tsutsui, Kenta; Ziman, Bruce; Stern, Michael D; Lakatta, Edward G; Maltsev, Victor A

2018-03-01

Cardiac pacemaker cells, including cells of the sinoatrial node, are heterogeneous in size, morphology, and electrophysiological characteristics. The exact extent to which these cells differ electrophysiologically is unclear yet is critical to understanding their functioning. We examined major ionic currents in individual intercaval pacemaker cells (IPCs) sampled from the paracristal, intercaval region (including the sinoatrial node) that were spontaneously beating after enzymatic isolation from rabbit hearts. The beating rate was measured at baseline and after inhibition of the Ca 2+ pump with cyclopiazonic acid. Thereafter, in each cell, we consecutively measured the density of funny current ( I f ), delayed rectifier K + current ( I K ) (a surrogate of repolarization capacity), and L-type Ca 2+ current ( I Ca,L ) using whole cell patch clamp . The ionic current densities varied to a greater extent than previously appreciated, with some IPCs demonstrating very small or zero I f . The density of none of the currents was correlated with cell size, while I Ca,L and I f densities were related to baseline beating rates. I f density was correlated with I K density but not with that of I Ca,L . Inhibition of Ca 2+ cycling had a greater beating rate slowing effect in IPCs with lower I f densities. Our numerical model simulation indicated that 1) IPCs with small (or zero) I f or small I Ca,L can operate via a major contribution of Ca 2+ clock, 2) I f -Ca 2+ -clock interplay could be important for robust pacemaking function, and 3) coupled I f - I K function could regulate maximum diastolic potential. Thus, we have demonstrated marked electrophysiological heterogeneity of IPCs. This heterogeneity is manifested in basal beating rate and response to interference of Ca 2+ cycling, which is linked to I f . NEW & NOTEWORTHY In the present study, a hitherto unrecognized range of heterogeneity of ion currents in pacemaker cells from the intercaval region is demonstrated. Relationships between basal beating rate and L-type Ca 2+ current and funny current ( I f ) density are uncovered, along with a positive relationship between I f and delayed rectifier K + current. Links are shown between the response to Ca 2+ cycling blockade and I f density.

Tracing impacts of partner abundance in facultative pollination mutualisms: from individuals to populations.

PubMed

Geib, Jennifer C; Galen, Candace

2012-07-01

Partner abundance affects costs and benefits in obligate mutualisms, but its role in facultative partnerships is less clear. We address this gap in a pollination web consisting of two clovers (Trifolium) that differ in specialization on a bumble bee pollinator Bombus balteatus. We examine how pollination niche breadth affects plant responses to pollinator abundance, comparing early-flowering (specialized) and late-flowering (generalized) cohorts of T. parryi and early T. parryi to T. dasyphyllum, a pollination generalist. Co-pollinators disrupt the link between B. halteatus visitation and pollination rate for both clovers. Only for early-flowering T. parryi do visitation, pollination, and seed set increase with density of B. balteatus. Bumble bee density also alters timing of seed germination in T. parryi, with seeds from plants receiving augmented B. balteatus germinating sooner than seeds of open-pollinated counterparts. Benefits saturate at intermediate bumble bee densities. Despite strong effects of B. balteatus density on individual plant fitness components, population models suggest little impact of B. balteatus density on lamda in T. parryi or T. dasyphyllum. Findings show that functional redundancy in a pollinator guild mediates host-plant responses to partner density. Unexpected effects of pollinator density on life history schedule have implications for recruitment under pollinator decline.

Response functions for neutron skyshine analysis

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

Gui, A.A.; Shultis, J.K.; Faw, R.E.

1997-02-01

Neutron and associated secondary photon line-beam response functions (LBRFs) for point monodirectional neutron sources are generated using the MCNP Monte Carlo code for use in neutron skyshine analysis employing the integral line-beam method. The LBRFs are evaluated at 14 neutron source energies ranging from 0.01 to 14 MeV and at 18 emission angles from 1 to 170 deg, as measured from the source-to-detector axis. The neutron and associated secondary photon conical-beam response functions (CBRFs) for azimuthally symmetric neutron sources are also evaluated at 13 neutron source energies in the same energy range and at 13 polar angles of source collimationmore » from 1 to 89 deg. The response functions are approximated by an empirical three-parameter function of the source-to-detector distance. These response function approximations are available for a source-to-detector distance up to 2,500 m and, for the first time, give dose equivalent responses that are required for modern radiological assessments. For the CBRFs, ground correction factors for neutrons and secondary photons are calculated and also approximated by empirical formulas for use in air-over-ground neutron skyshine problems with azimuthal symmetry. In addition, simple procedures are proposed for humidity and atmospheric density corrections.« less

Optimized Vertex Method and Hybrid Reliability

NASA Technical Reports Server (NTRS)

Smith, Steven A.; Krishnamurthy, T.; Mason, B. H.

2002-01-01

A method of calculating the fuzzy response of a system is presented. This method, called the Optimized Vertex Method (OVM), is based upon the vertex method but requires considerably fewer function evaluations. The method is demonstrated by calculating the response membership function of strain-energy release rate for a bonded joint with a crack. The possibility of failure of the bonded joint was determined over a range of loads. After completing the possibilistic analysis, the possibilistic (fuzzy) membership functions were transformed to probability density functions and the probability of failure of the bonded joint was calculated. This approach is called a possibility-based hybrid reliability assessment. The possibility and probability of failure are presented and compared to a Monte Carlo Simulation (MCS) of the bonded joint.

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

NASA Astrophysics Data System (ADS)

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

2017-02-01

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

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

DOE PAGES

Sosa Vazquez, Xochitl A.; Isborn, Christine M.

2015-12-22

Density functional theory is often the method of choice for modeling the energetics of large molecules and including explicit solvation effects. It is preferable to use a method that treats systems of different sizes and with different amounts of explicit solvent on equal footing. However, recent work suggests that approximate density functional theory has a size-dependent error in the computation of the ionization potential. We here investigate the lack of size-intensivity of the ionization potential computed with approximate density functionals in vacuum and solution. We show that local and semi-local approximations to exchange do not yield a constant ionization potentialmore » for an increasing number of identical isolated molecules in vacuum. Instead, as the number of molecules increases, the total energy required to ionize the system decreases. Rather surprisingly, we find that this is still the case in solution, whether using a polarizable continuum model or with explicit solvent that breaks the degeneracy of each solute, and we find that explicit solvent in the calculation can exacerbate the size-dependent delocalization error. We demonstrate that increasing the amount of exact exchange changes the character of the polarization of the solvent molecules; for small amounts of exact exchange the solvent molecules contribute a fraction of their electron density to the ionized electron, but for larger amounts of exact exchange they properly polarize in response to the cationic solute. As a result, in vacuum and explicit solvent, the ionization potential can be made size-intensive by optimally tuning a long-range corrected hybrid functional.« less

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

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

Sosa Vazquez, Xochitl A.; Isborn, Christine M., E-mail: cisborn@ucmerced.edu

2015-12-28

Density functional theory is often the method of choice for modeling the energetics of large molecules and including explicit solvation effects. It is preferable to use a method that treats systems of different sizes and with different amounts of explicit solvent on equal footing. However, recent work suggests that approximate density functional theory has a size-dependent error in the computation of the ionization potential. We here investigate the lack of size-intensivity of the ionization potential computed with approximate density functionals in vacuum and solution. We show that local and semi-local approximations to exchange do not yield a constant ionization potentialmore » for an increasing number of identical isolated molecules in vacuum. Instead, as the number of molecules increases, the total energy required to ionize the system decreases. Rather surprisingly, we find that this is still the case in solution, whether using a polarizable continuum model or with explicit solvent that breaks the degeneracy of each solute, and we find that explicit solvent in the calculation can exacerbate the size-dependent delocalization error. We demonstrate that increasing the amount of exact exchange changes the character of the polarization of the solvent molecules; for small amounts of exact exchange the solvent molecules contribute a fraction of their electron density to the ionized electron, but for larger amounts of exact exchange they properly polarize in response to the cationic solute. In vacuum and explicit solvent, the ionization potential can be made size-intensive by optimally tuning a long-range corrected hybrid functional.« less

Comparison of Fatigue Life Estimation Using Equivalent Linearization and Time Domain Simulation Methods

NASA Technical Reports Server (NTRS)

Mei, Chuh; Dhainaut, Jean-Michel

2000-01-01

The Monte Carlo simulation method in conjunction with the finite element large deflection modal formulation are used to estimate fatigue life of aircraft panels subjected to stationary Gaussian band-limited white-noise excitations. Ten loading cases varying from 106 dB to 160 dB OASPL with bandwidth 1024 Hz are considered. For each load case, response statistics are obtained from an ensemble of 10 response time histories. The finite element nonlinear modal procedure yields time histories, probability density functions (PDF), power spectral densities and higher statistical moments of the maximum deflection and stress/strain. The method of moments of PSD with Dirlik's approach is employed to estimate the panel fatigue life.

Dielectric function and plasmons in graphene: A self-consistent-field calculation within a Markovian master equation formalism

DOE PAGES

Karimi, F.; Davoody, A. H.; Knezevic, I.

2016-05-12

We introduce a method for calculating the dielectric function of nanostructures with an arbitrary band dispersion and Bloch wave functions. The linear response of a dissipative electronic system to an external electromagnetic field is calculated by a self-consistent-field approach within a Markovian master equation formalism (SCF-MMEF) coupled with full-wave electromagnetic equations. The SCF-MMEF accurately accounts for several concurrent scattering mechanisms. The method captures interband electron-hole-pair generation, as well as the interband and intraband electron scattering with phonons and impurities. We employ the SCF-MMEF to calculate the dielectric function, complex conductivity, and loss function for supported graphene. From the loss-function maximum,more » we obtain plasmon dispersion and propagation length for different substrate types [nonpolar diamondlike carbon (DLC) and polar SiO 2 and hBN], impurity densities, carrier densities, and temperatures. Plasmons on the two polar substrates are suppressed below the highest surface phonon energy, while the spectrum is broad on the nonpolar DLC. Plasmon propagation lengths are comparable on polar and nonpolar substrates and are on the order of tens of nanometers, considerably shorter than previously reported. As a result, they improve with fewer impurities, at lower temperatures, and at higher carrier densities.« less

Transgenerational Effects Alter Plant Defense and Resistance in Nature

PubMed Central

Colicchio, Jack

2017-01-01

Trichomes, or leaf hairs, are epidermal extensions that take a variety of forms and perform many functions in plants, including herbivore defense. In this study, I document genetically determined variation, within-generation plasticity, and a direct role of trichomes in herbivore defense for Mimulus guttatus. After establishing the relationship between trichomes and herbivory, I test for transgenerational effects of wounding on trichome density and herbivore resistance. Patterns of inter-annual variation in herbivore density and the high cost of plant defense makes plant-herbivore interactions a system in which transgenerational phenotypic plasticity (TPP) is apt to evolve. Here, I demonstrate that parental damage alters offspring trichome density and herbivore resistance in nature. Moreover, this response varies between populations. This is among the first studies to demonstrate that TPP contributes to variation in nature, and also suggests that selection can modify TPP in response to local conditions. PMID:28102915

Ab-initio investigation of Rb substitution in KTP single crystal

NASA Astrophysics Data System (ADS)

Ghoohestani, Marzieh; Arab, Ali; Hashemifar, S. Javad; Sadeghi, Hossein

2018-01-01

The effects of rubidium doping on the structural, electronic, and optical properties of KTiOPO4 (KTP) are investigated in the framework of density functional theory. The equilibrium structural parameters of KTP and RbTiOPO4 (RTP) are calculated within the local density and Perdew-Burke-Ernzerhof (PBE), Wu-Cohen, and PBEsol formulation of generalized gradient approximations. We discuss that PBEsol predicts better equilibrium parameters for the KTP alloy. In addition, the variation of lattice constants and Ti-O-Ti bond angles are evaluated as a function of rubidium concentration. The modern modified Becke-Johnson functional is applied for more accurate band gap determination in the pure and alloyed KTP/RTP compounds. The phenomenological pseudoinversion parameter is calculated for a qualitative understanding of the effect of impurity on a non-linear optical response of KTP. We also analyze the behavior of the dielectric function, dispersive refractive indices, and birefringence of KTP/RTP alloys.

Measurements of observables during detonator function

NASA Astrophysics Data System (ADS)

Smilowitz, Laura; Henson, Bryan; Remelius, Dennis

Thermal explosion and detonation are two phenomena which can both occur as the response of explosives to thermal or mechanical insults. Thermal explosion is typically considered in the safety envelope and detonation is considered in the performance regime of explosive behavior. However, the two regimes are tied together by a phenomenon called deflagration to detonation transition (DDT). In this talk, I will discuss experiments on commercial detonators aimed at understanding the mechanism for energy release during detonator function. Diagnostic development towards measuring temperature, pressure, and density during the extreme conditions and time scales of detonation will be discussed. Our current ability to perform table-top dynamic radiography on functioning detonators will be described. Dynamic measurements of temperature, pressure, and density will be shown and discussion of the function of a detonator will be given in terms of our current understanding of deflagration, detonation, and the transition between the two.

Self-consistent hybrid functionals for solids: a fully-automated implementation

NASA Astrophysics Data System (ADS)

Erba, A.

2017-08-01

A fully-automated algorithm for the determination of the system-specific optimal fraction of exact exchange in self-consistent hybrid functionals of the density-functional-theory is illustrated, as implemented into the public Crystal program. The exchange fraction of this new class of functionals is self-consistently updated proportionally to the inverse of the dielectric response of the system within an iterative procedure (Skone et al 2014 Phys. Rev. B 89, 195112). Each iteration of the present scheme, in turn, implies convergence of a self-consistent-field (SCF) and a coupled-perturbed-Hartree-Fock/Kohn-Sham (CPHF/KS) procedure. The present implementation, beside improving the user-friendliness of self-consistent hybrids, exploits the unperturbed and electric-field perturbed density matrices from previous iterations as guesses for subsequent SCF and CPHF/KS iterations, which is documented to reduce the overall computational cost of the whole process by a factor of 2.

Characterization, parameter estimation, and aircraft response statistics of atmospheric turbulence

NASA Technical Reports Server (NTRS)

Mark, W. D.

1981-01-01

A nonGaussian three component model of atmospheric turbulence is postulated that accounts for readily observable features of turbulence velocity records, their autocorrelation functions, and their spectra. Methods for computing probability density functions and mean exceedance rates of a generic aircraft response variable are developed using nonGaussian turbulence characterizations readily extracted from velocity recordings. A maximum likelihood method is developed for optimal estimation of the integral scale and intensity of records possessing von Karman transverse of longitudinal spectra. Formulas for the variances of such parameter estimates are developed. The maximum likelihood and least-square approaches are combined to yield a method for estimating the autocorrelation function parameters of a two component model for turbulence.

Comparative transcriptomics of Atlantic Salmo salar, chum Oncorhynchus keta and pink salmon O. gorbuscha during infections with salmon lice Lepeophtheirus salmonis.

PubMed

Sutherland, Ben J G; Koczka, Kim W; Yasuike, Motoshige; Jantzen, Stuart G; Yazawa, Ryosuke; Koop, Ben F; Jones, Simon R M

2014-03-15

Salmon species vary in susceptibility to infections with the salmon louse (Lepeophtheirus salmonis). Comparing mechanisms underlying responses in susceptible and resistant species is important for estimating impacts of infections on wild salmon, selective breeding of farmed salmon, and expanding our knowledge of fish immune responses to ectoparasites. Herein we report three L. salmonis experimental infection trials of co-habited Atlantic Salmo salar, chum Oncorhynchus keta and pink salmon O. gorbuscha, profiling hematocrit, blood cortisol concentrations, and transcriptomic responses of the anterior kidney and skin to the infection. In all trials, infection densities (lice per host weight (g)) were consistently highest on chum salmon, followed by Atlantic salmon, and lowest in pink salmon. At 43 days post-exposure, all lice had developed to motile stages, and infection density was uniformly low among species. Hematocrit was reduced in infected Atlantic and chum salmon, and cortisol was elevated in infected chum salmon. Systemic transcriptomic responses were profiled in all species and large differences in response functions were identified between Atlantic and Pacific (chum and pink) salmon. Pink and chum salmon up-regulated acute phase response genes, including complement and coagulation components, and down-regulated antiviral immune genes. The pink salmon response involved the largest and most diverse iron sequestration and homeostasis mechanisms. Pattern recognition receptors were up-regulated in all species but the active components were often species-specific. C-type lectin domain family 4 member M and acidic mammalian chitinase were specifically up-regulated in the resistant pink salmon. Experimental exposures consistently indicated increased susceptibility in chum and Atlantic salmon, and resistance in pink salmon, with differences in infection density occurring within the first three days of infection. Transcriptomic analysis suggested candidate resistance functions including local inflammation with cytokines, specific innate pattern recognition receptors, and iron homeostasis. Suppressed antiviral immunity in both susceptible and resistant species indicates the importance of future work investigating co-infections of viral pathogens and lice.

Distribution of CpG Motifs in Upstream Gene Domains in a Reef Coral and Sea Anemone: Implications for Epigenetics in Cnidarians.

PubMed

Marsh, Adam G; Hoadley, Kenneth D; Warner, Mark E

2016-01-01

Coral reefs are under assault from stressors including global warming, ocean acidification, and urbanization. Knowing how these factors impact the future fate of reefs requires delineating stress responses across ecological, organismal and cellular scales. Recent advances in coral reef biology have integrated molecular processes with ecological fitness and have identified putative suites of temperature acclimation genes in a Scleractinian coral Acropora hyacinthus. We wondered what unique characteristics of these genes determined their coordinate expression in response to temperature acclimation, and whether or not other corals and cnidarians would likewise possess these features. Here, we focus on cytosine methylation as an epigenetic DNA modification that is responsive to environmental stressors. We identify common conserved patterns of cytosine-guanosine dinucleotide (CpG) motif frequencies in upstream promoter domains of different functional gene groups in two cnidarian genomes: a coral (Acropora digitifera) and an anemone (Nematostella vectensis). Our analyses show that CpG motif frequencies are prominent in the promoter domains of functional genes associated with environmental adaptation, particularly those identified in A. hyacinthus. Densities of CpG sites in upstream promoter domains near the transcriptional start site (TSS) are 1.38x higher than genomic background levels upstream of -2000 bp from the TSS. The increase in CpG usage suggests selection to allow for DNA methylation events to occur more frequently within 1 kb of the TSS. In addition, observed shifts in CpG densities among functional groups of genes suggests a potential role for epigenetic DNA methylation within promoter domains to impact functional gene expression responses in A. digitifera and N. vectensis. Identifying promoter epigenetic sequence motifs among genes within specific functional groups establishes an approach to describe integrated cellular responses to environmental stress in reef corals and potential roles of epigenetics on survival and fitness in the face of global climate change.

Quantification of cell response to polymeric composites using a two-dimensional gradient platform.

PubMed

Lin, Nancy J; Hu, Haiqing; Sung, Lipin; Lin-Gibson, Sheng

2009-07-01

A simple and straightforward screening process to assess the toxicity and corresponding cell response of dental composites would be useful prior to extensive in vitro or in vivo characterization. To this end, gradient composite samples were prepared with variations in filler content/type and in degree of conversion (DC). The DC was determined using near infrared spectroscopy (NIR), and the surface morphology was evaluated by laser scanning confocal microscopy (LSCM). RAW 264.7 macrophage-like cells were cultured directly on the composite gradient samples, and cell viability, density, and area were measured at 24 h. All three measures of cell response varied as a function of material properties. For instance, compositions with higher filler content had no reduction in cell viability or cell density, even at low conversions of 52%, whereas significant decreases in viability and density were present when the filler content was 35% or below (by mass). The overall results demonstrate the complexity of the cell-material interactions, with properties including DC, filler type, filler mass ratio, and surface morphology influencing the cell response. The combinatorial approach described herein enables simultaneous screening of multiple compositions and material properties, providing a more thorough characterization of cell response for the improved selection of biocompatible composite formulations and processing conditions.

HLA class I expression predicts prognosis and therapeutic benefits from tyrosine kinase inhibitors in metastatic renal-cell carcinoma patients.

PubMed

Wang, Jiajun; Liu, Li; Qu, Yang; Xi, Wei; Xia, Yu; Bai, Qi; Xiong, Ying; Long, Qilai; Xu, Jiejie; Guo, Jianming

2018-01-01

Classical HLA class I antigen is highly involved in antigen presentation and adaptive immune response against tumor. In this study, we explored its predictive value for treatment response and survival in metastatic renal-cell carcinoma (mRCC) patients. A TKI cohort of 111 mRCC patients treated with sunitinib or sorafenib and a non-TKI cohort of 160 mRCC patients treated with interleukin-2 or interferon-α-based immunotherapy at a single institution were retrospectively enrolled. HLA class I expression and cytotoxic T lymphocyte (CTL) density was assessed by immunohistochemistry on tissue microarrays. Association between HLA class I and CTL was also assessed in the TCGA KIRC cohort. In the TKI cohort, down-regulated HLA class I was associated with lower objective response rate of TKI therapy (P = 0.004), shorter overall survival (OS) (P = 0.001), and shorter progression free survival (PFS) (P < 0.001). Multivariate Cox regression model defined HLA expression as an independent prognostic factor for both OS [hazard ratio 1.687 (95% CI 1.045-2.724), P = 0.032] and PFS [hazard ratio 2.139 (95% CI 1.376-3.326), P = 0.001]. In the non-TKI cohort, HLA class I was not significantly associated with survival. HLA class I expression was associated with CTL infiltration and function, and its prognostic value was more predominant in CTL high-density tumors (P < 0.001) rather than CTL low-density tumors (P = 0.294). Classical HLA class I expression can serve as a potential predictive biomarker for TKI therapy in mRCC patients. Its predictive value was restricted in CTL high-density tumors. However, further external validations and functional investigations are still required.

Influence of Green Tides in Coastal Nursery Grounds on the Habitat Selection and Individual Performance of Juvenile Fish

PubMed Central

Murillo, Laurence; Randon, Marine; Lebot, Clément

2017-01-01

Coastal ecosystems, which provide numerous essential ecological functions for fish, are threatened by the proliferation of green macroalgae that significantly modify habitat conditions in intertidal areas. Understanding the influence of green tides on the nursery function of these ecosystems is essential to determine their potential effects on fish recruitment success. In this study, the influence of green tides on juvenile fish was examined in an intertidal sandy beach area, the Bay of Saint-Brieuc (Northwestern France), during two annual cycles of green tides with varying levels of intensity. The responses of three nursery-dependent fish species, the pelagic Sprattus sprattus (L.), the demersal Dicentrarchus labrax (L.) and the benthic Pleuronectes platessa L., were analysed to determine the effects of green tides according to species-specific habitat niche and behaviour. The responses to this perturbation were investigated based on habitat selection and a comparison of individual performance between a control and an impacted site. Several indices on different integrative scales were examined to evaluate these responses (antioxidant defence capacity, muscle total lipid, morphometric condition and growth). Based on these analyses, green tides affect juvenile fish differently according to macroalgal density and species-specific tolerance, which is linked to their capacity to move and to their distribution in the water column. A decreasing gradient of sensitivity was observed from benthic to demersal and pelagic fish species. At low densities of green macroalgae, the three species stayed at the impacted site and the growth of plaice was reduced. At medium macroalgal densities, plaice disappeared from the impacted site and the growth of sea bass and the muscle total lipid content of sprat were reduced. Finally, when high macroalgal densities were reached, none of the studied species were captured at the impacted site. Hence, sites affected by green tides are less favourable nursery grounds for all the studied species, with species-specific effects related to macroalgal density. PMID:28125605

Influence of Green Tides in Coastal Nursery Grounds on the Habitat Selection and Individual Performance of Juvenile Fish.

PubMed

Le Luherne, Emilie; Le Pape, Olivier; Murillo, Laurence; Randon, Marine; Lebot, Clément; Réveillac, Elodie

2017-01-01

Coastal ecosystems, which provide numerous essential ecological functions for fish, are threatened by the proliferation of green macroalgae that significantly modify habitat conditions in intertidal areas. Understanding the influence of green tides on the nursery function of these ecosystems is essential to determine their potential effects on fish recruitment success. In this study, the influence of green tides on juvenile fish was examined in an intertidal sandy beach area, the Bay of Saint-Brieuc (Northwestern France), during two annual cycles of green tides with varying levels of intensity. The responses of three nursery-dependent fish species, the pelagic Sprattus sprattus (L.), the demersal Dicentrarchus labrax (L.) and the benthic Pleuronectes platessa L., were analysed to determine the effects of green tides according to species-specific habitat niche and behaviour. The responses to this perturbation were investigated based on habitat selection and a comparison of individual performance between a control and an impacted site. Several indices on different integrative scales were examined to evaluate these responses (antioxidant defence capacity, muscle total lipid, morphometric condition and growth). Based on these analyses, green tides affect juvenile fish differently according to macroalgal density and species-specific tolerance, which is linked to their capacity to move and to their distribution in the water column. A decreasing gradient of sensitivity was observed from benthic to demersal and pelagic fish species. At low densities of green macroalgae, the three species stayed at the impacted site and the growth of plaice was reduced. At medium macroalgal densities, plaice disappeared from the impacted site and the growth of sea bass and the muscle total lipid content of sprat were reduced. Finally, when high macroalgal densities were reached, none of the studied species were captured at the impacted site. Hence, sites affected by green tides are less favourable nursery grounds for all the studied species, with species-specific effects related to macroalgal density.

Independent control of electron energy and density using a rotating magnetic field in inductively coupled plasmas

NASA Astrophysics Data System (ADS)

Kondo, Takahiro; Ohta, Masayuki; Ito, Tsuyohito; Okada, Shigefumi

2013-09-01

Effects of a rotating magnetic field (RMF) on the electron energy distribution function (EEDF) and on the electron density are investigated with the aim of controlling the radical composition of inductively coupled plasmas. By adjusting the RMF frequency and generation power, the desired electron density and electron energy shift are obtained. Consequently, the amount and fraction of high-energy electrons, which are mostly responsible for direct dissociation processes of raw molecules, will be controlled externally. This controllability, with no electrode exposed to plasma, will enable us to control radical components and their flux during plasma processing.

Effects of hatchery fish density on emigration, growth, survival, and predation risk of natural steelhead parr in an experimental stream channel

USGS Publications Warehouse

Tatara, Christopher P.; Riley, Stephen C.; Berejikian, Barry A.

2011-01-01

Hatchery supplementation of steelhead Oncorhynchus mykiss raises concerns about the impacts on natural populations, including reduced growth and survival, displacement, and increased predation. The potential risks may be density dependent.We examined how hatchery stocking density and the opportunity to emigrate affect the responses of natural steelhead parr in an experimental stream channel and after 15 d found no density-dependent effects on growth, emigration, or survival at densities ranging from 1-6 hatchery parr/m2. The opportunity for steelhead parr to emigrate reduced predation by coastal cutthroat trout O. clarkii clarkii on both hatchery and natural steelhead parr. The cutthroat trout exhibited a type-I functional response (constant predation rate with increased prey density) for the hatchery and composite populations. In contrast, the predation rate on natural parr decreased as hatchery stocking density increased. Supplementation with hatchery parr at any experimental stocking density reduced the final natural parr density. This decline was explained by increased emigration fromthe supplemented groups. Natural parr had higher mean instantaneous growth rates than hatchery parr. The proportion of parr emigrating decreased as parr size increased over successive experimental trials. Smaller parr had lower survival and suffered higher predation. The final density of the composite population, a measure of supplementation effectiveness, increased with the hatchery steelhead stocking rate. Our results indicate that stocking larger hatchery parr (over 50 d postemergence) at densities within the carrying capacity would have low short-term impact on the growth, survival, and emigration of natural parr while increasing the density of the composite population; in addition, a stocking density greater than 3 fish/m2 might be a good starting point for the evaluation of parr stocking in natural streams.

Four-Component Relativistic Density-Functional Theory Calculations of Nuclear Spin-Rotation Constants: Relativistic Effects in p-Block Hydrides.

PubMed

Komorovsky, Stanislav; Repisky, Michal; Malkin, Elena; Demissie, Taye B; Ruud, Kenneth

2015-08-11

We present an implementation of the nuclear spin-rotation (SR) constants based on the relativistic four-component Dirac-Coulomb Hamiltonian. This formalism has been implemented in the framework of the Hartree-Fock and Kohn-Sham theory, allowing assessment of both pure and hybrid exchange-correlation functionals. In the density-functional theory (DFT) implementation of the response equations, a noncollinear generalized gradient approximation (GGA) has been used. The present approach enforces a restricted kinetic balance condition for the small-component basis at the integral level, leading to very efficient calculations of the property. We apply the methodology to study relativistic effects on the spin-rotation constants by performing calculations on XHn (n = 1-4) for all elements X in the p-block of the periodic table and comparing the effects of relativity on the nuclear SR tensors to that observed for the nuclear magnetic shielding tensors. Correlation effects as described by the density-functional theory are shown to be significant for the spin-rotation constants, whereas the differences between the use of GGA and hybrid density functionals are much smaller. Our calculated relativistic spin-rotation constants at the DFT level of theory are only in fair agreement with available experimental data. It is shown that the scaling of the relativistic effects for the spin-rotation constants (varying between Z(3.8) and Z(4.5)) is as strong as for the chemical shieldings but with a much smaller prefactor.

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

Quantitative evaluation of capillaroscopic microvascular changes in patients with established coronary heart disease.

PubMed

Sanchez-Garcia, M Esther; Ramirez-Lara, Irene; Gomez-Delgado, Francisco; Yubero-Serrano, Elena M; Leon-Acuña, Ana; Marin, Carmen; Alcala-Diaz, Juan F; Camargo, Antonio; Lopez-Moreno, Javier; Perez-Martinez, Pablo; Tinahones, Francisco José; Ordovas, Jose M; Caballero, Javier; Blanco-Molina, Angeles; Lopez-Miranda, Jose; Delgado-Lista, Javier

2018-02-23

Microcirculation disturbances have been associated to most of the cardiovascular risk factors as well as to multiple inflammatory diseases. However, whether these abnormalities are specifically augmented in patients with coronary heart disease is still unknown. We aimed to evaluate if there is a relationship between the presence of coronary heart disease and the existence of functional and structural capillary abnormalities evaluated in the cutaneous microcirculation by videocapillaroscopy. Two matched samples of 30 participants with and without coronary heart disease but with similar clinical and anthropometric characteristics were evaluated by videocapillaroscopy at the dorsal skin of the third finger of the non-dominant hand. We calculated basal capillary density as well as capillary density after a period of arterial and venous occlusion in order to evaluate functionality and maximum capillary density. We also measured capillary recruitment. Microvascular capillary density at rest was significantly lower in patients suffering from coronary heart disease than in controls. This fact was also found after dynamic tests (arterial and venous occlusion), suggesting functional impairments. Capillary recruitment of the samples was not different in our sample. In our study, patients with coronary heart disease exhibit functional and structural microvascular disturbances. Although this is a very preliminary study, these findings open the door for further studying the microvascular functionality in coronary patients and how it relates to the response to treatment and/or the prognosis of the disease. Copyright © 2017 Elsevier España, S.L.U. All rights reserved.

Functional trait responses to grazing are mediated by soil moisture and plant functional group identity

PubMed Central

Zheng, Shuxia; Li, Wenhuai; Lan, Zhichun; Ren, Haiyan; Wang, Kaibo

2015-01-01

Abundant evidence has shown that grazing alters plant functional traits, community structure and ecosystem functioning of grasslands. Few studies, however, have tested how plant responses to grazing are mediated by resource availability and plant functional group identity. We examined the effects of grazing on functional traits across a broad range of species along a soil moisture gradient in Inner Mongolia grassland. Our results showed that trait syndromes of plant size (individual biomass) and shoot growth (leaf N content and leaf density) distinguished plant species responses to grazing. The effects of grazing on functional traits were mediated by soil moisture and dependent on functional group identity. For most species, grazing decreased plant height but increased leaf N and specific leaf area (SLA) along the moisture gradient. Grazing enhanced the community-weighted attributes (leaf NCWM and SLACWM), which were triggered mainly by the positive trait responses of annuals and biennials and perennial grasses, and increased relative abundance of perennial forbs. Our results suggest that grazing-induced species turnover and increased intraspecific trait variability are two drivers for the observed changes in community weighted attributes. The dominant perennial bunchgrasses exhibited mixed tolerance–resistance strategies to grazing and mixed acquisitive–conservative strategies in resource utilization. PMID:26655858

Functional trait responses to grazing are mediated by soil moisture and plant functional group identity.

PubMed

Zheng, Shuxia; Li, Wenhuai; Lan, Zhichun; Ren, Haiyan; Wang, Kaibo

2015-12-11

Abundant evidence has shown that grazing alters plant functional traits, community structure and ecosystem functioning of grasslands. Few studies, however, have tested how plant responses to grazing are mediated by resource availability and plant functional group identity. We examined the effects of grazing on functional traits across a broad range of species along a soil moisture gradient in Inner Mongolia grassland. Our results showed that trait syndromes of plant size (individual biomass) and shoot growth (leaf N content and leaf density) distinguished plant species responses to grazing. The effects of grazing on functional traits were mediated by soil moisture and dependent on functional group identity. For most species, grazing decreased plant height but increased leaf N and specific leaf area (SLA) along the moisture gradient. Grazing enhanced the community-weighted attributes (leaf NCWM and SLACWM), which were triggered mainly by the positive trait responses of annuals and biennials and perennial grasses, and increased relative abundance of perennial forbs. Our results suggest that grazing-induced species turnover and increased intraspecific trait variability are two drivers for the observed changes in community weighted attributes. The dominant perennial bunchgrasses exhibited mixed tolerance-resistance strategies to grazing and mixed acquisitive-conservative strategies in resource utilization.

Spiers Memorial Lecture. Quantum chemistry: the first seventy years.

PubMed

McWeeny, Roy

2007-01-01

Present-day theoretical chemistry is rooted in Quantum Mechanics. The aim of the opening lecture is to trace the evolution of Quantum Chemistry from the Heitler-London paper of 1927 up to the end of the last century, emphasizing concepts rather than calculations. The importance of symmetry concepts became evident in the early years: one thinks of the necessary anti-symmetry of the wave function under electron permutations, the Pauli principle, the aufbau scheme, and the classification of spectroscopic states. But for chemists perhaps the key concept is embodied in the Hellmann-Feynman theorem, which provides a pictorial interpretation of chemical bonding in terms of classical electrostatic forces exerted on the nuclei by the electron distribution. Much of the lecture is concerned with various electron distribution functions--the electron density, the current density, the spin density, and other 'property densities'--and with their use in interpreting both molecular structure and molecular properties. Other topics touched upon include Response theory and propagators; Chemical groups in molecules and the group function approach; Atoms in molecules and Bader's theory; Electron correlation and the 'pair function'. Finally, some long-standing controversies, in particular the EPR paradox, are re-examined in the context of molecular dissociation. By admitting the concept of symmetry breaking, along with the use of the von Neumann-Dirac statistical ensemble, orthodox quantum mechanics can lead to a convincing picture of the dissociation mechanism.

Low-energy ion distribution functions on a magnetically quiet day at geostationary altitude /L = 7/

NASA Technical Reports Server (NTRS)

Singh, N.; Raitt, W. J.; Yasuhara, F.

1982-01-01

Ion energy and pitch angle distribution functions are examined for a magnetically quiet day using averaged data from ATS 6. For both field-aligned and perpendicular fluxes, the populations have a mixture of characteristic energies, and the distribution functions can be fairly well approximated by Maxwellian distributions over three different energy bands in the range 3-600 eV. Pitch angle distributions varying with local time, and energy distributions are used to compute total ion density. Pitch angle scattering mechanisms responsible for the observed transformation of pitch angle distribution are examined, and it is found that a magnetic noise of a certain power spectral density belonging to the electromagnetic ion cyclotron mode near the ion cyclotron frequency can be effective in trapping the field aligned fluxes by pitch angle scattering.

Dynamics of confined water reconstructed from inelastic x-ray scattering measurements of bulk response functions

NASA Astrophysics Data System (ADS)

Coridan, Robert H.; Schmidt, Nathan W.; Lai, Ghee Hwee; Abbamonte, Peter; Wong, Gerard C. L.

2012-03-01

Nanoconfined water and surface-structured water impacts a broad range of fields. For water confined between hydrophilic surfaces, measurements and simulations have shown conflicting results ranging from “liquidlike” to “solidlike” behavior, from bulklike water viscosity to viscosity orders of magnitude higher. Here, we investigate how a homogeneous fluid behaves under nanoconfinement using its bulk response function: The Green's function of water extracted from a library of S(q,ω) inelastic x-ray scattering data is used to make femtosecond movies of nanoconfined water. Between two confining surfaces, the structure undergoes drastic changes as a function of surface separation. For surface separations of ≈9 Å, although the surface-associated hydration layers are highly deformed, they are separated by a layer of bulklike water. For separations of ≈6 Å, the two surface-associated hydration layers are forced to reconstruct into a single layer that modulates between localized “frozen’ and delocalized “melted” structures due to interference of density fields. These results potentially reconcile recent conflicting experiments. Importantly, we find a different delocalized wetting regime for nanoconfined water between surfaces with high spatial frequency charge densities, where water is organized into delocalized hydration layers instead of localized hydration shells, and are strongly resistant to `freezing' down to molecular distances (<6 Å).

Inter-Cohort Cannibalism of Early Benthic Phase Blue King Crabs (Paralithodes platypus): Alternate Foraging Strategies in Different Habitats Lead to Different Functional Responses

PubMed Central

Daly, Benjamin; Long, W. Christopher

2014-01-01

Blue king crabs (Paralithodes platypus) are commercially and ecologically important in Alaska, USA, but population abundances have fluctuated over the past several decades likely resulting from a combination of environmental and biological factors, including recruitment variability. Cannibalism between cohorts may be a source of mortality limiting recruitment success in the wild, but the degree of inter-cohort cannibalism is unknown for early benthic phase blue king crabs. In laboratory experiments, we evaluated the effects of habitat type (sand and shell) on the predator functional response and foraging behavior of year-1 blue king crabs as predators of year-0 conspecifics and examined the effects of predator presence on crypsis of prey crabs. In sand, consumption rates increased with predator size and prey density until satiation, while predation rates in shell were low regardless of predator size or prey density. These differential predation rates yielded a type III functional response in sand but a type I functional response in shell habitat. Crypsis of prey crabs was generally high and did not change in the presence of predators. Predator foraging activity was reduced in shell and may be an adaptive behavior to balance foraging efficiency and susceptibility to larger predators. Our results demonstrate that early benthic phase blue king crabs are cannibalistic between cohorts in the laboratory and that shell material is extremely effective for reducing encounter rates with conspecific predators. The distribution and abundance of such habitat may be important for recruitment success in some populations. Future studies should compare benthic habitat and species assemblages in areas with variable abundances, such as the Pribilof Islands and Saint Matthew Island in the eastern Bering Sea, to better understand possible mechanisms for recruitment variability. PMID:24558414

Inter-cohort cannibalism of early benthic phase blue king crabs (Paralithodes platypus): alternate foraging strategies in different habitats lead to different functional responses.

PubMed

Daly, Benjamin; Long, W Christopher

2014-01-01

Blue king crabs (Paralithodes platypus) are commercially and ecologically important in Alaska, USA, but population abundances have fluctuated over the past several decades likely resulting from a combination of environmental and biological factors, including recruitment variability. Cannibalism between cohorts may be a source of mortality limiting recruitment success in the wild, but the degree of inter-cohort cannibalism is unknown for early benthic phase blue king crabs. In laboratory experiments, we evaluated the effects of habitat type (sand and shell) on the predator functional response and foraging behavior of year-1 blue king crabs as predators of year-0 conspecifics and examined the effects of predator presence on crypsis of prey crabs. In sand, consumption rates increased with predator size and prey density until satiation, while predation rates in shell were low regardless of predator size or prey density. These differential predation rates yielded a type III functional response in sand but a type I functional response in shell habitat. Crypsis of prey crabs was generally high and did not change in the presence of predators. Predator foraging activity was reduced in shell and may be an adaptive behavior to balance foraging efficiency and susceptibility to larger predators. Our results demonstrate that early benthic phase blue king crabs are cannibalistic between cohorts in the laboratory and that shell material is extremely effective for reducing encounter rates with conspecific predators. The distribution and abundance of such habitat may be important for recruitment success in some populations. Future studies should compare benthic habitat and species assemblages in areas with variable abundances, such as the Pribilof Islands and Saint Matthew Island in the eastern Bering Sea, to better understand possible mechanisms for recruitment variability.

Random function representation of stationary stochastic vector processes for probability density evolution analysis of wind-induced structures

NASA Astrophysics Data System (ADS)

Liu, Zhangjun; Liu, Zenghui

2018-06-01

This paper develops a hybrid approach of spectral representation and random function for simulating stationary stochastic vector processes. In the proposed approach, the high-dimensional random variables, included in the original spectral representation (OSR) formula, could be effectively reduced to only two elementary random variables by introducing the random functions that serve as random constraints. Based on this, a satisfactory simulation accuracy can be guaranteed by selecting a small representative point set of the elementary random variables. The probability information of the stochastic excitations can be fully emerged through just several hundred of sample functions generated by the proposed approach. Therefore, combined with the probability density evolution method (PDEM), it could be able to implement dynamic response analysis and reliability assessment of engineering structures. For illustrative purposes, a stochastic turbulence wind velocity field acting on a frame-shear-wall structure is simulated by constructing three types of random functions to demonstrate the accuracy and efficiency of the proposed approach. Careful and in-depth studies concerning the probability density evolution analysis of the wind-induced structure have been conducted so as to better illustrate the application prospects of the proposed approach. Numerical examples also show that the proposed approach possesses a good robustness.

Projector Augmented-Wave formulation of response to strain and electric field perturbation within the density-functional perturbation theory

NASA Astrophysics Data System (ADS)

Martin, Alexandre; Torrent, Marc; Caracas, Razvan

2015-03-01

A formulation of the response of a system to strain and electric field perturbations in the pseudopotential-based density functional perturbation theory (DFPT) has been proposed by D.R Hamman and co-workers. It uses an elegant formalism based on the expression of DFT total energy in reduced coordinates, the key quantity being the metric tensor and its first and second derivatives. We propose to extend this formulation to the Projector Augmented-Wave approach (PAW). In this context, we express the full elastic tensor including the clamped-atom tensor, the atomic-relaxation contributions (internal stresses) and the response to electric field change (piezoelectric tensor and effective charges). With this we are able to compute the elastic tensor for all materials (metals and insulators) within a fully analytical formulation. The comparison with finite differences calculations on simple systems shows an excellent agreement. This formalism has been implemented in the plane-wave based DFT ABINIT code. We apply it to the computation of elastic properties and seismic-wave velocities of iron with impurity elements. By analogy with the materials contained in meteorites, tested impurities are light elements (H, O, C, S, Si).

Measuring the dependence of the decay curve on the electron energy deposit in NaI(Tl)

NASA Astrophysics Data System (ADS)

Choong, W.-S.; Bizarri, G.; Cherepy, N. J.; Hull, G.; Moses, W. W.; Payne, S. A.

2011-08-01

We report on the first measurement of the decay times of NaI(Tl) as a function of the deposited electron energy. It has been suggested that the decay curve depends on the ionization density, which is correlated with the electron energy deposit in the scintillator. The ionization creates excitation states, which can decay radiatively and non-radiatively through a number of competing processes. As a result, the rate at which the excitation decays depends on the ionization density. A measurement of the decay curve as a function of the ionization density will allow us to probe the kinetic rates of the competing processes. The Scintillator Light Yield Non-proportionality Characterization Instrument (SLYNCI) measures the electron response of scintillators utilizing fast sampling ADCs to digitize the raw signals from the detectors, and so can provide a measurement of the light pulse shape from the scintillator. Using data collected with the SLYNCI instrument, the intrinsic scintillation profile is extracted on an event-by-event basis by deconvolving the raw signal with the impulse response of the system. Scintillation profiles with the same electron energy deposit are summed to obtain decay curves as a function of the deposited electron energy. The decay time constants are obtained by fitting the decay curves with a two-component exponential decay. While a slight dependence of the decay time constants on the electron energy deposit is observed, the results are not statistically significant.

Bispectrum supersample covariance

NASA Astrophysics Data System (ADS)

Chan, Kwan Chuen; Moradinezhad Dizgah, Azadeh; Noreña, Jorge

2018-02-01

Modes with wavelengths larger than the survey window can have significant impact on the covariance within the survey window. The supersample covariance has been recognized as an important source of covariance for the power spectrum on small scales, and it can potentially be important for the bispectrum covariance as well. In this paper, using the response function formalism, we model the supersample covariance contributions to the bispectrum covariance and the cross-covariance between the power spectrum and the bispectrum. The supersample covariances due to the long-wavelength density and tidal perturbations are investigated, and the tidal contribution is a few orders of magnitude smaller than the density one because in configuration space the bispectrum estimator involves angular averaging and the tidal response function is anisotropic. The impact of the super-survey modes is quantified using numerical measurements with periodic box and sub-box setups. For the matter bispectrum, the ratio between the supersample covariance correction and the small-scale covariance—which can be computed using a periodic box—is roughly an order of magnitude smaller than that for the matter power spectrum. This is because for the bispectrum, the small-scale non-Gaussian covariance is significantly larger than that for the power spectrum. For the cross-covariance, the supersample covariance is as important as for the power spectrum covariance. The supersample covariance prediction with the halo model response function is in good agreement with numerical results.

The role of the anterodorsal thalami nuclei in the regulation of adrenal medullary function, beta-adrenergic cardiac receptors and anxiety responses in maternally deprived rats under stressful conditions.

PubMed

Suárez, M M; Rivarola, M A; Molina, S M; Levin, G M; Enders, J; Paglini, P

2004-09-01

Maternal separation can interfere with growth and development of the brain and represents a significant risk factor for adult psychopathology. In rodents, prolonged separation from the mother affects the behavioral and endocrine responses to stress for the lifetime of the animal. Limbic structures such as the anterodorsal thalamic nuclei (ADTN) play an important role in the control of neuroendocrine and sympathetic-adrenal function. In view of these findings we hypothesized that the function of the ADTN may be affected in an animal model of maternal deprivation. To test this hypothesis female rats were isolated 4.5 h daily, during the first 3 weeks of life and tested as adults. We evaluated plasma epinephrine (E) and norepinephrine (NE), cardiac adrenoreceptors and anxiety responses after maternal deprivation and variable chronic stress (VCS) in ADTN-lesioned rats. Thirty days after ADTN lesion, in non-maternally deprived rats basal plasma NE concentration was greater and cardiac beta-adrenoreceptor density was lower than that in the sham-lesioned group. Maternal deprivation induced a significant increase in basal plasma NE concentration, which was greater in lesioned rats, and cardiac beta-adrenoreceptor density was decreased in lesioned rats. After VCS plasma catecholamine concentration was much greater in non-maternally deprived rats than in maternally-deprived rats; cardiac beta-adrenoreceptor density was decreased by VCS in both maternally-deprived and non-deprived rats, but more so in non-deprived rats, and further decreased by the ADTN lesion. In the plus maze test, the number of open arm entries was greater in the maternally deprived and in the stressed rats. Thus, sympathetic-adrenal medullary activation produced by VCS was much greater in non-deprived rats, and was linked to a down regulation of myocardial beta-adrenoceptors. The ADTN are not responsible for the reduced catecholamine responses to stress in maternally-deprived rats. Maternal deprivation or chronic stress also induced a long term anxiolytic effect, which was also not affected by ADTN lesion.

Search for ionisation density effects in the radiation absorption stage in LiF:Mg,Ti.

PubMed

Nail, I; Horowitz, Y S; Oster, L; Brandan, M E; Rodríguez-Villafuerte, M; Buenfil, A E; Ruiz-Trejo, C; Gamboa-Debuen, I; Avila, O; Tovar, V M; Olko, P; Ipe, N

2006-01-01

Optical absorption (OA) dose-response of LiF:Mg,Ti (TLD-100) is studied as a function of electron energy (ionisation density) and irradiation dose. Contrary to the situation in thermoluminescence dose-response where the supralinearity is strongly energy-dependent, no dependence of the OA dose filling constants on energy is observed. This result is interpreted as indicating a lack of competitive process in the radiation absorption stage. The lack of an energy dependence of the dose filling constant also suggests that the charge carrier migration distances are sufficiently large to smear out the differences in the non-uniform distribution of ionisation events created by the impinging gamma/electron radiation of various energies.

Ion beams in multi-species plasmas

NASA Astrophysics Data System (ADS)

Aguirre, E. M.; Scime, E. E.; Good, T. N.

2018-04-01

Argon and xenon ion velocity distribution functions are measured in Ar-He, Ar-Xe, and Xe-He expanding helicon plasmas to determine if ion beam velocity is enhanced by the presence of lighter ions. Contrary to observations in mixed gas sheath experiments, we find that adding a lighter ion does not increase the ion beam speed. The predominant effect is a reduction of ion beam velocity consistent with increased drag arising from increased gas pressure under all conditions: constant total gas pressure, equal plasma densities of different ions, and very different plasma densities of different ions. These results suggest that the physics responsible for the acceleration of multiple ion species in simple sheaths is not responsible for the ion acceleration observed in expanding helicon plasmas.

HUMAN RESPONDING ON RANDOM-INTERVAL SCHEDULES OF RESPONSE-COST PUNISHMENT: THE ROLE OF REDUCED REINFORCEMENT DENSITY

PubMed Central

Pietras, Cynthia J; Brandt, Andrew E; Searcy, Gabriel D

2010-01-01

An experiment with adult humans investigated the effects of response-contingent money loss (response-cost punishment) on monetary-reinforced responding. A yoked-control procedure was used to separate the effects on responding of the response-cost contingency from the effects of reduced reinforcement density. Eight adults pressed buttons for money on a three-component multiple reinforcement schedule. During baseline, responding in all components produced money gains according to a random-interval 20-s schedule. During punishment conditions, responding during the punishment component conjointly produced money losses according to a random-interval schedule. The value of the response-cost schedule was manipulated across conditions to systematically evaluate the effects on responding of response-cost frequency. Participants were assigned to one of two yoked-control conditions. For participants in the Yoked Punishment group, during punishment conditions money losses were delivered in the yoked component response independently at the same intervals that money losses were produced in the punishment component. For participants in the Yoked Reinforcement group, responding in the yoked component produced the same net earnings as produced in the punishment component. In 6 of 8 participants, contingent response cost selectively decreased response rates in the punishment component and the magnitude of the decrease was directly related to the punishment schedule value. Under punishment conditions, for participants in the Yoked Punishment group response rates in the yoked component also decreased, but the decrease was less than that observed in the punishment component, whereas for participants in the Yoked Reinforcement group response rates in the yoked component remained similar to rates in the no-punishment component. These results provide further evidence that contingent response cost functions similarly to noxious punishers in that it appears to suppress responding apart from its effects on reinforcement density. PMID:20676265

Response properties in the adsorption-desorption model on a triangular lattice

NASA Astrophysics Data System (ADS)

Šćepanović, J. R.; Stojiljković, D.; Jakšić, Z. M.; Budinski-Petković, Lj.; Vrhovac, S. B.

2016-06-01

The out-of-equilibrium dynamical processes during the reversible random sequential adsorption (RSA) of objects of various shapes on a two-dimensional triangular lattice are studied numerically by means of Monte Carlo simulations. We focused on the influence of the order of symmetry axis of the shape on the response of the reversible RSA model to sudden perturbations of the desorption probability Pd. We provide a detailed discussion of the significance of collective events for governing the time coverage behavior of shapes with different rotational symmetries. We calculate the two-time density-density correlation function C(t ,tw) for various waiting times tw and show that longer memory of the initial state persists for the more symmetrical shapes. Our model displays nonequilibrium dynamical effects such as aging. We find that the correlation function C(t ,tw) for all objects scales as a function of single variable ln(tw) / ln(t) . We also study the short-term memory effects in two-component mixtures of extended objects and give a detailed analysis of the contribution to the densification kinetics coming from each mixture component. We observe the weakening of correlation features for the deposition processes in multicomponent systems.

Uncertainties propagation and global sensitivity analysis of the frequency response function of piezoelectric energy harvesters

NASA Astrophysics Data System (ADS)

Ruiz, Rafael O.; Meruane, Viviana

2017-06-01

The goal of this work is to describe a framework to propagate uncertainties in piezoelectric energy harvesters (PEHs). These uncertainties are related to the incomplete knowledge of the model parameters. The framework presented could be employed to conduct prior robust stochastic predictions. The prior analysis assumes a known probability density function for the uncertain variables and propagates the uncertainties to the output voltage. The framework is particularized to evaluate the behavior of the frequency response functions (FRFs) in PEHs, while its implementation is illustrated by the use of different unimorph and bimorph PEHs subjected to different scenarios: free of uncertainties, common uncertainties, and uncertainties as a product of imperfect clamping. The common variability associated with the PEH parameters are tabulated and reported. A global sensitivity analysis is conducted to identify the Sobol indices. Results indicate that the elastic modulus, density, and thickness of the piezoelectric layer are the most relevant parameters of the output variability. The importance of including the model parameter uncertainties in the estimation of the FRFs is revealed. In this sense, the present framework constitutes a powerful tool in the robust design and prediction of PEH performance.

Hemocyte Density Increases with Developmental Stage in an Immune-Challenged Forest Caterpillar

PubMed Central

Stoepler, Teresa M.; Castillo, Julio C.; Lill, John T.; Eleftherianos, Ioannis

2013-01-01

The cellular arm of the insect immune response is mediated by the activity of hemocytes. While hemocytes have been well-characterized morphologically and functionally in model insects, few studies have characterized the hemocytes of non-model insects. Further, the role of ontogeny in mediating immune response is not well understood in non-model invertebrate systems. The goals of the current study were to (1) determine the effects of caterpillar size (and age) on hemocyte density in naïve caterpillars and caterpillars challenged with non-pathogenic bacteria, and (2) characterize the hemocyte activity and diversity of cell types present in two forest caterpillars: Euclea delphinii and Lithacodes fasciola (Limacodidae). We found that although early and late instar (small and large size, respectively) naïve caterpillars had similar constitutive hemocyte densities in both species, late instar Lithacodes caterpillars injected with non-pathogenic E. coli produced more than a twofold greater density of hemocytes than those in early instars. We also found that both caterpillar species contained plasmatocytes, granulocytes and oenocytoids, all of which are found in other lepidopteran species, but lacked spherulocytes. Granulocytes and plasmatocytes were found to be strongly phagocytic in both species, but granulocytes exhibited a higher phagocytic activity than plasmatocytes. Our results strongly suggest that for at least one measure of immunological response, the production of hemocytes in response to infection, response magnitudes can increase over ontogeny. While the underlying raison d’ être for this improvement remains unclear, these findings may be useful in explaining natural patterns of stage-dependent parasitism and pathogen infection. PMID:23940679

The Equation of State of Triamino-Trinitrobenzene from Density Functional Theory Molecular Dynamics

NASA Astrophysics Data System (ADS)

Wixom, Ryan R.

2017-06-01

The US-uP shock Hugoniot has long been the fundamental relationship used to experimentally define the unreacted equations of state of explosives. These experiments are typically performed on porous or composite samples, providing data that is specific to the density of the samples being tested. However, If the crystalline Hugoniot is known, analytical or numerical methods can be used to transform the US-uP relationship to describe the shock response of the porous material. To obtain an accurate crystalline equation of state for TATB, density functional theory based molecular dynamics were used to map out points on the Hugoniot. Since this method provides the pressure, temperature, density, and internal energy at each point on the Hugoniot, a complete equation of state can be constructed. Isotropic, uniaxial, hydrostatic, and isothermal compression of the simulation cell were used to examine TATB under different thermodynamic conditions. A cusp is observed in the Hugoniot that correlates to loss of aromaticity of the molecule. Results of the calculations will be presented and compared to the available experimental data. Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque NM.

On Bayesian Rules for Selecting 3PL Binary Items for Criterion-Referenced Interpretations and Creating Booklets for Bookmark Standard Setting.

ERIC Educational Resources Information Center

Huynh, Huynh

By noting that a Rasch or two parameter logistic (2PL) item belongs to the exponential family of random variables and that the probability density function (pdf) of the correct response (X=1) and the incorrect response (X=0) are symmetric with respect to the vertical line at the item location, it is shown that the conjugate prior for ability is…

Movement reveals scale dependence in habitat selection of a large ungulate

USGS Publications Warehouse

Northrup, Joseph; Anderson, Charles R.; Hooten, Mevin B.; Wittemyer, George

2016-01-01

Ecological processes operate across temporal and spatial scales. Anthropogenic disturbances impact these processes, but examinations of scale dependence in impacts are infrequent. Such examinations can provide important insight to wildlife–human interactions and guide management efforts to reduce impacts. We assessed spatiotemporal scale dependence in habitat selection of mule deer (Odocoileus hemionus) in the Piceance Basin of Colorado, USA, an area of ongoing natural gas development. We employed a newly developed animal movement method to assess habitat selection across scales defined using animal-centric spatiotemporal definitions ranging from the local (defined from five hour movements) to the broad (defined from weekly movements). We extended our analysis to examine variation in scale dependence between night and day and assess functional responses in habitat selection patterns relative to the density of anthropogenic features. Mule deer displayed scale invariance in the direction of their response to energy development features, avoiding well pads and the areas closest to roads at all scales, though with increasing strength of avoidance at coarser scales. Deer displayed scale-dependent responses to most other habitat features, including land cover type and habitat edges. Selection differed between night and day at the finest scales, but homogenized as scale increased. Deer displayed functional responses to development, with deer inhabiting the least developed ranges more strongly avoiding development relative to those with more development in their ranges. Energy development was a primary driver of habitat selection patterns in mule deer, structuring their behaviors across all scales examined. Stronger avoidance at coarser scales suggests that deer behaviorally mediated their interaction with development, but only to a degree. At higher development densities than seen in this area, such mediation may not be possible and thus maintenance of sufficient habitat with lower development densities will be a critical best management practice as development expands globally.

Polystyrene Foam EOS as a Function of Porosity and Fill Gas

NASA Astrophysics Data System (ADS)

Mulford, Roberta; Swift, Damian

2009-06-01

An accurate EOS for polystyrene foam is necessary for analysis of numerous experiments in shock compression, inertial confinement fusion, and astrophysics. Plastic to gas ratios vary between various samples of foam, according to the density and cell-size of the foam. A matrix of compositions has been investigated, allowing prediction of foam response as a function of the plastic-to-air ratio. The EOS code CHEETAH allows participation of the air in the decomposition reaction of the foam, Differences between air-filled, nitrogen-blown, and CO2-blown foams are investigated, to estimate the importance of allowing air to react with plastic products during decomposition. Results differ somewhat from the conventional EOS, which are generated from values for plastic extrapolated to low densities.

Electronic, phonon and superconducting properties of LaPtBi half-Heusler compound

NASA Astrophysics Data System (ADS)

Shrivastava, Deepika; Sanyal, Sankar P.

2018-05-01

In the framework of density functional theory based on plane wave pseudopotential method and linear response technique, we have studied the electronic, phonon and superconducting properties of LaPtBi half-Heusler compound. The electronic band structure and density of states show that it is gapless semiconductor which is consistent with previous results. The positive phonon frequencies confirm the stability of this compound in cubic MgAgAs phase. Superconductivity is studied in terms of Eliashberg spectral function (α2F(ω)), electron-phonon coupling constants (λ). The value of electron-phonon coupling parameter is found to be 0.41 and the superconducting transition temperature is calculated to be 0.76 K, in excellent agreement with the experimentally reported values.

Evaluation of submarine strain-gage systems for monitoring coastal sediment migration

NASA Technical Reports Server (NTRS)

Shideler, G. L.; Mcgrath, D. G.

1973-01-01

Single and multiple strain-gage systems were respectively evaluated as in situ point and areal sensors for monitoring sand-height variations in coastal environments. Static loading tests indicate that gage response pressure is linear for sand heights up to 24 inches. Response pressures are a function of both sand height and aggregate density, with density being influenced by both sediment texture and degree of compaction. Poorer sediment sorting and greater compaction result in higher response pressures. Field tests in a beach foreshore environment indicate that the gage systems are effective qualitative instruments for monitoring long-period migration trends of beach sediments; whereas, short-period responses are not sufficiently reliable. The durability and compactness of the gage systems must be substantially increased for effective field operations. It is recommended that the systems' qualitative potentials be further developed, whereas their development as quantitative instruments be terminated. Further development should emphasize the construction of remote recording systems designed for semipermanent installation.

Modal characterization of the ASCIE segmented optics testbed: New algorithms and experimental results

NASA Technical Reports Server (NTRS)

Carrier, Alain C.; Aubrun, Jean-Noel

1993-01-01

New frequency response measurement procedures, on-line modal tuning techniques, and off-line modal identification algorithms are developed and applied to the modal identification of the Advanced Structures/Controls Integrated Experiment (ASCIE), a generic segmented optics telescope test-bed representative of future complex space structures. The frequency response measurement procedure uses all the actuators simultaneously to excite the structure and all the sensors to measure the structural response so that all the transfer functions are measured simultaneously. Structural responses to sinusoidal excitations are measured and analyzed to calculate spectral responses. The spectral responses in turn are analyzed as the spectral data become available and, which is new, the results are used to maintain high quality measurements. Data acquisition, processing, and checking procedures are fully automated. As the acquisition of the frequency response progresses, an on-line algorithm keeps track of the actuator force distribution that maximizes the structural response to automatically tune to a structural mode when approaching a resonant frequency. This tuning is insensitive to delays, ill-conditioning, and nonproportional damping. Experimental results show that is useful for modal surveys even in high modal density regions. For thorough modeling, a constructive procedure is proposed to identify the dynamics of a complex system from its frequency response with the minimization of a least-squares cost function as a desirable objective. This procedure relies on off-line modal separation algorithms to extract modal information and on least-squares parameter subset optimization to combine the modal results and globally fit the modal parameters to the measured data. The modal separation algorithms resolved modal density of 5 modes/Hz in the ASCIE experiment. They promise to be useful in many challenging applications.

Critical Seismic Vector Random Excitations for Multiply Supported Structures

NASA Astrophysics Data System (ADS)

Sarkar, A.; Manohar, C. S.

1998-05-01

A method for determining critical power spectral density matrix models for earthquake excitations which maximize steady response variance of linear multiply supported extended structures and which also satisfy constraints on input variance, zero crossing rates, frequency content and transmission time lag has been developed. The optimization problem is shown to be non-linear in nature and solutions are obtained by using an iterative technique which is based on linear programming method. A constraint on entropy rate as a measure of uncertainty which can be expected in realistic earthquake ground motions is proposed which makes the critical excitations more realistic. Two special cases are also considered. Firstly, when knowledge of autospectral densities is available, the critical response is shown to be produced by fully coherent excitations which are neither in-phase nor out-of-phase. The critical phase between the excitation components depends on structural parameters, but independent of the auto-spectral densities of the excitations. Secondly, when the knowledge of autospectral densities and phase spectrum of the excitations is available, the critical response is shown to be produced by a system dependent coherence function representing neither fully coherent nor fully incoherent ground motions. The applications of these special cases are discussed in the context of land-based extended structures and secondary systems such as nuclear piping assembly. Illustrative examples on critical inputs and response of sdof and a long-span suspended cable which demonstrated the various features of the approach developed are presented.

Genetic effects on bone mass and turnover-relevance to black/white differences.

PubMed

Parfitt, A M

1997-08-01

The mass of a bone is given by its volume and its apparent density--mass per unit external volume. Most measurements of so-called density are of mass incompletely normalized by some index of bone size. Genes control about 60% to 75% of the variance of peak bone mass/density and a much smaller proportion of the variance in rate of loss. Genetic influence on bone mass/density are mediated in large part by body size, bone size, and muscle mass. Most of the fifty-fold increase in bone mass from birth to maturity is due to bone growth, which is linked to muscle growth and bodily growth. Three-D apparent bone density in the vertebrae increases about 15% during the pubertal growth spurt. The genetic potential for bone accumulation can be frustrated by insufficient calcium intake, disruption of the calendar of puberty and inadequate physical activity. The growing skeleton is much more responsive than the mature skeleton to the osteotrophic effect of exercise, which is mediated by the detection of deviations from a target value for strain, and orchestration of cellular responses that restore the target value, processes collectively termed the mechanostat. Production of metaphyseal cancellous bone and growth in length are both linked to endochondral ossification, which is driven by growth plate cartilage cell proliferation. Production of diaphyseal cortical bone and growth in width are both linked to periosteal apposition, which is driven by osteoblast precursor proliferation. During adolescence trabeculae and cortices become thicker by net endosteal apposition, which increases apparent density. Two lines of evidence support a genetic basis for black/white differences in bone mass. First, the magnitude (10% to 40%) is incommensurate with known nongenetic factors. Second, the difference is already evident in the fetus and increases progressively during growth, especially in adolescence; the difference in peak bone mass persists throughout life. The genetic determination of bone mass is mediated by two classes of gene. The first regulates growth of the body, including muscles and bones, under the control of a master gene or set of genes whose products function as the sizostat. The second regulates the increase in apparent bone density in response to load bearing, under the control of a master gene or set of genes whose products function as the mechanostat.

Open-Ended Recursive Approach for the Calculation of Multiphoton Absorption Matrix Elements

PubMed Central

2015-01-01

We present an implementation of single residues for response functions to arbitrary order using a recursive approach. Explicit expressions in terms of density-matrix-based response theory for the single residues of the linear, quadratic, cubic, and quartic response functions are also presented. These residues correspond to one-, two-, three- and four-photon transition matrix elements. The newly developed code is used to calculate the one-, two-, three- and four-photon absorption cross sections of para-nitroaniline and para-nitroaminostilbene, making this the first treatment of four-photon absorption in the framework of response theory. We find that the calculated multiphoton absorption cross sections are not very sensitive to the size of the basis set as long as a reasonably large basis set with diffuse functions is used. The choice of exchange–correlation functional, however, significantly affects the calculated cross sections of both charge-transfer transitions and other transitions, in particular, for the larger para-nitroaminostilbene molecule. We therefore recommend the use of a range-separated exchange–correlation functional in combination with the augmented correlation-consistent double-ζ basis set aug-cc-pVDZ for the calculation of multiphoton absorption properties. PMID:25821415

Kinetic damping in the spectra of the spherical impedance probe

NASA Astrophysics Data System (ADS)

Oberrath, J.

2018-04-01

The impedance probe is a measurement device to measure plasma parameters, such as electron density. It consists of one electrode connected to a network analyzer via a coaxial cable and is immersed into a plasma. A bias potential superposed with an alternating potential is applied to the electrode and the response of the plasma is measured. Its dynamical interaction with the plasma in an electrostatic, kinetic description can be modeled in an abstract notation based on functional analytic methods. These methods provide the opportunity to derive a general solution, which is given as the response function of the probe–plasma system. It is defined by the matrix elements of the resolvent of an appropriate dynamical operator. Based on the general solution, a residual damping for vanishing pressure can be predicted and can only be explained by kinetic effects. In this paper, an explicit response function of the spherical impedance probe is derived. Therefore, the resolvent is determined by its algebraic representation based on an expansion in orthogonal basis functions. This allows one to compute an approximated response function and its corresponding spectra. These spectra show additional damping due to kinetic effects and are in good agreement with former kinetically determined spectra.

Phase space explorations in time dependent density functional theory

NASA Astrophysics Data System (ADS)

Rajam, Aruna K.

Time dependent density functional theory (TDDFT) is one of the useful tools for the study of the dynamic behavior of correlated electronic systems under the influence of external potentials. The success of this formally exact theory practically relies on approximations for the exchange-correlation potential which is a complicated functional of the co-ordinate density, non-local in space and time. Adiabatic approximations (such as ALDA), which are local in time, are most commonly used in the increasing applications of the field. Going beyond ALDA, has been proved difficult leading to mathematical inconsistencies. We explore the regions where the theory faces challenges, and try to answer some of them via the insights from two electron model systems. In this thesis work we propose a phase-space extension of the TDDFT. We want to answer the challenges the theory is facing currently by exploring the one-body phase-space. We give a general introduction to this theory and its mathematical background in the first chapter. In second chapter, we carryout a detailed study of instantaneous phase-space densities and argue that the functionals of distributions can be a better alternative to the nonlocality issue of the exchange-correlation potentials. For this we study in detail the interacting and the non-interacting phase-space distributions for Hookes atom model. The applicability of ALDA-based TDDFT for the dynamics in strongfields can become severely problematic due to the failure of single-Slater determinant picture.. In the third chapter, we analyze how the phase-space distributions can shine some light into this problem. We do a comparative study of Kohn-Sham and interacting phase-space and momentum distributions for single ionization and double ionization systems. Using a simple model of two-electron systems, we have showed that the momentum distribution computed directly from the exact KS system contains spurious oscillations: a non-classical description of the essentially classical two-electron dynamics. In Time dependent density matrix functional theory (TDDMFT), the evolution scheme of the 1RDM (first order reduced density matrix) contains second-order reduced density matrix (2RDM), which has to be expressed in terms of 1RDMs. Any non-correlated approximations (Hartree-Fock) for 2RDM would fail to capture the natural occupations of the system. In our fourth chapter, we show that by applying the quasi-classical and semi-classical approximations one can capture the natural occupations of the excited systems. We study a time-dependent Moshinsky atom model for this. The fifth chapter contains a comparative work on the existing non-local exchange-correlation kernels that are based on current density response frame work and the co-moving frame work. We show that the two approaches though coinciding with each other in linear response regime, actually turn out to be different in non-linear regime.

Selective inhibition of alpha1B-adrenergic receptor expression and function using a phosphorothioate antisense oligodeoxynucleotide.

PubMed

Gonzalez-Cabrera, P J; Iversen, P L; Liu, M F; Scofield, M A; Jeffries, W B

1998-06-01

To investigate alpha1B-adrenoceptor function, we developed a phosphorothioate antisense oligodeoxynucleotide (AO) to inhibit the expression of the alpha1B-adrenoceptor subtype in DDT1 MF2 cells. We measured the cellular uptake of the AO and its effect on alpha1B-adrenoceptor mRNA expression, protein density, and coupling to phospholipase C. Cells treated with either a control oligodeoxynucleotide (CO) or medium alone served as control groups. Confocal microscopy demonstrated that DDT1 MF2 cells internalized carboxyfluorescein-labeled (FAM) AO within 30 min. Analysis of cellular lysates showed that approximately 50% of the intracellular FAM-AO was present as an intact 18-mer for up to 48 hr. Incubation of cells with AO for 48 hr decreased alpha1B-adrenoceptor density ([3H]prazosin Bmax) versus control groups by 12% (1 microM AO) and 72% (10 microM AO). In time course experiments, AO (10 microM) reduced alpha1B-adrenoceptor density by 28, 64, and 68% versus controls after 24, 48, and 72 hr of exposure, respectively. alpha1B-Adrenoceptor mRNA concentration (measured by RT-PCR) was reduced by 25% in cells treated for 48 hr with 10 microM AO versus controls. AO pretreatment (10 microM, 48 hr) reduced the maximum response to agonist-stimulated [3H]inositol phosphate accumulation. The maximal response of the full agonist norepinephrine was reduced by 30% after AO treatment, and by 73% for the partial agonist naphazoline. In contrast, AO did not affect histamine-stimulated total [3H]inositol phosphate accumulation. Thus, AO effectively reduced alpha1B-adrenoceptor subtype expression and function in vitro, suggesting a potential to selectively inhibit alpha1B-adrenoceptor function in vivo.

Predator diversity and environmental change modify the strengths of trophic and nontrophic interactions.

PubMed

Sentis, Arnaud; Gémard, Charlène; Jaugeon, Baptiste; Boukal, David S

2017-07-01

Understanding the dependence of species interaction strengths on environmental factors and species diversity is crucial to predict community dynamics and persistence in a rapidly changing world. Nontrophic (e.g. predator interference) and trophic components together determine species interaction strengths, but the effects of environmental factors on these two components remain largely unknown. This impedes our ability to fully understand the links between environmental drivers and species interactions. Here, we used a dynamical modelling framework based on measured predator functional responses to investigate the effects of predator diversity, prey density, and temperature on trophic and nontrophic interaction strengths within a freshwater food web. We found that (i) species interaction strengths cannot be predicted from trophic interactions alone, (ii) nontrophic interaction strengths vary strongly among predator assemblages, (iii) temperature has opposite effects on trophic and nontrophic interaction strengths, and (iv) trophic interaction strengths decrease with prey density, whereas the dependence of nontrophic interaction strengths on prey density is concave up. Interestingly, the qualitative impacts of temperature and prey density on the strengths of trophic and nontrophic interactions were independent of predator identity, suggesting a general pattern. Our results indicate that taking multiple environmental factors and the nonlinearity of density-dependent species interactions into account is an important step towards a better understanding of the effects of environmental variations on complex ecological communities. The functional response approach used in this study opens new avenues for (i) the quantification of the relative importance of the trophic and nontrophic components in species interactions and (ii) a better understanding how environmental factors affect these interactions and the dynamics of ecological communities. © 2016 John Wiley & Sons Ltd.

The subcellular distribution of T-type Ca2+ channels in interneurons of the lateral geniculate nucleus.

PubMed

Allken, Vaneeda; Chepkoech, Joy-Loi; Einevoll, Gaute T; Halnes, Geir

2014-01-01

Inhibitory interneurons (INs) in the lateral geniculate nucleus (LGN) provide both axonal and dendritic GABA output to thalamocortical relay cells (TCs). Distal parts of the IN dendrites often enter into complex arrangements known as triadic synapses, where the IN dendrite plays a dual role as postsynaptic to retinal input and presynaptic to TC dendrites. Dendritic GABA release can be triggered by retinal input, in a highly localized process that is functionally isolated from the soma, but can also be triggered by somatically elicited Ca(2+)-spikes and possibly by backpropagating action potentials. Ca(2+)-spikes in INs are predominantly mediated by T-type Ca(2+)-channels (T-channels). Due to the complex nature of the dendritic signalling, the function of the IN is likely to depend critically on how T-channels are distributed over the somatodendritic membrane (T-distribution). To study the relationship between the T-distribution and several IN response properties, we here run a series of simulations where we vary the T-distribution in a multicompartmental IN model with a realistic morphology. We find that the somatic response to somatic current injection is facilitated by a high T-channel density in the soma-region. Conversely, a high T-channel density in the distal dendritic region is found to facilitate dendritic signalling in both the outward direction (increases the response in distal dendrites to somatic input) and the inward direction (the soma responds stronger to distal synaptic input). The real T-distribution is likely to reflect a compromise between several neural functions, involving somatic response patterns and dendritic signalling.

The Subcellular Distribution of T-Type Ca2+ Channels in Interneurons of the Lateral Geniculate Nucleus

PubMed Central

Allken, Vaneeda; Chepkoech, Joy-Loi; Einevoll, Gaute T.; Halnes, Geir

2014-01-01

Inhibitory interneurons (INs) in the lateral geniculate nucleus (LGN) provide both axonal and dendritic GABA output to thalamocortical relay cells (TCs). Distal parts of the IN dendrites often enter into complex arrangements known as triadic synapses, where the IN dendrite plays a dual role as postsynaptic to retinal input and presynaptic to TC dendrites. Dendritic GABA release can be triggered by retinal input, in a highly localized process that is functionally isolated from the soma, but can also be triggered by somatically elicited Ca2+-spikes and possibly by backpropagating action potentials. Ca2+-spikes in INs are predominantly mediated by T-type Ca2+-channels (T-channels). Due to the complex nature of the dendritic signalling, the function of the IN is likely to depend critically on how T-channels are distributed over the somatodendritic membrane (T-distribution). To study the relationship between the T-distribution and several IN response properties, we here run a series of simulations where we vary the T-distribution in a multicompartmental IN model with a realistic morphology. We find that the somatic response to somatic current injection is facilitated by a high T-channel density in the soma-region. Conversely, a high T-channel density in the distal dendritic region is found to facilitate dendritic signalling in both the outward direction (increases the response in distal dendrites to somatic input) and the inward direction (the soma responds stronger to distal synaptic input). The real T-distribution is likely to reflect a compromise between several neural functions, involving somatic response patterns and dendritic signalling. PMID:25268996

Linking functional response and bioenergetics to estimate juvenile salmon growth in a reservoir food web.

PubMed

Haskell, Craig A; Beauchamp, David A; Bollens, Stephen M

2017-01-01

Juvenile salmon (Oncorhynchus spp.) use of reservoir food webs is understudied. We examined the feeding behavior of subyearling Chinook salmon (O. tshawytscha) and its relation to growth by estimating the functional response of juvenile salmon to changes in the density of Daphnia, an important component of reservoir food webs. We then estimated salmon growth across a broad range of water temperatures and daily rations of two primary prey, Daphnia and juvenile American shad (Alosa sapidissima) using a bioenergetics model. Laboratory feeding experiments yielded a Type-II functional response curve: C = 29.858 P *(4.271 + P)-1 indicating that salmon consumption (C) of Daphnia was not affected until Daphnia densities (P) were < 30 · L-1. Past field studies documented Daphnia densities in lower Columbia River reservoirs of < 3 · L-1 in July but as high as 40 · L-1 in August. Bioenergetics modeling indicated that subyearlings could not achieve positive growth above 22°C regardless of prey type or consumption rate. When feeding on Daphnia, subyearlings could not achieve positive growth above 20°C (water temperatures they commonly encounter in the lower Columbia River during summer). At 16-18°C, subyearlings had to consume about 27,000 Daphnia · day-1 to achieve positive growth. However, when feeding on juvenile American shad, subyearlings had to consume 20 shad · day-1 at 16-18°C, or at least 25 shad · day-1 at 20°C to achieve positive growth. Using empirical consumption rates and water temperatures from summer 2013, subyearlings exhibited negative growth during July (-0.23 to -0.29 g · d-1) and August (-0.05 to -0.07 g · d-1). By switching prey from Daphnia to juvenile shad which have a higher energy density, subyearlings can partially compensate for the effects of higher water temperatures they experience in the lower Columbia River during summer. However, achieving positive growth as piscivores requires subyearlings to feed at higher consumption rates than they exhibited empirically. While our results indicate compromised growth in reservoir habitats, the long-term repercussions to salmon populations in the Columbia River Basin are unknown.

Exact nonstationary responses of rectangular thin plate on Pasternak foundation excited by stochastic moving loads

NASA Astrophysics Data System (ADS)

Chen, Guohai; Meng, Zeng; Yang, Dixiong

2018-01-01

This paper develops an efficient method termed as PE-PIM to address the exact nonstationary responses of pavement structure, which is modeled as a rectangular thin plate resting on bi-parametric Pasternak elastic foundation subjected to stochastic moving loads with constant acceleration. Firstly, analytical power spectral density (PSD) functions of random responses for thin plate are derived by integrating pseudo excitation method (PEM) with Duhamel's integral. Based on PEM, the new equivalent von Mises stress (NEVMS) is proposed, whose PSD function contains all cross-PSD functions between stress components. Then, the PE-PIM that combines the PEM with precise integration method (PIM) is presented to achieve efficiently stochastic responses of the plate by replacing Duhamel's integral with the PIM. Moreover, the semi-analytical Monte Carlo simulation is employed to verify the computational results of the developed PE-PIM. Finally, numerical examples demonstrate the high accuracy and efficiency of PE-PIM for nonstationary random vibration analysis. The effects of velocity and acceleration of moving load, boundary conditions of the plate and foundation stiffness on the deflection and NEVMS responses are scrutinized.

Tracking the evolution of crossmodal plasticity and visual functions before and after sight restoration

PubMed Central

Dormal, Giulia; Lepore, Franco; Harissi-Dagher, Mona; Albouy, Geneviève; Bertone, Armando; Rossion, Bruno

2014-01-01

Visual deprivation leads to massive reorganization in both the structure and function of the occipital cortex, raising crucial challenges for sight restoration. We tracked the behavioral, structural, and neurofunctional changes occurring in an early and severely visually impaired patient before and 1.5 and 7 mo after sight restoration with magnetic resonance imaging. Robust presurgical auditory responses were found in occipital cortex despite residual preoperative vision. In primary visual cortex, crossmodal auditory responses overlapped with visual responses and remained elevated even 7 mo after surgery. However, these crossmodal responses decreased in extrastriate occipital regions after surgery, together with improved behavioral vision and with increases in both gray matter density and neural activation in low-level visual regions. Selective responses in high-level visual regions involved in motion and face processing were observable even before surgery and did not evolve after surgery. Taken together, these findings demonstrate that structural and functional reorganization of occipital regions are present in an individual with a long-standing history of severe visual impairment and that such reorganizations can be partially reversed by visual restoration in adulthood. PMID:25520432

Physiological responses and lipid storage of the coral Lophelia pertusa at varying food density.

PubMed

Baussant, Thierry; Nilsen, Marianne; Ravagnan, Elisa; Westerlund, Stig; Ramanand, Sreerekha

2017-01-01

Despite the importance of the cold-water coral Lophelia pertusa to deep-sea reef ecosystem functioning, current knowledge of key physiological responses to available food resources is scarce. Scenarios with varying food density may help to understand how corals deal with seasonal variations in the dark ocean and might be used to study consequences of anthropogenic activities potentially affecting food availability. Thus, the physiological responses of L. pertusa to varying food (Artemia salina nauplii) concentration, ranging from 20% to 300% of carbon equivalent turned over by basal coral respiration, were investigated. A starvation group was also included. Measurements of respiration, growth, mucus production, and energy reserves (storage fatty acids) were performed at several time intervals over 26 weeks. In general, data showed a stronger effect of experimental time on measured responses, but no significant influence of food density treatment. In starved corals, respiration rate declined to 52% of initial respiration, while skeleton growth rate was maintained at the same rate as Artemia-fed corals throughout the investigation. Mucus production measured as the sum of dissolved organic carbon (DOC) and particulate organic carbon (POC) was also similar across food treatments, but POC production exceeded that of DOC at the highest food density. No marked effect was observed on storage fatty acids. These results confirm that L. pertusa is highly resilient to environmental conditions with suboptimal food densities over a time scale of months. Regulation of several physiological processes, including respiration and mucus production, possibly in combination with an opportunistic feeding strategy, contributed to this tolerance to maintain viable corals. Thus, it appears that L. pertusa is well adapted to life in the deep sea.

Response of soft-bottom macrobenthic assemblages to artisanal trawling fisheries in a subtropical estuary

NASA Astrophysics Data System (ADS)

Ortega, Ileana; Colling, Leonir André; Dumont, Luiz Felipe Cestari

2018-07-01

Bottom trawling is one of the most harmful and widespread activities affecting benthic habitats and fauna. In this study, we analyzed the impact of shrimp trawling fisheries on the densities, assemblage structure and vertical stratification of the benthic macrofauna in shallow mudflats of the Patos Lagoon Estuary (Brazil). Experimental trawls of different intensities were performed during three shrimp fishing seasons (2015-2017), comparing macrofauna among before and after trawling, and a control zone. The changes in macrofaunal assemblages were more consistently related to natural variability than to trawling impact, being mostly influenced by sediment structure and salinity variation. The trawling impact was mainly detected in the area with higher percentages of fine sediments, with different macrofaunal responses in each month and stratum. Some non-significant decreases on total densities after trawling were observed, mainly on the superficial stratum, and signs of burial activities. The response to trawling disturbance of each species was different and it highly depended on their natural variability. Only five species showed significant variation to the trawling treatment (Erodona mactroides, Heleobia australis, H. charruana, Heteromastus similis and Laeonereis acuta), with temporally different responses. Decreasing densities were more related to the high impact treatment. In some seasons, decreases on the abundance of Monokalliapseudes schubarti after high impact trawls were up to 60% of the seasonal mean densities. Trawling fisheries may reduce macrobenthic densities but not their vertical stratification. The impact of trawling on key species may compromise the ecosystem function, as benthic macrofauna provide food sources for many aquatic resources. This study highlights trawling impacts in an estuarine nursery area, which should be fully considered since they may be reflected in the trophic webs.

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

PubMed Central

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

2015-01-01

We investigated how density-dependent processes and subsequent variation in nutritional condition of individuals influenced both timing and duration of sexual segregation and selection of resources. During 1999–2001, we experimentally created two population densities of North American elk (Cervus elaphus), a high-density population at 20 elk/km2, and a low-density population at 4 elk/km2 to test hypotheses relative to timing and duration of sexual segregation and variation in selection of resources. We used multi-response permutation procedures to investigate patterns of sexual segregation, and resource selection functions to document differences in selection of resources by individuals in high- and low-density populations during sexual segregation and aggregation. The duration of sexual segregation was 2 months longer in the high-density population and likely was influenced by individuals in poorer nutritional condition, which corresponded with later conception and parturition, than at low density. Males and females in the high-density population overlapped in selection of resources to a greater extent than in the low-density population, probably resulting from density-dependent effects of increased intraspecific competition and lower availability of resources. PMID:25691992

ERP Energy and Cognitive Activity Correlates

NASA Astrophysics Data System (ADS)

Schillaci, Michael Jay; Vendemia, Jennifer M. C.

2014-03-01

We propose a novel analysis approach for high-density event related scalp potential (ERP) data where the integrated channel-power is used to attain an energy density functional state for channel-clusters of neurophysiological significance. The method is applied to data recorded during a two-stimulus, directed lie paradigm and shows that deceptive responses emit between 8% and 10% less power. A time course analysis of these cognitive activity measures over posterior and anterior regions of the cortex suggests that neocortical interactions, reflecting the differing workload demands during executive and semantic processes, take about 50% longer for the case of deception. These results suggest that the proposed method may provide a useful tool for the analysis of ERP correlates of high-order cognitive functioning. We also report on a possible equivalence between the energy functional distribution and near-infrared signatures that have been measured with other modalities.

Negative differential resistance and switch behavior of T-BxNy (x, y = 5, 6, 11) molecular junctions

NASA Astrophysics Data System (ADS)

Wang, Shi-Liang; Yang, Chuan-Lu; Wang, Mei-Shan; Ma, Xiao-Guang; Xin, Jian-Guo

2017-05-01

The electronic transport properties of T-BxNy (x, y = 5, 6, 11) molecular junction are investigated based on first-principle density functional theory and non-equilibrium Green's function method. Strong negative differential resistance (NDR) behavior is observed for T-B5N6 molecule under negative and positive bias voltages, with an obvious switch effect for T-B6N5. However, only small NDR is shown for the complex of the two molecules. The projected device density of states, the spatial distribution of molecular orbitals, and the effect of transmission spectra under various bias voltages on the electronic transport properties are analyzed. The obvious effect of bias voltage on the changes in the electronic distribution of frontier molecular orbitals is responsible for the NDR or switch behavior. Therefore, different functional molecular devices can be obtained with different structures of T-BxNy.

Structural, electronic, mechanical, and dynamical properties of graphene oxides: A first principles study

NASA Astrophysics Data System (ADS)

Dabhi, Shweta D.; Gupta, Sanjay D.; Jha, Prafulla K.

2014-05-01

We report the results of a theoretical study on the structural, electronic, mechanical, and vibrational properties of some graphene oxide models (GDO, a-GMO, z-GMO, ep-GMO and mix-GMO) at ambient pressure. The calculations are based on the ab-initio plane-wave pseudo potential density functional theory, within the generalized gradient approximations for the exchange and correlation functional. The calculated values of lattice parameters, bulk modulus, and its first order pressure derivative are in good agreement with other reports. A linear response approach to the density functional theory is used to derive the phonon frequencies. We discuss the contribution of the phonons in the dynamical stability of graphene oxides and detailed analysis of zone centre phonon modes in all the above mentioned models. Our study demonstrates a wide range of energy gap available in the considered models of graphene oxide and hence the possibility of their use in nanodevices.

Functional traits determine tree growth and ecosystem productivity of a tropical montane forest: Insights from a long-term nutrient manipulation experiment.

PubMed

Báez, Selene; Homeier, Jürgen

2018-01-01

Trait-response effects are critical to forecast community structure and biomass production in highly diverse tropical forests. Ecological theory and few observation studies indicate that trees with acquisitive functional traits would respond more strongly to higher resource availability than those with conservative traits. We assessed how long-term tree growth in experimental nutrient addition plots (N, P, and N + P) varied as a function of morphological traits, tree size, and species identity. We also evaluated how trait-based responses affected stand scale biomass production considering the community structure. We found that tree growth depended on interactions between functional traits and the type or combination of nutrients added. Common species with acquisitive functional traits responded more strongly to nutrient addition, mainly to N + P. Phosphorous enhanced the growth rates of species with acquisitive and conservative traits, had mostly positive effects on common species and neutral or negative effects in rare species. Moreover, trees receiving N + P grew faster irrespective of their initial size relative to trees in control or to trees in other treatment plots. Finally, species responses were highly idiosyncratic suggesting that community processes including competition and niche dimensionality may be altered under increased resource availability. We found no statistically significant effects of nutrient additions on aboveground biomass productivity because acquisitive species had a limited potential to increase their biomass, possibly due to their generally lower wood density. In contrast, P addition increased the growth rates of species characterized by more conservative resource strategies (with higher wood density) that were poorly represented in the plant community. We provide the first long-term experimental evidence that trait-based responses, community structure, and community processes modulate the effects of increased nutrient availability on biomass productivity in a tropical forest. © 2017 John Wiley & Sons Ltd.

Bone marrow support of the heart in pressure overload is lost with aging.

PubMed

Sopko, Nikolai A; Turturice, Benjamin A; Becker, Mitchell E; Brown, Chase R; Dong, Feng; Popović, Zoran B; Penn, Marc S

2010-12-21

Exogenous stem cell delivery is under investigation to prevent and treat cardiac dysfunction. It is less studied as to the extent endogenous bone marrow derived stem cells contribute to cardiac homeostais in response to stress and the affects of aging on this stress response. To determine the role of bone marrow (BM) derived stem cells on cardiac homeostasis in response to pressure overload (PO) and how this response is altered by aging. Young (8 weeks) and old (>40 weeks) C57/b6 mice underwent homo- and heterochronic BM transplantation prior to transverse aortic constriction (TAC). We found that older BM is associated with decreased cardiac function following TAC. This decreased function is associated with decrease in BM cell engraftment, increased myocyte apoptosis, decreased myocyte hypertrophy, increased myocardial fibrosis and decreased cardiac function. Additionally, there is a decrease in activation of resident cells within the heart in response to PO in old mice. Interestingly, these effects are not due to alterations in vascular density or inflammation in response to PO or differences in ex vivo stem cell migration between young and old mice. BM derived stem cells are activated in response to cardiac PO, and the recruitment of BM derived cells are involved in cardiac myocyte hypertrophy and maintenance of function in response to PO which is lost with aging.

Uncertainty quantification of voice signal production mechanical model and experimental updating

NASA Astrophysics Data System (ADS)

Cataldo, E.; Soize, C.; Sampaio, R.

2013-11-01

The aim of this paper is to analyze the uncertainty quantification in a voice production mechanical model and update the probability density function corresponding to the tension parameter using the Bayes method and experimental data. Three parameters are considered uncertain in the voice production mechanical model used: the tension parameter, the neutral glottal area and the subglottal pressure. The tension parameter of the vocal folds is mainly responsible for the changing of the fundamental frequency of a voice signal, generated by a mechanical/mathematical model for producing voiced sounds. The three uncertain parameters are modeled by random variables. The probability density function related to the tension parameter is considered uniform and the probability density functions related to the neutral glottal area and the subglottal pressure are constructed using the Maximum Entropy Principle. The output of the stochastic computational model is the random voice signal and the Monte Carlo method is used to solve the stochastic equations allowing realizations of the random voice signals to be generated. For each realization of the random voice signal, the corresponding realization of the random fundamental frequency is calculated and the prior pdf of this random fundamental frequency is then estimated. Experimental data are available for the fundamental frequency and the posterior probability density function of the random tension parameter is then estimated using the Bayes method. In addition, an application is performed considering a case with a pathology in the vocal folds. The strategy developed here is important mainly due to two things. The first one is related to the possibility of updating the probability density function of a parameter, the tension parameter of the vocal folds, which cannot be measured direct and the second one is related to the construction of the likelihood function. In general, it is predefined using the known pdf. Here, it is constructed in a new and different manner, using the own system considered.

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

NASA Astrophysics Data System (ADS)

Sander, Tobias; Kresse, Georg

2017-02-01

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

Ground-state densities from the Rayleigh-Ritz variation principle and from density-functional theory.

PubMed

Kvaal, Simen; Helgaker, Trygve

2015-11-14

The relationship between the densities of ground-state wave functions (i.e., the minimizers of the Rayleigh-Ritz variation principle) and the ground-state densities in density-functional theory (i.e., the minimizers of the Hohenberg-Kohn variation principle) is studied within the framework of convex conjugation, in a generic setting covering molecular systems, solid-state systems, and more. Having introduced admissible density functionals as functionals that produce the exact ground-state energy for a given external potential by minimizing over densities in the Hohenberg-Kohn variation principle, necessary and sufficient conditions on such functionals are established to ensure that the Rayleigh-Ritz ground-state densities and the Hohenberg-Kohn ground-state densities are identical. We apply the results to molecular systems in the Born-Oppenheimer approximation. For any given potential v ∈ L(3/2)(ℝ(3)) + L(∞)(ℝ(3)), we establish a one-to-one correspondence between the mixed ground-state densities of the Rayleigh-Ritz variation principle and the mixed ground-state densities of the Hohenberg-Kohn variation principle when the Lieb density-matrix constrained-search universal density functional is taken as the admissible functional. A similar one-to-one correspondence is established between the pure ground-state densities of the Rayleigh-Ritz variation principle and the pure ground-state densities obtained using the Hohenberg-Kohn variation principle with the Levy-Lieb pure-state constrained-search functional. In other words, all physical ground-state densities (pure or mixed) are recovered with these functionals and no false densities (i.e., minimizing densities that are not physical) exist. The importance of topology (i.e., choice of Banach space of densities and potentials) is emphasized and illustrated. The relevance of these results for current-density-functional theory is examined.

Local population density and group composition influence the signal-preference relationship in Enchenopa treehoppers (Hemiptera: Membracidae).

PubMed

Fowler-Finn, K D; Cruz, D C; Rodríguez, R L

2017-01-01

Many animals exhibit social plasticity - changes in phenotype or behaviour in response to experience with conspecifics that change how evolutionary processes like sexual selection play out. Here, we asked whether social plasticity arising from variation in local population density in male advertisement signals and female mate preferences influences the form of sexual selection. We manipulated local density and determined whether this changed how the distribution of male signals overlapped with female preferences - the signal preference relationship. We specifically look at the shape of female mate preference functions, which, when compared to signal distributions, provide hypotheses about the form of sexual selection. We used Enchenopa binotata treehoppers, a group of plant-feeding insects that exhibit natural variation in local densities across individual host plants, populations, species and years. We measured male signal frequency and female preference functions across the density treatments. We found that male signals varied across local social groups, but not according to local density. By contrast, female preferences varied with local density - favouring higher signal frequencies in denser environments. Thus, local density changes the signal-preference relationship and, consequently, the expected form of sexual selection. We found no influence of sex ratio on the signal-preference relationship. Our findings suggest that plasticity arising from variation in local group density and composition can alter the form of sexual selection with potentially important consequences both for the maintenance of variation and for speciation. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Effect of stretching on the ballistic conductance of Au nanocontacts in presence of CO: A density functional study

NASA Astrophysics Data System (ADS)

Sclauzero, Gabriele; Dal Corso, Andrea; Smogunov, Alexander

2012-04-01

CO adsorption on an Au monatomic chain is studied within density functional theory in nanocontact geometries as a function of the contact stretching. We compare the bridge and atop adsorption sites of CO, finding that the bridge site is energetically favored at all strains studied here. Atop adsorption gives rise to an almost complete suppression of the ballistic conductance of the nanocontact, while adsorption at the bridge site results in a conductance value close to 0.6G0, in agreement with previous experimental data. We show that only the bridge site can qualitatively account for the evolution of the conductance as a function of the contact stretching observed in the experimental conductance traces. The numerical discrepancy between the theoretical and experimental conductance slopes is rationalized through a simple model for the elastic response of the metallic leads. We also verify that our conductance values are not affected by the specific choice of the nanocontact geometry by comparing two different atomistic models for the tips.

Global excitation of wave phenomena in a dissipative multiconstituent medium. III - Response characteristics for different sources in the earth's thermosphere

NASA Technical Reports Server (NTRS)

Mayr, H. G.; Harris, I.; Varosi, F.; Herrero, F. A.

1987-01-01

A linear trasnfer function model of the earth's thermosphere which includes the electric field momentum source is used to study the differences in the response characteristics for Joule heating and momentum coupling in the thermosphere. It is found that, for Joule/particle heating, the temperature and density perturbations contain a relatively large trapped component which has the property of a low-pass filter, with slow decay after the source is turned off. The decay time is sensitive to the altitude of energy deposition and is significantly reduced as the source peak moves from 125 to 150 km. For electric field momentum coupling, the trapped components in the temperature and density perturbations are relatively small. In the curl field of the velocity, however, the trapped component dominates, but compared with the temperature and density its decay time is much shorter. Outside the source region the form of excitation is of secondary importance for the generation of the various propagating gravity wave modes.

Use of nonlinear programming to optimize performance response to energy density in broiler feed formulation.

PubMed

Guevara, V R

2004-02-01

A nonlinear programming optimization model was developed to maximize margin over feed cost in broiler feed formulation and is described in this paper. The model identifies the optimal feed mix that maximizes profit margin. Optimum metabolizable energy level and performance were found by using Excel Solver nonlinear programming. Data from an energy density study with broilers were fitted to quadratic equations to express weight gain, feed consumption, and the objective function income over feed cost in terms of energy density. Nutrient:energy ratio constraints were transformed into equivalent linear constraints. National Research Council nutrient requirements and feeding program were used for examining changes in variables. The nonlinear programming feed formulation method was used to illustrate the effects of changes in different variables on the optimum energy density, performance, and profitability and was compared with conventional linear programming. To demonstrate the capabilities of the model, I determined the impact of variation in prices. Prices for broiler, corn, fish meal, and soybean meal were increased and decreased by 25%. Formulations were identical in all other respects. Energy density, margin, and diet cost changed compared with conventional linear programming formulation. This study suggests that nonlinear programming can be more useful than conventional linear programming to optimize performance response to energy density in broiler feed formulation because an energy level does not need to be set.

Functional Response of Eretmocerus delhiensis on Trialeurodes vaporariorum by Parasitism and Host Feeding

PubMed Central

Ebrahimifar, Jafar; Allahyari, Hossein

2017-01-01

The parasitoid wasp, Eretmocerus delhiensis (Hymenoptera, Aphelinidae) is a thelytokous and syn-ovigenic parasitoid. To evaluate E. delhiensis as a biocontrol agent in greenhouse, the killing efficiency of this parasitoid by parasitism and host-feeding, were studied. Killing efficiency can be compared by estimation of functional response parameters. Laboratory experiments were performed in controllable conditions to evaluate the functional response of E. delhiensis at eight densities (2, 4, 8, 16, 32, 64, 100, and 120 third nymphal stage) of Trialeurodes vaporariorum (Hemiptera, Aleyrodidae) on two hosts including; tomato and prickly lettuce. The maximum likelihood estimates from regression logistic analysis revealed type II functional response for two host plants and the type of functional response was not affected by host plant. Roger’s model was used to fit the data. The attack rate (a) for E. delhiensis was 0.0286 and 0.0144 per hour on tomato and 0.0434 and 0.0170 per hour on prickly lettuce for parasitism and host feeding, respectively. Furthermore, estimated handling times (Th) were 0.4911 and 1.4453 h on tomato and 0.5713 and 1.5001 h on prickly lettuce for parasitism and host feeding, respectively. Based on 95% confidence interval, functional response parameters were significantly different between the host plants solely in parasitism. Results of this study opens new insight in the host parasitoid interactions, subsequently needs further investigation before utilizing it for management and reduction of greenhouse whitefly. PMID:28423420

Density-dependent prophylaxis in the mealworm beetle Tenebrio molitor L. (Coleoptera: Tenebrionidae): cuticular melanization is an indicator of investment in immunity.

PubMed Central

Barnes, A I; Siva-Jothy, M T

2000-01-01

If there are costs involved with the maintenance of pathogen resistance, then higher investment in this trait is expected when the risk of pathogenesis is high. One situation in which the risk of pathogenesis is elevated is at increased conspecific density. This paper reports the results of a study of density-dependent polyphenism in pathogen resistance and immune function in the mealworm beetle Tenebrio molitor. Beetles reared at high larval densities showed lower mortality when exposed to a generalist entomopathogenic fungus and a higher degree of cuticular melanization than those reared solitarily. The degree of cuticular melanization was a strong indicator of resistance, with darker beetles being more resistant than lighter ones regardless of rearing density. No differences were found between rearing densities in the levels of phenoloxidase, an enzyme key to the insect immune response. The results show that pathogen resistance is phenotypically plastic in T. molitor, suggesting that the maintenance of this trait is costly. PMID:10687824

Expression Patterns of Odorant Receptors and Response Properties of Olfactory Sensory Neurons in Aged Mice

PubMed Central

Lee, Anderson C.; Tian, Huikai; Grosmaitre, Xavier

2009-01-01

The sense of smell deteriorates in normal aging, but the underling mechanisms are still elusive. Here we investigated age-related alterations in expression patterns of odorant receptor (OR) genes and functional properties of olfactory sensory neurons (OSNs)—2 critical factors that define the odor detection threshold in the olfactory epithelium. Using in situ hybridization for 9 representative OR genes, we compared the cell densities of each OR in coronal nose sections at different ages (3–27 months). The cell density for different ORs peaked at different time points and a decline was observed for 6 of 9 ORs at advanced ages. Using patch clamp recordings, we then examined the odorant responses of individual OSNs coexpressing a defined OR (MOR23) and green fluorescent protein. The MOR23 neurons recorded from aged animals maintained a similar sensitivity and dynamic range in response to the cognate odorant (lyral) as those from younger mice. The results indicate that although the cell densities of OSNs expressing certain types of ORs decline at advanced ages, individual OSNs can retain their sensitivity. The implications of these findings in age-related olfactory deterioration are discussed. PMID:19759360

Expression patterns of odorant receptors and response properties of olfactory sensory neurons in aged mice.

PubMed

Lee, Anderson C; Tian, Huikai; Grosmaitre, Xavier; Ma, Minghong

2009-10-01

The sense of smell deteriorates in normal aging, but the underling mechanisms are still elusive. Here we investigated age-related alterations in expression patterns of odorant receptor (OR) genes and functional properties of olfactory sensory neurons (OSNs)-2 critical factors that define the odor detection threshold in the olfactory epithelium. Using in situ hybridization for 9 representative OR genes, we compared the cell densities of each OR in coronal nose sections at different ages (3-27 months). The cell density for different ORs peaked at different time points and a decline was observed for 6 of 9 ORs at advanced ages. Using patch clamp recordings, we then examined the odorant responses of individual OSNs coexpressing a defined OR (MOR23) and green fluorescent protein. The MOR23 neurons recorded from aged animals maintained a similar sensitivity and dynamic range in response to the cognate odorant (lyral) as those from younger mice. The results indicate that although the cell densities of OSNs expressing certain types of ORs decline at advanced ages, individual OSNs can retain their sensitivity. The implications of these findings in age-related olfactory deterioration are discussed.

Spectral decompositions of multiple time series: a Bayesian non-parametric approach.

PubMed

Macaro, Christian; Prado, Raquel

2014-01-01

We consider spectral decompositions of multiple time series that arise in studies where the interest lies in assessing the influence of two or more factors. We write the spectral density of each time series as a sum of the spectral densities associated to the different levels of the factors. We then use Whittle's approximation to the likelihood function and follow a Bayesian non-parametric approach to obtain posterior inference on the spectral densities based on Bernstein-Dirichlet prior distributions. The prior is strategically important as it carries identifiability conditions for the models and allows us to quantify our degree of confidence in such conditions. A Markov chain Monte Carlo (MCMC) algorithm for posterior inference within this class of frequency-domain models is presented.We illustrate the approach by analyzing simulated and real data via spectral one-way and two-way models. In particular, we present an analysis of functional magnetic resonance imaging (fMRI) brain responses measured in individuals who participated in a designed experiment to study pain perception in humans.

An atomic orbital based real-time time-dependent density functional theory for computing electronic circular dichroism band spectra

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

Goings, Joshua J.; Li, Xiaosong, E-mail: xsli@uw.edu

2016-06-21

One of the challenges of interpreting electronic circular dichroism (ECD) band spectra is that different states may have different rotatory strength signs, determined by their absolute configuration. If the states are closely spaced and opposite in sign, observed transitions may be washed out by nearby states, unlike absorption spectra where transitions are always positive additive. To accurately compute ECD bands, it is necessary to compute a large number of excited states, which may be prohibitively costly if one uses the linear-response time-dependent density functional theory (TDDFT) framework. Here we implement a real-time, atomic-orbital based TDDFT method for computing the entiremore » ECD spectrum simultaneously. The method is advantageous for large systems with a high density of states. In contrast to previous implementations based on real-space grids, the method is variational, independent of nuclear orientation, and does not rely on pseudopotential approximations, making it suitable for computation of chiroptical properties well into the X-ray regime.« less

In situ study of heavy ion irradiation response of immiscible Cu/Fe multilayers

DOE PAGES

Chen, Youxing; Li, Nan; Bufford, Daniel Charles; ...

2016-04-09

By providing active defect sinks that capture and annihilate radiation induced defect clusters immiscible metallic multilayers with incoherent interfaces can effectively reduce defect density in ion irradiated metals. Although it is anticipated that defect density within the layers should vary as a function of distance to the layer interface, there is, to date, little in situ TEM evidence to validate this hypothesis. In our study monolithic Cu films and Cu/Fe multilayers with individual layer thickness, h, of 100 and 5 nm were subjected to in situ Cu ion irradiation at room temperature to nominally 1 displacement-per-atom inside a transmission electronmore » microscope. Rapid formation and propagation of defect clusters were observed in monolithic Cu, whereas fewer defects with smaller dimensions were generated in Cu/Fe multilayers with smaller h. Moreover, in situ video shows that the cumulative defect density in Cu/Fe 100 nm multilayers indeed varies, as a function of distance to the layer interfaces, supporting a long postulated hypothesis.« less

Bifurcation Analysis of a Predator-Prey System with Ratio-Dependent Functional Response

NASA Astrophysics Data System (ADS)

Jiang, Xin; She, Zhikun; Feng, Zhaosheng; Zheng, Xiuliang

2017-12-01

In this paper, we are concerned with the structural stability of a density dependent predator-prey system with ratio-dependent functional response. Starting with the geometrical analysis of hyperbolic curves, we obtain that the system has one or two positive equilibria under various conditions. Inspired by the S-procedure and semi-definite programming, we use the sum of squares decomposition based method to ensure the global asymptotic stability of the positive equilibrium through the associated polynomial Lyapunov functions. By exploring the monotonic property of the trace of the Jacobian matrix with respect to r under the given different conditions, we analytically verify that there is a corresponding unique r∗ such that the trace is equal to zero and prove the existence of Hopf bifurcation, respectively.

Ordinary dielectric function of corundumlike α -Ga2O3 from 40 meV to 20 eV

NASA Astrophysics Data System (ADS)

Feneberg, Martin; Nixdorf, Jakob; Neumann, Maciej D.; Esser, Norbert; Artús, Lluis; Cuscó, Ramon; Yamaguchi, Tomohiro; Goldhahn, Rüdiger

2018-04-01

The linear optical response of metastable α -Ga2O3 is investigated by spectroscopic ellipsometry. We determine the ordinary dielectric function from lattice vibrations up to the vacuum ultraviolet spectral range at room temperature for a sample with a (0001 ) surface. Three out of four Eu infrared-active phonon modes are unambiguously determined, and their frequencies are in good agreement with density functional theory calculations. The dispersion of the refractive index in the visible and ultraviolet part of the spectrum is determined. High-energy interband transitions are characterized up to 20 eV . By comparison with the optical response of α -Al2O3 and with theoretical results, a tentative assignment of interband transitions is proposed.

Spin-Multiplet Components and Energy Splittings by Multistate Density Functional Theory.

PubMed

Grofe, Adam; Chen, Xin; Liu, Wenjian; Gao, Jiali

2017-10-05

Kohn-Sham density functional theory has been tremendously successful in chemistry and physics. Yet, it is unable to describe the energy degeneracy of spin-multiplet components with any approximate functional. This work features two contributions. (1) We present a multistate density functional theory (MSDFT) to represent spin-multiplet components and to determine multiplet energies. MSDFT is a hybrid approach, taking advantage of both wave function theory and density functional theory. Thus, the wave functions, electron densities and energy density-functionals for ground and excited states and for different components are treated on the same footing. The method is illustrated on valence excitations of atoms and molecules. (2) Importantly, a key result is that for cases in which the high-spin components can be determined separately by Kohn-Sham density functional theory, the transition density functional in MSDFT (which describes electronic coupling) can be defined rigorously. The numerical results may be explored to design and optimize transition density functionals for configuration coupling in multiconfigurational DFT.

Limited spatial response to direct predation risk by African herbivores following predator reintroduction.

PubMed

Davies, Andrew B; Tambling, Craig J; Kerley, Graham I H; Asner, Gregory P

2016-08-01

Predators affect ecosystems not only through direct mortality of prey, but also through risk effects on prey behavior, which can exert strong influences on ecosystem function and prey fitness. However, how functionally different prey species respond to predation risk and how prey strategies vary across ecosystems and in response to predator reintroduction are poorly understood. We investigated the spatial distributions of six African herbivores varying in foraging strategy and body size in response to environmental factors and direct predation risk by recently reintroduced lions in the thicket biome of the Addo Elephant National Park, South Africa, using camera trap surveys, GPS telemetry, kill site locations and Light Detection and Ranging. Spatial distributions of all species, apart from buffalo, were driven primarily by environmental factors, with limited responses to direct predation risk. Responses to predation risk were instead indirect, with species distributions driven by environmental factors, and diel patterns being particularly pronounced. Grazers were more responsive to the measured variables than browsers, with more observations in open areas. Terrain ruggedness was a stronger predictor of browser distributions than was vegetation density. Buffalo was the only species to respond to predator encounter risk, avoiding areas with higher lion utilization. Buffalo therefore behaved in similar ways to when lions were absent from the study area. Our results suggest that direct predation risk effects are relatively weak when predator densities are low and the time since reintroduction is short and emphasize the need for robust, long-term monitoring of predator reintroductions to place such events in the broader context of predation risk effects.

Markedly Divergent Tree Assemblage Responses to Tropical Forest Loss and Fragmentation across a Strong Seasonality Gradient.

PubMed

Orihuela, Rodrigo L L; Peres, Carlos A; Mendes, Gabriel; Jarenkow, João A; Tabarelli, Marcelo

2015-01-01

We examine the effects of forest fragmentation on the structure and composition of tree assemblages within three seasonal and aseasonal forest types of southern Brazil, including evergreen, Araucaria, and deciduous forests. We sampled three southernmost Atlantic Forest landscapes, including the largest continuous forest protected areas within each forest type. Tree assemblages in each forest type were sampled within 10 plots of 0.1 ha in both continuous forests and 10 adjacent forest fragments. All trees within each plot were assigned to trait categories describing their regeneration strategy, vertical stratification, seed-dispersal mode, seed size, and wood density. We detected differences among both forest types and landscape contexts in terms of overall tree species richness, and the density and species richness of different functional groups in terms of regeneration strategy, seed dispersal mode and woody density. Overall, evergreen forest fragments exhibited the largest deviations from continuous forest plots in assemblage structure. Evergreen, Araucaria and deciduous forests diverge in the functional composition of tree floras, particularly in relation to regeneration strategy and stress tolerance. By supporting a more diversified light-demanding and stress-tolerant flora with reduced richness and abundance of shade-tolerant, old-growth species, both deciduous and Araucaria forest tree assemblages are more intrinsically resilient to contemporary human-disturbances, including fragmentation-induced edge effects, in terms of species erosion and functional shifts. We suggest that these intrinsic differences in the direction and magnitude of responses to changes in landscape structure between forest types should guide a wide range of conservation strategies in restoring fragmented tropical forest landscapes worldwide.

Markedly Divergent Tree Assemblage Responses to Tropical Forest Loss and Fragmentation across a Strong Seasonality Gradient

PubMed Central

Orihuela, Rodrigo L. L.; Peres, Carlos A.; Mendes, Gabriel; Jarenkow, João A.; Tabarelli, Marcelo

2015-01-01

We examine the effects of forest fragmentation on the structure and composition of tree assemblages within three seasonal and aseasonal forest types of southern Brazil, including evergreen, Araucaria, and deciduous forests. We sampled three southernmost Atlantic Forest landscapes, including the largest continuous forest protected areas within each forest type. Tree assemblages in each forest type were sampled within 10 plots of 0.1 ha in both continuous forests and 10 adjacent forest fragments. All trees within each plot were assigned to trait categories describing their regeneration strategy, vertical stratification, seed-dispersal mode, seed size, and wood density. We detected differences among both forest types and landscape contexts in terms of overall tree species richness, and the density and species richness of different functional groups in terms of regeneration strategy, seed dispersal mode and woody density. Overall, evergreen forest fragments exhibited the largest deviations from continuous forest plots in assemblage structure. Evergreen, Araucaria and deciduous forests diverge in the functional composition of tree floras, particularly in relation to regeneration strategy and stress tolerance. By supporting a more diversified light-demanding and stress-tolerant flora with reduced richness and abundance of shade-tolerant, old-growth species, both deciduous and Araucaria forest tree assemblages are more intrinsically resilient to contemporary human-disturbances, including fragmentation-induced edge effects, in terms of species erosion and functional shifts. We suggest that these intrinsic differences in the direction and magnitude of responses to changes in landscape structure between forest types should guide a wide range of conservation strategies in restoring fragmented tropical forest landscapes worldwide. PMID:26309252

Acute SSRI-induced anxiogenic and brain metabolic effects are attenuated 6 months after initial MDMA-induced depletion.

PubMed

Andó, Rómeó D; Adori, Csaba; Kirilly, Eszter; Molnár, Eszter; Kovács, Gábor G; Ferrington, Linda; Kelly, Paul A T; Bagdy, György

2010-03-05

To assess the functional state of the serotonergic system, the acute behavioural and brain metabolic effect of SSRI antidepressants were studied during the recovery period after MDMA-induced neuronal damage. The effects of the SSRI fluoxetine and the serotonin receptor agonist meta-chloro-phenylpiperazine (m-CPP) were investigated in the social interaction test in Dark Agouti rats, 6 months after treatment with a single dose of MDMA (15 or 30 mg kg(-1), i.p.). At earlier time points these doses of MDMA have been shown to cause 30-60% loss in axonal densities in several brain regions. Densities of the serotonergic axons were assessed using serotonin-transporter and tryptophan-hydroxylase immunohistochemistry. In a parallel group of animals, brain function was examined following an acute challenge with either fluoxetine or citalopram, using 2-deoxyglucose autoradiographic imaging. Six months after MDMA treatment the densities of serotonergic axons were decreased in only a few brain areas including hippocampus and thalamus. Basal anxiety was unaltered in MDMA-treated animals. However, the acute anxiogenic effects of fluoxetine, but not m-CPP, were attenuated in animals pretreated with MDMA. The metabolic response to both citalopram and fluoxetine was normal in most of the brain areas examined with the exception of ventromedial thalamus and hippocampal sub-fields where the response was attenuated. These data provide evidence that 6 months after MDMA-induced damage serotonergic axons show recovery in most brain areas, but serotonergic functions to challenges with SSRIs including anxiety and aggression remain altered. Copyright 2009 Elsevier B.V. All rights reserved.

Plane wave density functional molecular dynamics study of exothermic reactions of Al/CuO thermites

NASA Astrophysics Data System (ADS)

Oloriegbe, Suleiman; Sewell, Thomas; Chen, Zhen; Jiang, Shan; Gan, Yong

2014-03-01

Exothermic reactions between nanosize aluminum (Al) and copper oxide (CuO) structures are of current interest because of their high reaction enthalpy and energy density which exceed those of traditional monomolecular energetic compounds such as TNT, RDX, and HMX. In this work, molecular dynamics simulations with forces obtained from plane wave density functional theory are used to investigate the atomic-scale and electronic processes that occur during the fast thermite reactions between Al and CuO nanostructures under adiabatic conditions. Aluminum surfaces in contact with O-exposed and Cu-exposed CuO surfaces are studied. Starting from initial temperature T = 800 K, we have observed: faster chemical reaction at the oxygen-rich interface during the initial 0.5 ps, linear temperature rise, and fast oxygen diffusion into the Al region with the rate 1.87 X 10-3 cm2/s. The density-derived electrostatic and chemical method is used to evaluate the net atomic charges and charge transfer during the important redox processes. High charge density around the oxygen-exposed interface may be responsible for the faster initial reactions at that interface. The overall reaction rate, determined using the time evolution of Cu-O charge orbital overlap population, is approximately first order.

Geometric characterization and simulation of planar layered elastomeric fibrous biomaterials

PubMed Central

Carleton, James B.; D'Amore, Antonio; Feaver, Kristen R.; Rodin, Gregory J.; Sacks, Michael S.

2014-01-01

Many important biomaterials are composed of multiple layers of networked fibers. While there is a growing interest in modeling and simulation of the mechanical response of these biomaterials, a theoretical foundation for such simulations has yet to be firmly established. Moreover, correctly identifying and matching key geometric features is a critically important first step for performing reliable mechanical simulations. The present work addresses these issues in two ways. First, using methods of geometric probability we develop theoretical estimates for the mean linear and areal fiber intersection densities for two-dimensional fibrous networks. These densities are expressed in terms of the fiber density and the orientation distribution function, both of which are relatively easy-to-measure properties. Secondly, we develop a random walk algorithm for geometric simulation of two-dimensional fibrous networks which can accurately reproduce the prescribed fiber density and orientation distribution function. Furthermore, the linear and areal fiber intersection densities obtained with the algorithm are in agreement with the theoretical estimates. Both theoretical and computational results are compared with those obtained by post-processing of SEM images of actual scaffolds. These comparisons reveal difficulties inherent to resolving fine details of multilayered fibrous networks. The methods provided herein can provide a rational means to define and generate key geometric features from experimentally measured or prescribed scaffold structural data. PMID:25311685

The Expansion of Two-Year Colleges: Tests of Institutional and Political Economy Theories in a Dynamic Model.

ERIC Educational Resources Information Center

Blau, Judith R.; And Others

Traditional theoretical explanations for the rate of expansion of educational institutions have included the "organizational ecology" model of new foundings as a function of population density, the "institutional theory" argument that foundings are responsive to societal/consumer demand, and theories of political economy which describe foundings…

Frequency of anti-collision observing responses by solo pilots as a function of traffic density, ATC traffic warnings, and competing behavior.

DOT National Transportation Integrated Search

1973-04-01

Eighteen instrument-rated pilots were flown in two-hour simulated solo missions during which the frequency of traffic, ATC warnings, and ATC clearances were varied, while the visibility of the target was held constant at 100%. : In order to observe t...

Efficient block preconditioned eigensolvers for linear response time-dependent density functional theory

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

Vecharynski, Eugene; Brabec, Jiri; Shao, Meiyue

We present two efficient iterative algorithms for solving the linear response eigen- value problem arising from the time dependent density functional theory. Although the matrix to be diagonalized is nonsymmetric, it has a special structure that can be exploited to save both memory and floating point operations. In particular, the nonsymmetric eigenvalue problem can be transformed into a product eigenvalue problem that is self-adjoint with respect to a K-inner product. This product eigenvalue problem can be solved efficiently by a modified Davidson algorithm and a modified locally optimal block preconditioned conjugate gradient (LOBPCG) algorithm that make use of the K-innermore » product. The solution of the product eigenvalue problem yields one component of the eigenvector associated with the original eigenvalue problem. However, the other component of the eigenvector can be easily recovered in a postprocessing procedure. Therefore, the algorithms we present here are more efficient than existing algorithms that try to approximate both components of the eigenvectors simultaneously. The efficiency of the new algorithms is demonstrated by numerical examples.« less

The chronic infusion of nicotine into the developing chick embryo does not alter the density of (-)-[3H]nicotine-binding sites or vestibular function

NASA Technical Reports Server (NTRS)

Roll, R. L.; Jones, T. A.; Benowitz, N. L.; Morley, B. J.

1993-01-01

(-)-Nicotine (1.2 mg/day) or saline was infused into chick embryos (Gallus domesticus) for 10 days beginning 12 h beyond the eight day of incubation (E8 + 12 h). Twelve h beyond the eighteenth day of incubation (E18 + 12 h), the eggs were opened to access the embryos and subcutaneous skull electrodes placed. Short latency vestibular response thresholds and input/output functions were determined to assess neurophysiological consequences of chronic nicotine administration. Samples of serum and extraembryonic (amniotic and albumen) fluid were analyzed by gas chromatography-mass spectrometry to determine the levels of nicotine and its major metabolite, cotinine. The brains were removed and divided into diencephalon and mesencephalon and the density of (-)-[3H]nicotine binding sites in each brain area was measured. Nicotine and cotinine were found in the serum and extraembryonic fluid, but nicotinic receptors were not up-regulated in the brains of animals infused with nicotine in comparison to controls. Vestibular response thresholds also did not differ between nicotine-treated and control animals.

A density functional theory study of the correlation between analyte basicity, ZnPc adsorption strength, and sensor response.

PubMed

Tran, N L; Bohrer, F I; Trogler, W C; Kummel, A C

2009-05-28

Density functional theory (DFT) simulations were used to determine the binding strength of 12 electron-donating analytes to the zinc metal center of a zinc phthalocyanine molecule (ZnPc monomer). The analyte binding strengths were compared to the analytes' enthalpies of complex formation with boron trifluoride (BF(3)), which is a direct measure of their electron donating ability or Lewis basicity. With the exception of the most basic analyte investigated, the ZnPc binding energies were found to correlate linearly with analyte basicities. Based on natural population analysis calculations, analyte complexation to the Zn metal of the ZnPc monomer resulted in limited charge transfer from the analyte to the ZnPc molecule, which increased with analyte-ZnPc binding energy. The experimental analyte sensitivities from chemiresistor ZnPc sensor data were proportional to an exponential of the binding energies from DFT calculations consistent with sensitivity being proportional to analyte coverage and binding strength. The good correlation observed suggests DFT is a reliable method for the prediction of chemiresistor metallophthalocyanine binding strengths and response sensitivities.

Response of the Shockley surface state on Cu(111) to an external electrical field: A density-functional theory study

NASA Astrophysics Data System (ADS)

Berland, Kristian; Hyldgaard, Per; Einstein, T. L.

2011-03-01

We study the response of the Cu(111) Shockley surface state to an external electrical field E by combining a density-functional theory calculation for a finite slab geometry with an analysis of the Kohn-Sham wavefunctions to obtain a well-converged characterization. We find that the surface state displays isotropic dispersion, quadratic until the Fermi wave vector but with a significant quartic contribution beyond. We find that the shift in band minimum and effective mass depend linearly on E. Most change in electrostatic potential profile, and charge transfer occurs outside the outermost copper atoms, and most of the screening is due to bulk electrons. Our analysis is facilitated by a method used to decouple the Kohn-Sham states due to the finite slab geometry, using a rotation in Hilbert space. We discuss applications to tuning the Fermi wavelength and so the many patterns attributed to metallic surface states. Supported by (KB and PH) Swedish Vetenskapsrådet VR 621-2008-4346 and (TLE) NSF CHE 07-50334 & UMD MRSEC DMR 05-20471.

Polarizable embedding with a multiconfiguration short-range density functional theory linear response method

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

Hedegård, Erik Donovan, E-mail: erik.hedegard@phys.chem.ethz.ch; Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense; Olsen, Jógvan Magnus Haugaard

2015-03-21

We present here the coupling of a polarizable embedding (PE) model to the recently developed multiconfiguration short-range density functional theory method (MC-srDFT), which can treat multiconfigurational systems with a simultaneous account for dynamical and static correlation effects. PE-MC-srDFT is designed to combine efficient treatment of complicated electronic structures with inclusion of effects from the surrounding environment. The environmental effects encompass classical electrostatic interactions as well as polarization of both the quantum region and the environment. Using response theory, molecular properties such as excitation energies and oscillator strengths can be obtained. The PE-MC-srDFT method and the additional terms required for linearmore » response have been implemented in a development version of DALTON. To benchmark the PE-MC-srDFT approach against the literature data, we have investigated the low-lying electronic excitations of acetone and uracil, both immersed in water solution. The PE-MC-srDFT results are consistent and accurate, both in terms of the calculated solvent shift and, unlike regular PE-MCSCF, also with respect to the individual absolute excitation energies. To demonstrate the capabilities of PE-MC-srDFT, we also investigated the retinylidene Schiff base chromophore embedded in the channelrhodopsin protein. While using a much more compact reference wave function in terms of active space, our PE-MC-srDFT approach yields excitation energies comparable in quality to CASSCF/CASPT2 benchmarks.« less

Understanding Short-Term Nonmigrating Tidal Variability in the Ionospheric Dynamo Region from SABER Using Information Theory and Bayesian Statistics

NASA Astrophysics Data System (ADS)

Kumari, K.; Oberheide, J.

2017-12-01

Nonmigrating tidal diagnostics of SABER temperature observations in the ionospheric dynamo region reveal a large amount of variability on time-scales of a few days to weeks. In this paper, we discuss the physical reasons for the observed short-term tidal variability using a novel approach based on Information theory and Bayesian statistics. We diagnose short-term tidal variability as a function of season, QBO, ENSO, and solar cycle and other drivers using time dependent probability density functions, Shannon entropy and Kullback-Leibler divergence. The statistical significance of the approach and its predictive capability is exemplified using SABER tidal diagnostics with emphasis on the responses to the QBO and solar cycle. Implications for F-region plasma density will be discussed.

Correlated hydrogen bonding fluctuations and vibrational cross peaks in N-methyl acetamide: simulation based on a complete electrostatic density functional theory map.

PubMed

Hayashi, Tomoyuki; Mukamel, Shaul

2006-11-21

The coherent nonlinear response of the entire amide line shapes of N-methyl acetamide to three infrared pulses is simulated using an electrostatic density functional theory map. Positive and negative cross peaks contain signatures of correlations between the fundamentals and the combination state. The amide I-A and I-III cross-peak line shapes indicate positive correlation and anticorrelation of frequency fluctuations, respectively. These can be ascribed to correlated hydrogen bonding at C[double bond]O and N-H sites. The amide I frequency is negatively correlated with the hydrogen bond on carbonyl C[double bond]O, whereas the amide A and III are negatively and positively correlated, respectively, with the hydrogen bond on amide N-H.

Maintaining ecosystem resilience: functional responses of tree cavity nesters to logging in temperate forests of the Americas.

PubMed

Ibarra, José Tomás; Martin, Michaela; Cockle, Kristina L; Martin, Kathy

2017-06-30

Logging often reduces taxonomic diversity in forest communities, but little is known about how this biodiversity loss affects the resilience of ecosystem functions. We examined how partial logging and clearcutting of temperate forests influenced functional diversity of birds that nest in tree cavities. We used point-counts in a before-after-control-impact design to examine the effects of logging on the value, range, and density of functional traits in bird communities in Canada (21 species) and Chile (16 species). Clearcutting, but not partial logging, reduced diversity in both systems. The effect was much more pronounced in Chile, where logging operations removed critical nesting resources (large decaying trees), than in Canada, where decaying aspen Populus tremuloides were retained on site. In Chile, logging was accompanied by declines in species richness, functional richness (amount of functional niche occupied by species), community-weighted body mass (average mass, weighted by species densities), and functional divergence (degree of maximization of divergence in occupied functional niche). In Canada, clearcutting did not affect species richness but nevertheless reduced functional richness and community-weighted body mass. Although some cavity-nesting birds can persist under intensive logging operations, their ecosystem functions may be severely compromised unless future nest trees can be retained on logged sites.

Probabilistic Aeroelastic Analysis Developed for Turbomachinery Components

NASA Technical Reports Server (NTRS)

Reddy, T. S. R.; Mital, Subodh K.; Stefko, George L.; Pai, Shantaram S.

2003-01-01

Aeroelastic analyses for advanced turbomachines are being developed for use at the NASA Glenn Research Center and industry. However, these analyses at present are used for turbomachinery design with uncertainties accounted for by using safety factors. This approach may lead to overly conservative designs, thereby reducing the potential of designing higher efficiency engines. An integration of the deterministic aeroelastic analysis methods with probabilistic analysis methods offers the potential to design efficient engines with fewer aeroelastic problems and to make a quantum leap toward designing safe reliable engines. In this research, probabilistic analysis is integrated with aeroelastic analysis: (1) to determine the parameters that most affect the aeroelastic characteristics (forced response and stability) of a turbomachine component such as a fan, compressor, or turbine and (2) to give the acceptable standard deviation on the design parameters for an aeroelastically stable system. The approach taken is to combine the aeroelastic analysis of the MISER (MIStuned Engine Response) code with the FPI (fast probability integration) code. The role of MISER is to provide the functional relationships that tie the structural and aerodynamic parameters (the primitive variables) to the forced response amplitudes and stability eigenvalues (the response properties). The role of FPI is to perform probabilistic analyses by utilizing the response properties generated by MISER. The results are a probability density function for the response properties. The probabilistic sensitivities of the response variables to uncertainty in primitive variables are obtained as a byproduct of the FPI technique. The combined analysis of aeroelastic and probabilistic analysis is applied to a 12-bladed cascade vibrating in bending and torsion. Out of the total 11 design parameters, 6 are considered as having probabilistic variation. The six parameters are space-to-chord ratio (SBYC), stagger angle (GAMA), elastic axis (ELAXS), Mach number (MACH), mass ratio (MASSR), and frequency ratio (WHWB). The cascade is considered to be in subsonic flow with Mach 0.7. The results of the probabilistic aeroelastic analysis are the probability density function of predicted aerodynamic damping and frequency for flutter and the response amplitudes for forced response.

Characterizing the performance of an affordable, multichannel conductivity probe for density measurements in stratified flows

NASA Astrophysics Data System (ADS)

Subramanian, Balaji; Carminati, Marco; Luzzatto-Fegiz, Paolo

2017-11-01

In stratified flows, conductivity (combined with temperature) is often used to measure density. The conductivity probes typically used can resolve very fine spatial scales, but on the downside they are fragile, expensive, sensitive to environmental noise and have only single channel capability. Recently a low-cost, robust, arduino-based probe called Conduino was developed, which can be valuable in a wide range of applications where resolving extremely small spatial scales is not needed. This probe uses micro-USB connectors as actual conductivity sensors with a custom designed electronic board for simultaneous acquisition from multiple probes, with conductivity resolution comparable to commercially available PME conductivity probe. A detailed assessment of performance of this Conduino probe is described here. To establish time response and sensitivity as a function of electrode geometry, we build a variety of shapes for different kinds of applications, with tip spacing ranging from 0.5-2.5 mm, and with electrode length ranging from 2.3-6 mm. We set up a two-layer density profile and traverse it rapidly, yielding a time response comparable to PME. The Conduino's multi-channel capability is used to operate probe arrays, which helps to construct density fields in stratified flows.

Predicting invasive species impacts: a community module functional response approach reveals context dependencies.

PubMed

Paterson, Rachel A; Dick, Jaimie T A; Pritchard, Daniel W; Ennis, Marilyn; Hatcher, Melanie J; Dunn, Alison M

2015-03-01

Predatory functional responses play integral roles in predator-prey dynamics, and their assessment promises greater understanding and prediction of the predatory impacts of invasive species. Other interspecific interactions, however, such as parasitism and higher-order predation, have the potential to modify predator-prey interactions and thus the predictive capability of the comparative functional response approach. We used a four-species community module (higher-order predator; focal native or invasive predators; parasites of focal predators; native prey) to compare the predatory functional responses of native Gammarus duebeni celticus and invasive Gammarus pulex amphipods towards three invertebrate prey species (Asellus aquaticus, Simulium spp., Baetis rhodani), thus, quantifying the context dependencies of parasitism and a higher-order fish predator on these functional responses. Our functional response experiments demonstrated that the invasive amphipod had a higher predatory impact (lower handling time) on two of three prey species, which reflects patterns of impact observed in the field. The community module also revealed that parasitism had context-dependent influences, for one prey species, with the potential to further reduce the predatory impact of the invasive amphipod or increase the predatory impact of the native amphipod in the presence of a higher-order fish predator. Partial consumption of prey was similar for both predators and occurred increasingly in the order A. aquaticus, Simulium spp. and B. rhodani. This was associated with increasing prey densities, but showed no context dependencies with parasitism or higher-order fish predator. This study supports the applicability of comparative functional responses as a tool to predict and assess invasive species impacts incorporating multiple context dependencies. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

X-ray detection with zinc-blende (cubic) GaN Schottky diodes

NASA Astrophysics Data System (ADS)

Gohil, T.; Whale, J.; Lioliou, G.; Novikov, S. V.; Foxon, C. T.; Kent, A. J.; Barnett, A. M.

2016-07-01

The room temperature X-ray responses as functions of time of two n type cubic GaN Schottky diodes (200 μm and 400 μm diameters) are reported. The current densities as functions of time for both diodes showed fast turn-on transients and increases in current density when illuminated with X-ray photons of energy up to 35 keV. The diodes were also electrically characterized: capacitance, implied depletion width and dark current measurements as functions of applied bias at room temperature are presented. At -5 V reverse bias, the capacitances of the diodes were measured to be (84.05 ± 0.01) pF and (121.67 ± 0.02) pF, respectively. At -5 V reverse bias, the dark current densities of the diodes were measured to be (347.2 ± 0.4) mA cm-2 and (189.0 ± 0.2) mA cm-2, respectively. The Schottky barrier heights of the devices (0.52 ± 0.07) eV and (0.63 ± 0.09) eV, respectively, were extracted from the forward dark current characteristics.

Implementation of the zooplankton functional response in plankton models: State of the art, recent challenges and future directions

NASA Astrophysics Data System (ADS)

Morozov, Andrew; Poggiale, Jean-Christophe; Cordoleani, Flora

2012-09-01

The conventional way of describing grazing in plankton models is based on a zooplankton functional response framework, according to which the consumption rate is computed as the product of a certain function of food (the functional response) and the density/biomass of herbivorous zooplankton. A large amount of literature on experimental feeding reports the existence of a zooplankton functional response in microcosms and small mesocosms, which goes a long way towards explaining the popularity of this framework both in mean-field (e.g. NPZD models) and spatially resolved models. On the other hand, the complex foraging behaviour of zooplankton (feeding cycles) as well as spatial heterogeneity of food and grazer distributions (plankton patchiness) across time and space scales raise questions as to the existence of a functional response of herbivores in vivo. In the current review, we discuss limitations of the ‘classical’ zooplankton functional response and consider possible ways to amend this framework to cope with the complexity of real planktonic ecosystems. Our general conclusion is that although the functional response of herbivores often does not exist in real ecosystems (especially in the form observed in the laboratory), this framework can be rather useful in modelling - but it does need some amendment which can be made based on various techniques of model reduction. We also show that the shape of the functional response depends on the spatial resolution (‘frame’) of the model. We argue that incorporating foraging behaviour and spatial heterogeneity in plankton models would not necessarily require the use of individual based modelling - an approach which is now becoming dominant in the literature. Finally, we list concrete future directions and challenges and emphasize the importance of a closer collaboration between plankton biologists and modellers in order to make further progress towards better descriptions of zooplankton grazing.

Electrophysiological basis for the ability of olanzapine to improve verbal memory and functional outcome in patients with schizophrenia: a LORETA analysis of P300.

PubMed

Higuchi, Yuko; Sumiyoshi, Tomiki; Kawasaki, Yasuhiro; Matsui, Mie; Arai, Hirofumi; Kurachi, Masayoshi

2008-04-01

Abnormality of P300 waveforms of event-related potentials (ERPs) has been suggested to represent an aspect of the pathophysiology of schizophrenia. Previous work points to the contribution of altered neural function in discrete brain regions in the left hemisphere to psychotic symptoms and cognitive deficits of schizophrenia. In this study, we sought to determine: 1) if patients with schizophrenia elicit a decreased P300 current source density in brain areas, such as the superior temporal gyrus (STG); 2) if decreased P300 generator density in the left STG is recovered by treatment with the most widely-used antipsychotic drug olanzapine; and 3) if the recovery of P300 source density is associated with improvements of cognitive and functional status. P300 in response to an auditory oddball task, as well as verbal learning memory, psychopathology, and quality of life were evaluated in 16 right-handed patients with schizophrenia before and after treatment with olanzapine for 6 months. ERP data were also obtained from 16 right-handed age and gender-matched normal volunteers. Low resolution electromagnetic tomography (LORETA) analysis was used to obtain current density images of P300. Patients with schizophrenia showed significantly smaller LORETA values in several brain regions in the left side, particularly STG, middle frontal gyrus, and precentral gyrus, compared with control subjects. Six-month treatment with olanzapine significantly increased P300 source density only in the left STG. Positive symptoms, negative symptoms, verbal learning memory, and quality of life were also improved during treatment. Significant correlations were found between the increase in LORETA values of left STG vs. improvements of negative symptoms, as measured by Scale for the Assessment of the Negative Symptoms, and verbal learning memory, as measured by the Japanese Verbal Learning Test. Improvement of quality of life, as evaluated by the Quality of Life Scale, were significantly associated with an increase in LORETA values of middle frontal gyrus, and tended to correlate with that of precentral gyrus. The results of this study suggest that changes in cortical activity, as measured by ERPs, are responsible for the ability of some antipsychotic drugs to improve cognition and functional outcome in patients with schizophrenia.

Porous, Dexamethasone-loaded polyurethane coatings extend performance window of implantable glucose sensors in vivo.

PubMed

Vallejo-Heligon, Suzana G; Brown, Nga L; Reichert, William M; Klitzman, Bruce

2016-01-01

Continuous glucose sensors offer the promise of tight glycemic control for insulin dependent diabetics; however, utilization of such systems has been hindered by issues of tissue compatibility. Here we report on the in vivo performance of implanted glucose sensors coated with Dexamethasone-loaded (Dex-loaded) porous coatings employed to mediate the tissue-sensor interface. Two animal studies were conducted to (1) characterize the tissue modifying effects of the porous Dex-loaded coatings deployed on sensor surrogate implants and (2) investigate the effects of the same coatings on the in vivo performance of Medtronic MiniMed SOF-SENSOR™ glucose sensors. The tissue response to implants was evaluated by quantifying macrophage infiltration, blood vessel formation, and collagen density around implants. Sensor function was assessed by measuring changes in sensor sensitivity and time lag, calculating the Mean Absolute Relative Difference (MARD) for each sensor treatment, and performing functional glucose challenge test at relevant time points. Implants treated with porous Dex-loaded coatings diminished inflammation and enhanced vascularization of the tissue surrounding the implants. Functional sensors with Dex-loaded porous coatings showed enhanced sensor sensitivity over a 21-day period when compared to controls. Enhanced sensor sensitivity was accompanied with an increase in sensor signal lag and MARD score. These results indicate that Dex-loaded porous coatings were able to elicit an attenuated tissue response, and that such tissue microenvironment could be conducive towards extending the performance window of glucose sensors in vivo. In the present article, a coating to extend the functionality of implantable glucose sensors in vivo was developed. Our study showed that the delivery of an anti-inflammatory agent with the presentation of micro-sized topographical cues from coatings may lead to improved long-term glucose sensor function in vivo. We believe that improved function of sensors treated with the novel coatings was a result of the observed decreases in inflammatory cell density and increases in vessel density of the tissue adjacent to the devices. Furthermore, extending the in vivo functionality of implantable glucose sensors may lead to greater adoption of these devices by diabetic patients. Copyright © 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

A frequency domain global parameter estimation method for multiple reference frequency response measurements

NASA Astrophysics Data System (ADS)

Shih, C. Y.; Tsuei, Y. G.; Allemang, R. J.; Brown, D. L.

1988-10-01

A method of using the matrix Auto-Regressive Moving Average (ARMA) model in the Laplace domain for multiple-reference global parameter identification is presented. This method is particularly applicable to the area of modal analysis where high modal density exists. The method is also applicable when multiple reference frequency response functions are used to characterise linear systems. In order to facilitate the mathematical solution, the Forsythe orthogonal polynomial is used to reduce the ill-conditioning of the formulated equations and to decouple the normal matrix into two reduced matrix blocks. A Complex Mode Indicator Function (CMIF) is introduced, which can be used to determine the proper order of the rational polynomials.

Cholinergic depletion in nucleus accumbens impairs mesocortical dopamine activation and cognitive function in rats.

PubMed

Laplante, François; Zhang, Zi-Wei; Huppé-Gourgues, Frédéric; Dufresne, Marc M; Vaucher, Elvire; Sullivan, Ron M

2012-11-01

In rats, selective depletion of the cholinergic interneurons in the ventral striatum (nucleus accumbens or N.Acc.) results in heightened behavioural sensitivity to amphetamine and impaired sensorimotor gating processes, suggesting a hyper-responsiveness to dopamine (DA) activity in the N.Acc. We hypothesized that local cholinergic depletion may also trigger distal functional alterations, particularly in prefrontal cortex (PFC). Adult male Sprague-Dawley rats were injected bilaterally in the N.Acc. with an immunotoxin targeting choline acetyltransferase. Two weeks later, cognitive function was assessed using the delayed alternation paradigm in the T-maze. The rats were then implanted with voltammetric recording electrodes in the ventromedial PFC to measure in vivo extracellular DA release in response to mild tail pinch stress. The PFC was also examined for density of tyrosine hydroxylase (TH)-labelled varicosities. In another cohort of control and lesioned rats, we measured post mortem tissue content of DA. Depletion of cholinergic neurons (restricted to N.Acc.) significantly impaired delayed alternation performance across delay intervals. While (basal) post mortem indices of PFC DA function were unaffected by N.Acc. lesions, in vivo mesocortical DA activation was markedly reduced; this deficit correlated significantly with cognitive impairments. TH-labelled varicosities however, were unaffected in cortical layer V relative to controls. These data suggest that selective depletion of cholinergic interneurons in N.Acc. triggers widespread functional impairments in mesocorticolimbic DA function and cognition. The possible relevance of these findings is also discussed in relation to schizophrenia, where reduced density of cholinergic neurons in ventral striatum has been reported. Copyright © 2012 Elsevier Ltd. All rights reserved.

Multiconfiguration Pair-Density Functional Theory.

PubMed

Li Manni, Giovanni; Carlson, Rebecca K; Luo, Sijie; Ma, Dongxia; Olsen, Jeppe; Truhlar, Donald G; Gagliardi, Laura

2014-09-09

We present a new theoretical framework, called Multiconfiguration Pair-Density Functional Theory (MC-PDFT), which combines multiconfigurational wave functions with a generalization of density functional theory (DFT). A multiconfigurational self-consistent-field (MCSCF) wave function with correct spin and space symmetry is used to compute the total electronic density, its gradient, the on-top pair density, and the kinetic and Coulomb contributions to the total electronic energy. We then use a functional of the total density, its gradient, and the on-top pair density to calculate the remaining part of the energy, which we call the on-top-density-functional energy in contrast to the exchange-correlation energy of Kohn-Sham DFT. Because the on-top pair density is an element of the two-particle density matrix, this goes beyond the Hohenberg-Kohn theorem that refers only to the one-particle density. To illustrate the theory, we obtain first approximations to the required new type of density functionals by translating conventional density functionals of the spin densities using a simple prescription, and we perform post-SCF density functional calculations using the total density, density gradient, and on-top pair density from the MCSCF calculations. Double counting of dynamic correlation or exchange does not occur because the MCSCF energy is not used. The theory is illustrated by applications to the bond energies and potential energy curves of H2, N2, F2, CaO, Cr2, and NiCl and the electronic excitation energies of Be, C, N, N(+), O, O(+), Sc(+), Mn, Co, Mo, Ru, N2, HCHO, C4H6, c-C5H6, and pyrazine. The method presented has a computational cost and scaling similar to MCSCF, but a quantitative accuracy, even with the present first approximations to the new types of density functionals, that is comparable to much more expensive multireference perturbation theory methods.

The effect of subambient to elevated atmospheric CO₂ concentration on vascular function in Helianthus annuus: implications for plant response to climate change.

PubMed

Rico, Christopher; Pittermann, Jarmila; Polley, H Wayne; Aspinwall, Michael J; Fay, Phillip A

2013-09-01

Plant gas exchange is regulated by stomata, which coordinate leaf-level water loss with xylem transport. Stomatal opening responds to internal concentrations of CO₂ in the leaf, but changing CO₂ can also lead to changes in stomatal density that influence transpiration. Given that stomatal conductance increases under subambient concentrations of CO₂ and, conversely, that plants lose less water at elevated concentrations, can downstream effects of atmospheric CO₂ be observed in xylem tissue? We approached this problem by evaluating leaf stomatal density, xylem transport, xylem anatomy and resistance to cavitation in Helianthus annuus plants grown under three CO₂ regimes ranging from pre-industrial to elevated concentrations. Xylem transport, conduit size and stomatal density all increased at 290 ppm relative to ambient and elevated CO₂ concentrations. The shoots of the 290-ppm-grown plants were most vulnerable to cavitation, whereas xylem cavitation resistance did not differ in 390- and 480-ppm-grown plants. Our data indicate that, even as an indirect driver of water loss, CO₂ can affect xylem structure and water transport by coupling stomatal and xylem hydraulic functions during plant development. This plastic response has implications for plant water use under variable concentrations of CO₂, as well as the evolution of efficient xylem transport. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

Empirical Orthogonal Function (EOF) Analysis of Storm-Time GPS Total Electron Content Variations

NASA Astrophysics Data System (ADS)

Thomas, E. G.; Coster, A. J.; Zhang, S.; McGranaghan, R. M.; Shepherd, S. G.; Baker, J. B.; Ruohoniemi, J. M.

2016-12-01

Large perturbations in ionospheric density are known to occur during geomagnetic storms triggered by dynamic structures in the solar wind. These ionospheric storm effects have long attracted interest due to their impact on the propagation characteristics of radio wave communications. Over the last two decades, maps of vertically-integrated total electron content (TEC) based on data collected by worldwide networks of Global Positioning System (GPS) receivers have dramatically improved our ability to monitor the spatiotemporal dynamics of prominent storm-time features such as polar cap patches and storm enhanced density (SED) plumes. In this study, we use an empirical orthogonal function (EOF) decomposition technique to identify the primary modes of spatial and temporal variability in the storm-time GPS TEC response at midlatitudes over North America during more than 100 moderate geomagnetic storms from 2001-2013. We next examine the resulting time-varying principal components and their correlation with various geophysical indices and parameters in order to derive an analytical representation. Finally, we use a truncated reconstruction of the EOF basis functions and parameterization of the principal components to produce an empirical representation of the geomagnetic storm-time response of GPS TEC for all magnetic local times local times and seasons at midlatitudes in the North American sector.

Brevicoryne brassicae aphids interfere with transcriptome responses of Arabidopsis thaliana to feeding by Plutella xylostella caterpillars in a density-dependent manner.

PubMed

Kroes, Anneke; Broekgaarden, Colette; Castellanos Uribe, Marcos; May, Sean; van Loon, Joop J A; Dicke, Marcel

2017-01-01

Plants are commonly attacked by multiple herbivorous species. Yet, little is known about transcriptional patterns underlying plant responses to multiple insect attackers feeding simultaneously. Here, we assessed transcriptomic responses of Arabidopsis thaliana plants to simultaneous feeding by Plutella xylostella caterpillars and Brevicoryne brassicae aphids in comparison to plants infested by P. xylostella caterpillars alone, using microarray analysis. We particularly investigated how aphid feeding interferes with the transcriptomic response to P. xylostella caterpillars and whether this interference is dependent on aphid density and time since aphid attack. Various JA-responsive genes were up-regulated in response to feeding by P. xylostella caterpillars. The additional presence of aphids, both at low and high densities, clearly affected the transcriptional plant response to caterpillars. Interestingly, some important modulators of plant defense signalling, including WRKY transcription factor genes and ABA-dependent genes, were differentially induced in response to simultaneous aphid feeding at low or high density compared with responses to P. xylostella caterpillars feeding alone. Furthermore, aphids affected the P. xylostella-induced transcriptomic response in a density-dependent manner, which caused an acceleration in plant response against dual insect attack at high aphid density compared to dual insect attack at low aphid density. In conclusion, our study provides evidence that aphids influence the caterpillar-induced transcriptional response of A. thaliana in a density-dependent manner. It highlights the importance of addressing insect density to understand how plant responses to single attackers interfere with responses to other attackers and thus underlines the importance of the dynamics of transcriptional plant responses to multiple herbivory.

Highly efficient implementation of pseudospectral time-dependent density-functional theory for the calculation of excitation energies of large molecules.

PubMed

Cao, Yixiang; Hughes, Thomas; Giesen, Dave; Halls, Mathew D; Goldberg, Alexander; Vadicherla, Tati Reddy; Sastry, Madhavi; Patel, Bhargav; Sherman, Woody; Weisman, Andrew L; Friesner, Richard A

2016-06-15

We have developed and implemented pseudospectral time-dependent density-functional theory (TDDFT) in the quantum mechanics package Jaguar to calculate restricted singlet and restricted triplet, as well as unrestricted excitation energies with either full linear response (FLR) or the Tamm-Dancoff approximation (TDA) with the pseudospectral length scales, pseudospectral atomic corrections, and pseudospectral multigrid strategy included in the implementations to improve the chemical accuracy and to speed the pseudospectral calculations. The calculations based on pseudospectral time-dependent density-functional theory with full linear response (PS-FLR-TDDFT) and within the Tamm-Dancoff approximation (PS-TDA-TDDFT) for G2 set molecules using B3LYP/6-31G*(*) show mean and maximum absolute deviations of 0.0015 eV and 0.0081 eV, 0.0007 eV and 0.0064 eV, 0.0004 eV and 0.0022 eV for restricted singlet excitation energies, restricted triplet excitation energies, and unrestricted excitation energies, respectively; compared with the results calculated from the conventional spectral method. The application of PS-FLR-TDDFT to OLED molecules and organic dyes, as well as the comparisons for results calculated from PS-FLR-TDDFT and best estimations demonstrate that the accuracy of both PS-FLR-TDDFT and PS-TDA-TDDFT. Calculations for a set of medium-sized molecules, including Cn fullerenes and nanotubes, using the B3LYP functional and 6-31G(**) basis set show PS-TDA-TDDFT provides 19- to 34-fold speedups for Cn fullerenes with 450-1470 basis functions, 11- to 32-fold speedups for nanotubes with 660-3180 basis functions, and 9- to 16-fold speedups for organic molecules with 540-1340 basis functions compared to fully analytic calculations without sacrificing chemical accuracy. The calculations on a set of larger molecules, including the antibiotic drug Ramoplanin, the 46-residue crambin protein, fullerenes up to C540 and nanotubes up to 14×(6,6), using the B3LYP functional and 6-31G(**) basis set with up to 8100 basis functions show that PS-FLR-TDDFT CPU time scales as N(2.05) with the number of basis functions. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

The influence of low frequency sound on the changes of EEG signal morphology

NASA Astrophysics Data System (ADS)

Damijan, Z.; Wiciak, J.

2006-11-01

The effects of low frequency sound on the changes of morphology of the spectral power density function of EEG signals were studied as a part of the research program f = 40 Hz, Lp = 110 dB HP. The research program involved 33 experiments. A quantitative analysis was conducted of the driving response effect for the fundamental frequency and its harmonics to find the frequency of the driving response effect occurrence depending on the sex of participants.

Optimised effective potential for ground states, excited states, and time-dependent phenomena

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

Gross, E.K.U.

1996-12-31

(1) The optimized effective potential method is a variant of the traditional Kohn-Sham scheme. In this variant, the exchange-correlation energy E{sub xc} is an explicit functional of single-particle orbitals. The exchange-correlation potential, given as usual by the functional derivative v{sub xc} = {delta}E{sub xc}/{delta}{rho}, then satisfies as integral equation involving the single-particle orbitals. This integral equation in solved semi-analytically using a scheme recently proposed by Krieger, Li and Iafrate. If the exact (Fock) exchange-energy functional is employed together with the Colle-Salvetti orbital functional for the correlation energy, the mean absolute deviation of the resulting ground-state energies from the exact nonrelativisticmore » values is CT mH for the first-row atoms, as compared to 4.5 mH in a state-of-the-art CI calculation. The proposed scheme is thus significantly more accurate than the conventional Kohn-Sham method while the numerical effort involved is about the same as for an ordinary Hanree-Fock calculation. (2) A time-dependent generalization of the optimized-potential method is presented and applied to the linear-response regime. Since time-dependent density functional theory leads to a formally exact representation of the frequency-dependent linear density response and since the latter, as a function of frequency, has poles at the excitation energies of the fully interacting system, the formalism is suitable for the calculation of excitation energies. A simple additive correction to the Kohn-Sham single-particle excitation energies will be deduced and first results for atomic and molecular singlet and triplet excitation energies will be presented. (3) Beyond the regime of linear response, the time-dependent optimized-potential method is employed to describe atoms in strong emtosecond laser pulses. Ionization yields and harmonic spectra will be presented and compared with experimental data.« less

Reformulation of Density Functional Theory for N-Representable Densities and the Resolution of the v-Representability Problem

DOE PAGES

Gonis, A.; Zhang, X. G.; Stocks, G. M.; ...

2015-10-23

Density functional theory for the case of general, N-representable densities is reformulated in terms of density functional derivatives of expectation values of operators evaluated with wave functions leading to a density, making no reference to the concept of potential. The developments provide a complete solution of the v-representability problem by establishing a mathematical procedure that determines whether a density is v-representable and in the case of an affirmative answer determines the potential (within an additive constant) as a derivative with respect to the density of a constrained search functional. It also establishes the existence of an energy functional of themore » density that, for v-representable densities, assumes its minimum value at the density describing the ground state of an interacting many-particle system. The theorems of Hohenberg and Kohn emerge as special cases of the formalism.« less

Thermodynamic responses of electronic systems.

PubMed

Franco-Pérez, Marco; Ayers, Paul W; Gázquez, José L; Vela, Alberto

2017-09-07

We present how the framework of the temperature-dependent chemical reactivity theory can describe the panorama of different types of interactions between an electronic system and external reagents. The key reactivity indicators are responses of an appropriate state function (like the energy or grand potential) to the variables that determine the state of the system (like the number of electrons/chemical potential, external potential, and temperature). We also consider the response of the average electron density to appropriate perturbations. We present computable formulas for these reactivity indicators and discuss their chemical utility for describing electronic, electrostatic, and thermal changes associated with chemical processes.

Thermodynamic responses of electronic systems

NASA Astrophysics Data System (ADS)

Franco-Pérez, Marco; Ayers, Paul W.; Gázquez, José L.; Vela, Alberto

2017-09-01

We present how the framework of the temperature-dependent chemical reactivity theory can describe the panorama of different types of interactions between an electronic system and external reagents. The key reactivity indicators are responses of an appropriate state function (like the energy or grand potential) to the variables that determine the state of the system (like the number of electrons/chemical potential, external potential, and temperature). We also consider the response of the average electron density to appropriate perturbations. We present computable formulas for these reactivity indicators and discuss their chemical utility for describing electronic, electrostatic, and thermal changes associated with chemical processes.

Dielectric response in Bloch’s hydrodynamic model of an electron-ion plasma

NASA Astrophysics Data System (ADS)

Ishikawa, K.; Felderhof, B. U.

The linear response of an electron-ion plasma to an applied oscillating electric field is studied within the framework of Bloch’s classical hydrodynamic model. The ions are assumed to be fixed in space and distributed according to a known probability distribution. The linearized equations of motion for electron density and flow velocity are studied with the aid of a multiple scattering analysis and cluster expansion. This allows systematic reduction of the many-ion problem to a composition of few-ion problems, and shows how the longitudinal dielectric response function can in principle be calculated.

Consistent individual differences and population plasticity in network-derived sociality: An experimental manipulation of density in a gregarious ungulate

PubMed Central

O’Brien, Paul P.; Vander Wal, Eric

2018-01-01

In many taxa, individual social traits appear to be consistent across time and context, thus meeting the criteria for animal personality. How these differences are maintained in response to changes in population density is unknown, particularly in large mammals, such as ungulates. Using a behavioral reaction norm (BRN) framework, we examined how among- and within-individual variation in social connectedness, measured using social network analyses, change as a function of population density. We studied a captive herd of elk (Cervus canadensis) separated into a group of male elk and a group of female elk. Males and females were exposed to three different density treatments and we recorded social associations between individuals with proximity-detecting radio-collars fitted to elk. We constructed social networks using dyadic association data and calculated three social network metrics reflective of social connectedness: eigenvector centrality, graph strength, and degree. Elk exhibited consistent individual differences in social connectedness across densities; however, they showed little individual variation in their response to changes in density, i.e., individuals oftentimes responded plastically, but in the same manner to changes in density. Female elk had highest connectedness at an intermediate density. In contrast, male elk increased connectedness with increasing density. Whereas this may suggest that the benefits of social connectedness outweigh the costs of increased competition at higher density for males, females appear to exhibit a threshold in social benefits (e.g. predator detection and forage information). Our study illustrates the importance of viewing social connectedness as a density-dependent trait, particularly in the context of plasticity. Moreover, we highlight the need to revisit our understanding of density dependence as a population-level phenomenon by accounting for consistent individual differences not only in social connectedness, but likely in other ecological processes (e.g., predator-prey dynamics, mate choice, disease transfer). PMID:29494640

Track structure simulations at relativistic energies: an update on cross section calculations

NASA Astrophysics Data System (ADS)

Dingfelder, Michael

Charged particle track structure simulations follow the primary, as well as all (produced) sec-ondary particles in an event-by-event matter, from starting or ejection energies down to total stopping. They provide detailed information on the spacial distributions of energy depositions, interaction types, and radical species produced. These quantities provide a starting point to describe the interaction of the radiation with matter of biological interest and to explore and estimate the effects of radiation quality on various biological responses of these systems. Of special interest is liquid water which serves as surrogate for soft tissue. Ionization and excitation cross sections for bare charged particles can be calculated within the framework of the (relativistic) plane-wave Born approximation or the (relativistic) Bethe approximation. Both theories rely on a realistic model of the dielectric response function of the material under consideration and need to address relativistic medium polarization effects like the Fermi-density effect in a consistent way. In this talk we will review and present new and updated aspects of charged particle cross section calculations for relativistic heavy ions with liquid water and other materials of biological interest. This includes an updated model for the dielectric response function of liquid water to better reflect new data from inelastic X-ray scattering (IXS) experiments using synchrotron radiation and a model for the dielectric response function of calcium, which serves as a bone surrogate. We will also discuss the implementation of relativistic effect, especially of the Fermi-density effect into the cross section calculations. This work is supported by the National Aeronautics and Space Administration (NASA), grant no. NNJ04HF39G.

Flexoelectricity from density-functional perturbation theory

NASA Astrophysics Data System (ADS)

Stengel, Massimiliano

2013-11-01

We derive the complete flexoelectric tensor, including electronic and lattice-mediated effects, of an arbitrary insulator in terms of the microscopic linear response of the crystal to atomic displacements. The basic ingredient, which can be readily calculated from first principles in the framework of density-functional perturbation theory, is the quantum-mechanical probability current response to a long-wavelength acoustic phonon. Its second-order Taylor expansion in the wave vector q around the Γ (q=0) point in the Brillouin zone naturally yields the flexoelectric tensor. At order one in q we recover Martin's theory of piezoelectricity [Martin, Phys. Rev. B 5, 1607 (1972)], thus providing an alternative derivation thereof. To put our derivations on firm theoretical grounds, we perform a thorough analysis of the nonanalytic behavior of the dynamical matrix and other response functions in a vicinity of Γ. Based on this analysis, we find that there is an ambiguity in the specification of the “zero macroscopic field” condition in the flexoelectric case; such arbitrariness can be related to an analytic band-structure term, in close analogy to the theory of deformation potentials. As a by-product, we derive a rigorous generalization of the Cochran-Cowley formula [Cochran and Cowley, J. Phys. Chem. Solids 23, 447 (1962)] to higher orders in q. This can be of great utility in building reliable atomistic models of electromechanical phenomena, as well as for improving the accuracy of the calculation of phonon dispersion curves. Finally, we discuss the physical interpretation of the various contributions to the flexoelectric response, either in the static or dynamic regime, and we relate our findings to earlier theoretical works on the subject.

Testing functional trait-based mechanisms underpinning plant responses to grazing and linkages to ecosystem functioning in grasslands

NASA Astrophysics Data System (ADS)

Zheng, S. X.; Li, W. H.; Lan, Z. C.; Ren, H. Y.; Wang, K. B.; Bai, Y. F.

2014-09-01

Abundant evidence has shown that grazing alters plant functional traits, ecological strategies, community structure, and ecosystem functioning of grasslands. Few studies, however, have examined how plant responses to grazing are mediated by resource availability and functional group identity. We test functional trait-based mechanisms underlying the responses of different life forms to grazing and linkages to ecosystem functioning along a soil moisture gradient in the Inner Mongolia grassland. A principal component analysis (PCA) based on 9 traits × 276 species matrix showed that the plant size spectrum (i.e., individual biomass), leaf economics spectrum (leaf N content and leaf density), and light competition spectrum (height and stem-leaf biomass ratio) distinguished plant species responses to grazing. The three life forms exhibited differential strategies as indicated by trait responses to grazing. The annuals and biennials adopted grazing-tolerant strategies associated with high growth rate, reflected by high leaf N content and specific leaf area. The perennial grasses exhibited grazing-tolerant strategies associated with great regrowth capacity and high palatability scores, whereas perennial forbs showed grazing-avoidant strategies with short stature and low palatability scores. In addition, the dominant perennial bunchgrasses exhibited mixed tolerance-resistance strategies to grazing and mixed acquisitive-conservative strategies in resource utilization. Grazing increased the relative abundance of perennial forbs with low palatability in the wet and fertile meadow, but it promoted perennial grasses with high palatability in the dry and infertile typical steppe. Our findings suggest that the effects of grazing on plant functional traits are dependent on both the abiotic (e.g., soil moisture) and biotic (e.g., plant functional group identity and composition) factors. Grazing-induced shifts in functional group composition are largely dependent on resource availability, particularly water availability.

Exchange-correlation energies of atoms from efficient density functionals: influence of the electron density

DOE PAGES

Tao, Jianmin; Ye, Lin -Hui; Duan, Yuhua

2017-11-20

The primary goal of Kohn–Sham density functional theory is to evaluate the exchange-correlation contribution to electronic properties. However, the accuracy of a density functional can be affected by the electron density. Here we apply the nonempirical Tao–Mo (TM) semilocal functional to study the influence of the electron density on the exchange and correlation energies of atoms and ions, and compare the results with the commonly used nonempirical semilocal functionals local spin-density approximation (LSDA), Perdew–Burke–Ernzerhof (PBE), Tao–Perdew–Staroverov–Scuseria (TPSS), and hybrid functional PBE0. We find that the spin-restricted Hartree–Fock density yields the exchange and correlation energies in good agreement with the Optimizedmore » Effective Potential method, particularly for spherical atoms and ions. However, the errors of these semilocal and hybrid functionals become larger for self-consistent densities. We further find that the quality of the electron density have greater effect on the exchange-correlation energies of kinetic energy density-dependent meta-GGA functionals TPSS and TM than on those of the LSDA and GGA, and therefore, should have greater influence on the performance of meta-GGA functionals. Lastly, we show that the influence of the density quality on PBE0 is slightly reduced, compared to that of PBE, due to the exact mixing.« less

Exchange-correlation energies of atoms from efficient density functionals: influence of the electron density

NASA Astrophysics Data System (ADS)

Tao, Jianmin; Ye, Lin-Hui; Duan, Yuhua

2017-12-01

The primary goal of Kohn-Sham density functional theory is to evaluate the exchange-correlation contribution to electronic properties. However, the accuracy of a density functional can be affected by the electron density. Here we apply the nonempirical Tao-Mo (TM) semilocal functional to study the influence of the electron density on the exchange and correlation energies of atoms and ions, and compare the results with the commonly used nonempirical semilocal functionals local spin-density approximation (LSDA), Perdew-Burke-Ernzerhof (PBE), Tao-Perdew-Staroverov-Scuseria (TPSS), and hybrid functional PBE0. We find that the spin-restricted Hartree-Fock density yields the exchange and correlation energies in good agreement with the Optimized Effective Potential method, particularly for spherical atoms and ions. However, the errors of these semilocal and hybrid functionals become larger for self-consistent densities. We further find that the quality of the electron density have greater effect on the exchange-correlation energies of kinetic energy density-dependent meta-GGA functionals TPSS and TM than on those of the LSDA and GGA, and therefore, should have greater influence on the performance of meta-GGA functionals. Finally, we show that the influence of the density quality on PBE0 is slightly reduced, compared to that of PBE, due to the exact mixing.

Exchange-correlation energies of atoms from efficient density functionals: influence of the electron density

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

Tao, Jianmin; Ye, Lin -Hui; Duan, Yuhua

The primary goal of Kohn–Sham density functional theory is to evaluate the exchange-correlation contribution to electronic properties. However, the accuracy of a density functional can be affected by the electron density. Here we apply the nonempirical Tao–Mo (TM) semilocal functional to study the influence of the electron density on the exchange and correlation energies of atoms and ions, and compare the results with the commonly used nonempirical semilocal functionals local spin-density approximation (LSDA), Perdew–Burke–Ernzerhof (PBE), Tao–Perdew–Staroverov–Scuseria (TPSS), and hybrid functional PBE0. We find that the spin-restricted Hartree–Fock density yields the exchange and correlation energies in good agreement with the Optimizedmore » Effective Potential method, particularly for spherical atoms and ions. However, the errors of these semilocal and hybrid functionals become larger for self-consistent densities. We further find that the quality of the electron density have greater effect on the exchange-correlation energies of kinetic energy density-dependent meta-GGA functionals TPSS and TM than on those of the LSDA and GGA, and therefore, should have greater influence on the performance of meta-GGA functionals. Lastly, we show that the influence of the density quality on PBE0 is slightly reduced, compared to that of PBE, due to the exact mixing.« less

A unifying approach to lattice dynamical and electronic properties of solids

NASA Astrophysics Data System (ADS)

Falter, C.

1988-06-01

A unified analysis of lattice dynamical and electronic properties of solids with special emphasis on the interaction between electrons and phonons is presented. The article is roughly divided into two parts reflecting different points of view. The density response of the electrons provides the link between these parts. In the first part, the microscopic theory in terms of the density response in crystals is discussed. Relations are pointed out between the density response approach and the density functional theory. The latter is used for a representation of the exchange-correlation interaction and the microscopic force constants. Relevant methods, as recently proposed by various authors for the calculation of the density response in inhomogeneous solids are discussed. Particular attention is paid to the development of a renormalized response description. Applications of this method to lattice dynamical and electronic properties are presented. In the second part an alternative physical concept, the quasi-ion approach, is outlined. This concept is shown to provide a microscopic basis for electronic charge localization in crystals and proves the importance of the correlation between crystal symmetry and many-body effects. Is is derived that within linear response theory an appropriate decomposition of the valence charge density leads uniquely to a spatially localized density contribution at the individual ion which follows its motion rigidly. The composite consisting of this partial density and the ion core is taken to be an individual entity, denoted as quasi-ion, from which the crystal is built up. In a certain sense this is a generalization of Ziman's concept of neutral pseudo-atoms being approximately valid in simple metals. New insight into the bonding mechanism and charge relaxation processes is shown to follow from this concept. In particular, we discuss the covalent, ionic and metallic bonding mechanisms, using the localized picture provided by the partial densities, on the same basis. The quasi-ion approach is also applied to the calculation of phonon-induced charge density redistributions and to the construction of a simplified formulation of microscopic lattice dynamics. Investigations of the phonon dispersion for different bonding types are given within a rigid quasi-ion model and extensions of this model are outlined. Among other things, these calculations indicate that bonding dynamics of (covalent) molecules and crystals can be described by relative rotations of the quasi-ions under the condition of rotational invariance of the system. Finally, possible applications of the quasi-ion concept to an approximate formulation of anharmonic lattice dynamics and the interaction between electrons and phonons are discussed. A numerical investigation of this interaction is presented and compared with the results from the rigid-ion model. As a consequence of the quasi-ion concept a consistent calculation of the phonon dispersion, the electronic band structure and the electron-phonon interaction becomes possible.

Linear Response Function of Bond-Order

PubMed Central

Suzuki, Nayuta; Mitsuta, Yuki; Okumura, Mitsutaka; Yamanaka, Shusuke

2016-01-01

We present the linear response function of bond-orders (LRF-BO) based on a real space integration scheme for molecular systems. As in the case of the LRF of density, the LRF-BO is defined as the response of the bond order of the molecule for the virtual perturbation. Our calculations show that the LRF-BO enables us not only to detect inductive and resonating effects of conjugating systems, but also to predict pKa values on substitution groups via linear relationships between the Hammett constants and the LRF-BO values for meta- and para-substituted benzoic acids. More importantly, the LRF-BO values for the O-H bonds strongly depend on the sites to which the virtual perturbation is applied, implying that the LRF-BO values include essential information about reaction mechanism of the acid-dissociation of substituted benzoic acids. PMID:27792148

Modeling ultrafast solvated electronic dynamics using time-dependent density functional theory and polarizable continuum model.

PubMed

Liang, Wenkel; Chapman, Craig T; Ding, Feizhi; Li, Xiaosong

2012-03-01

A first-principles solvated electronic dynamics method is introduced. Solvent electronic degrees of freedom are coupled to the time-dependent electronic density of a solute molecule by means of the implicit reaction field method, and the entire electronic system is propagated in time. This real-time time-dependent approach, incorporating the polarizable continuum solvation model, is shown to be very effective in describing the dynamical solvation effect in the charge transfer process and yields a consistent absorption spectrum in comparison to the conventional linear response results in solution. © 2012 American Chemical Society

Flow induced crystallisation of penetrable particles

NASA Astrophysics Data System (ADS)

Scacchi, Alberto; Brader, Joseph M.

2018-03-01

For a system of Brownian particles interacting via a soft exponential potential we investigate the interaction between equilibrium crystallisation and spatially varying shear flow. For thermodynamic state points within the liquid part of the phase diagram, but close to the crystallisation phase boundary, we observe that imposing a Poiseuille flow can induce nonequilibrium crystalline ordering in regions of low shear gradient. The physical mechanism responsible for this phenomenon is shear-induced particle migration, which causes particles to drift preferentially towards the center of the flow channel, thus increasing the local density in the channel center. The method employed is classical dynamical density functional theory.

Flow induced crystallisation of penetrable particles.

PubMed

Scacchi, Alberto; Brader, Joseph M

2018-03-07

For a system of Brownian particles interacting via a soft exponential potential we investigate the interaction between equilibrium crystallisation and spatially varying shear flow. For thermodynamic state points within the liquid part of the phase diagram, but close to the crystallisation phase boundary, we observe that imposing a Poiseuille flow can induce nonequilibrium crystalline ordering in regions of low shear gradient. The physical mechanism responsible for this phenomenon is shear-induced particle migration, which causes particles to drift preferentially towards the center of the flow channel, thus increasing the local density in the channel center. The method employed is classical dynamical density functional theory.

The significance of translation regulation in the stress response

PubMed Central

2013-01-01

Background The stress response in bacteria involves the multistage control of gene expression but is not entirely understood. To identify the translational response of bacteria in stress conditions and assess its contribution to the regulation of gene expression, the translational states of all mRNAs were compared under optimal growth condition and during nutrient (isoleucine) starvation. Results A genome-scale study of the translational response to nutritional limitation was performed in the model bacterium Lactococcus lactis. Two measures were used to assess the translational status of each individual mRNA: the fraction engaged in translation (ribosome occupancy) and ribosome density (number of ribosomes per 100 nucleotides). Under isoleucine starvation, half of the mRNAs considered were translationally down-regulated mainly due to decreased ribosome density. This pattern concerned genes involved in growth-related functions such as translation, transcription, and the metabolism of fatty acids, phospholipids and bases, contributing to the slowdown of growth. Only 4% of the mRNAs were translationally up-regulated, mostly related to prophagic expression in response to stress. The remaining genes exhibited antagonistic regulations of the two markers of translation. Ribosome occupancy increased significantly for all the genes involved in the biosynthesis of isoleucine, although their ribosome density had decreased. The results revealed complex translational regulation of this pathway, essential to cope with isoleucine starvation. To elucidate the regulation of global gene expression more generally, translational regulation was compared to transcriptional regulation under isoleucine starvation and to other post-transcriptional regulations related to mRNA degradation and mRNA dilution by growth. Translational regulation appeared to accentuate the effects of transcriptional changes for down-regulated growth-related functions under isoleucine starvation although mRNA stabilization and lower dilution by growth counterbalanced this effect. Conclusions We show that the contribution of translational regulation to the control of gene expression is significant in the stress response. Post-transcriptional regulation is complex and not systematically co-directional with transcription regulation. Post-transcriptional regulation is important to the understanding of gene expression control. PMID:23985063

In Situ Poling and Imidization of Amorphous Piezoelectric Polyimides

NASA Technical Reports Server (NTRS)

Park, Cheol; Ounaies, Zoubeida; Wise, Kristopher E.; Harrison, Joycelyn S.; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

An amorphous piezoelectric polyimide containing polar functional groups has been developed using a combination of experimental and molecular modeling for potential use in high temperature applications. This amorphous polyimide, (Beta-CN)APB/ODPA, has exhibited good thermal stability and piezoelectric response at temperatures up to 150C. Density functional calculations predicted that a partially cured amic acid (open imide ring) possesses a dipole moment four times larger than the fully imidized closed ring. In situ poling and imidization of the partially cured (Beta-CN)APB/ODPA, was studied in an attempt to maximize the degree of dipolar orientation and the resultant piezoelectric response. A positive corona poling was used to minimize localized arcing during poling and to allow use of higher poling fields without dielectric breakdown. The dielectric relaxation strength, remanent polarization, and piezoelectric response were evaluated as a function of the poling profile. The partially cured, corona poled polymers exhibited higher dielectric relaxation strength (delta varepsilon), remanent polarization (Pr) and piezoelectric strain coefficient (d33) than the fully cured, conventionally poled ones.

An Examination of the Neural Unreliability Thesis of Autism

PubMed Central

Butler, John S.; Molholm, Sophie; Andrade, Gizely N.; Foxe, John J.

2017-01-01

Abstract An emerging neuropathological theory of Autism, referred to here as “the neural unreliability thesis,” proposes greater variability in moment-to-moment cortical representation of environmental events, such that the system shows general instability in its impulse response function. Leading evidence for this thesis derives from functional neuroimaging, a methodology ill-suited for detailed assessment of sensory transmission dynamics occurring at the millisecond scale. Electrophysiological assessments of this thesis, however, are sparse and unconvincing. We conducted detailed examination of visual and somatosensory evoked activity using high-density electrical mapping in individuals with autism (N = 20) and precisely matched neurotypical controls (N = 20), recording large numbers of trials that allowed for exhaustive time-frequency analyses at the single-trial level. Measures of intertrial coherence and event-related spectral perturbation revealed no convincing evidence for an unreliability account of sensory responsivity in autism. Indeed, results point to robust, highly reproducible response functions marked for their exceedingly close correspondence to those in neurotypical controls PMID:27923839

An Examination of the Neural Unreliability Thesis of Autism.

PubMed

Butler, John S; Molholm, Sophie; Andrade, Gizely N; Foxe, John J

2017-01-01

An emerging neuropathological theory of Autism, referred to here as "the neural unreliability thesis," proposes greater variability in moment-to-moment cortical representation of environmental events, such that the system shows general instability in its impulse response function. Leading evidence for this thesis derives from functional neuroimaging, a methodology ill-suited for detailed assessment of sensory transmission dynamics occurring at the millisecond scale. Electrophysiological assessments of this thesis, however, are sparse and unconvincing. We conducted detailed examination of visual and somatosensory evoked activity using high-density electrical mapping in individuals with autism (N = 20) and precisely matched neurotypical controls (N = 20), recording large numbers of trials that allowed for exhaustive time-frequency analyses at the single-trial level. Measures of intertrial coherence and event-related spectral perturbation revealed no convincing evidence for an unreliability account of sensory responsivity in autism. Indeed, results point to robust, highly reproducible response functions marked for their exceedingly close correspondence to those in neurotypical controls. © The Author 2016. Published by Oxford University Press.

Self-Interaction Error in Density Functional Theory: An Appraisal.

PubMed

Bao, Junwei Lucas; Gagliardi, Laura; Truhlar, Donald G

2018-05-03

Self-interaction error (SIE) is considered to be one of the major sources of error in most approximate exchange-correlation functionals for Kohn-Sham density-functional theory (KS-DFT), and it is large with all local exchange-correlation functionals and with some hybrid functionals. In this work, we consider systems conventionally considered to be dominated by SIE. For these systems, we demonstrate that by using multiconfiguration pair-density functional theory (MC-PDFT), the error of a translated local density-functional approximation is significantly reduced (by a factor of 3) when using an MCSCF density and on-top density, as compared to using KS-DFT with the parent functional; the error in MC-PDFT with local on-top functionals is even lower than the error in some popular KS-DFT hybrid functionals. Density-functional theory, either in MC-PDFT form with local on-top functionals or in KS-DFT form with some functionals having 50% or more nonlocal exchange, has smaller errors for SIE-prone systems than does CASSCF, which has no SIE.

Spatial structure in the diet of imperial eagles Aquila heliaca in Kazakhstan

USGS Publications Warehouse

Katzner, T.E.; Bragin, E.A.; Knick, S.T.; Smith, A.T.

2006-01-01

We evaluated the relationship between spatial variability in prey and food habits of eastern imperial eagles Aquila heliaca at a 90,000 ha national nature reserve in north-central Kazakhstan. Eagle diet varied greatly within the population and the spatial structure of eagle diet within the population varied according to the scale of measurement. Patterns in dietary response were inconsistent with expectations if either ontogenetic imprinting or competition determined diet choice, but they met expectations if functional response determined diet. Eagles nesting near a high-density prey resource used that resource almost exclusively. In contrast, in locations with no single high-density prey species, eagles' diet was more diverse. Our results demonstrate that spatial structuring of diet of vertebrate predators can provide important insight into the mechanisms that drive dietary decisions. ?? OIKOS.

Halogen bond: a long overlooked interaction.

PubMed

Cavallo, Gabriella; Metrangolo, Pierangelo; Pilati, Tullio; Resnati, Giuseppe; Terraneo, Giancarlo

2015-01-01

Because of their high electronegativity, halogen atoms are typically considered, in most of their derivatives, as sites of high electron density and it is commonly accepted that they can form attractive interactions by functioning as the electron donor site (nucleophilic site). This is the case when they work as hydrogen bond acceptor sites. However, the electron density in covalently bound halogens is anisotropically distributed. There is a region of higher electron density, accounting for the ability of halogens to function as electron donor sites in attractive interactions, and a region of lower electron density where the electrostatic potential is frequently positive (mainly in the heavier halogens). This latter region is responsible for the ability of halogen atoms to function as the electron-acceptor site (electrophilic site) in attractive interactions formed with a variety of lone pair-possessing atoms, anions, and π-systems. This ability is quite general and is shown by a wide diversity of halogenated compounds (e.g., organohalogen derivatives and dihalogens). According to the definition proposed by the International Union of Pure and Applied Chemistry, any attractive interactions wherein the halogen atom is the electrophile is named halogen bond (XB). In this chapter, it is discussed how the practice and the concept of XB developed and a brief history of the interaction is presented. Papers (either from the primary or secondary literature) which have reported major experimental findings in the field or which have given important theoretical contributions for the development of the concept are recollected in order to trace how a unifying and comprehensive categorization emerged encompassing all interactions wherein halogen atoms function as the electrophilic site.

Acousto-exciton interaction in a gas of 2D indirect dipolar excitons in the presence of disorder

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

Kovalev, V. M.; Chaplik, A. V., E-mail: chaplik@isp.nsc.ru

2016-03-15

A theory for the linear and quadratic responses of a 2D gas of indirect dipolar excitons to an external surface acoustic wave perturbation in the presence of a static random potential is considered. The theory is constructed both for high temperatures, definitely greater than the exciton gas condensation temperature, and at zero temperature by taking into account the Bose–Einstein condensation effects. The particle Green functions, the density–density correlation function, and the quadratic response function are calculated by the “cross” diagram technique. The results obtained are used to calculate the absorption of Rayleigh surface waves and the acoustic exciton gas dragmore » by a Rayleigh wave. The damping of Bogoliubov excitations in an exciton condensate due to theirs scattering by a random potential has also been determined.« less

Evaluating and interpreting the chemical relevance of the linear response kernel for atoms II: open shell.

PubMed

Boisdenghien, Zino; Fias, Stijn; Van Alsenoy, Christian; De Proft, Frank; Geerlings, Paul

2014-07-28

Most of the work done on the linear response kernel χ(r,r') has focussed on its atom-atom condensed form χAB. Our previous work [Boisdenghien et al., J. Chem. Theory Comput., 2013, 9, 1007] was the first effort to truly focus on the non-condensed form of this function for closed (sub)shell atoms in a systematic fashion. In this work, we extend our method to the open shell case. To simplify the plotting of our results, we average our results to a symmetrical quantity χ(r,r'). This allows us to plot the linear response kernel for all elements up to and including argon and to investigate the periodicity throughout the first three rows in the periodic table and in the different representations of χ(r,r'). Within the context of Spin Polarized Conceptual Density Functional Theory, the first two-dimensional plots of spin polarized linear response functions are presented and commented on for some selected cases on the basis of the atomic ground state electronic configurations. Using the relation between the linear response kernel and the polarizability we compare the values of the polarizability tensor calculated using our method to high-level values.

Matricellular homologs in the foreign body response: hevin suppresses inflammation, but hevin and SPARC together diminish angiogenesis.

PubMed

Barker, Thomas H; Framson, Paul; Puolakkainen, Pauli A; Reed, May; Funk, Sarah E; Sage, E Helene

2005-03-01

Implanted foreign materials, used to restore or assist tissue function, elicit an initial acute inflammatory response followed by chronic fibrosis that leads to the entrapment of the biomaterial in a thick, poorly vascularized collagenous capsule. Matricellular proteins, secreted macromolecules that interact with extracellular matrix proteins but do not in themselves serve structural roles, have been identified as important mediators of the foreign body response that includes inflammation, angiogenesis, and collagen synthesis and assembly. In this report we delineate functions of hevin and SPARC, two homologs of the SPARC family of matricellular proteins, in the foreign body response. Despite their sequence similarity, hevin and SPARC mediate different aspects of this fibrotic response. Using mice with targeted gene deletions, we show that hevin is central to the progression of biomaterial-induced inflammation whereas SPARC regulates the formation of the collagenous capsule. Although vascular density within the capsule is unaltered in the absence of either protein, SPARC-hevin double-null capsules show substantially increased numbers of vessels, indicating compensatory functions for these two proteins in the inhibition of angiogenesis. These results provide important information for further development of implant technology.

IRT-LR-DIF with Estimation of the Focal-Group Density as an Empirical Histogram

ERIC Educational Resources Information Center

Woods, Carol M.

2008-01-01

Item response theory-likelihood ratio-differential item functioning (IRT-LR-DIF) is used to evaluate the degree to which items on a test or questionnaire have different measurement properties for one group of people versus another, irrespective of group-mean differences on the construct. Usually, the latent distribution is presumed normal for both…

Investment in constitutive immune function by north American elk experimentally maintained at two different population densities

Treesearch

Cynthia J. Downs; Kelley M. Stewart; Brian L. Dick; Daniel E Crocker

2015-01-01

Natural selection favors individuals that respond with effective and appropriate immune responses to macro or microparasites. Animals living in populations close to ecological carrying capacity experience increased intraspecific competition, and as a result are often in poor nutritional condition. Nutritional condition, in turn, affects the amount of endogenous...

Human-mediated loss of phylogenetic and functional diversity in coral reef fishes.

PubMed

D'agata, Stéphanie; Mouillot, David; Kulbicki, Michel; Andréfouët, Serge; Bellwood, David R; Cinner, Joshua E; Cowman, Peter F; Kronen, Mecki; Pinca, Silvia; Vigliola, Laurent

2014-03-03

Beyond the loss of species richness, human activities may also deplete the breadth of evolutionary history (phylogenetic diversity) and the diversity of roles (functional diversity) carried out by species within communities, two overlooked components of biodiversity. Both are, however, essential to sustain ecosystem functioning and the associated provision of ecosystem services, particularly under fluctuating environmental conditions. We quantified the effect of human activities on the taxonomic, phylogenetic, and functional diversity of fish communities in coral reefs, while teasing apart the influence of biogeography and habitat along a gradient of human pressure across the Pacific Ocean. We detected nonlinear relationships with significant breaking points in the impact of human population density on phylogenetic and functional diversity of parrotfishes, at 25 and 15 inhabitants/km(2), respectively, while parrotfish species richness decreased linearly along the same population gradient. Over the whole range, species richness decreased by 11.7%, while phylogenetic and functional diversity dropped by 35.8% and 46.6%, respectively. Our results call for caution when using species richness as a benchmark for measuring the status of ecosystems since it appears to be less responsive to variation in human population densities than its phylogenetic and functional counterparts, potentially imperiling the functioning of coral reef ecosystems. Copyright © 2014 Elsevier Ltd. All rights reserved.

Universal fermionic spectral functions from string theory.

PubMed

Gauntlett, Jerome P; Sonner, Julian; Waldram, Daniel

2011-12-09

We carry out the first holographic calculation of a fermionic response function for a strongly coupled d=3 system with an explicit D=10 or D=11 supergravity dual. By considering the supersymmetry current, we obtain a universal result applicable to all d=3 N=2 SCFTs with such duals. Surprisingly, the spectral function does not exhibit a Fermi surface, despite the fact that the system is at finite charge density. We show that it has a phonino pole and at low frequencies there is a depletion of spectral weight with a power-law scaling which is governed by a locally quantum critical point.

Thermosphere Response to Geomagnetic Variability during Solar Minimum Conditions

NASA Astrophysics Data System (ADS)

Forbes, Jeffrey; Gasperini, Federico; Zhang, Xiaoli; Doornbos, Eelco; Bruinsma, Sean; Haeusler, Kathrin; Hagan, Maura

2015-04-01

The response of thermosphere mass density to variable geomagnetic activity at solar minimum is revealed as a function of height utilizing accelerometer data from GRACE near 480 km, CHAMP near 320 km, and GOCE near 260 km during the period October-December, 2009. The GOCE data at 260 km, and to some degree the CHAMP measurements at 320 km, reveal the interesting feature that the response maximum occurs at low latitudes, rather than at high latitudes where the geomagnetic energy input is presumed to be deposited. The latitude distribution of the response is opposite to what one might expect based on thermal expansion and/or increase in mean molecular weight due to vertical transport of N2 at high latitudes. We speculate that what is observed reflects the consequences of an equatorward meridional circulation with downward motion and compressional heating at low latitudes. A numerical simulation using the National Center for Atmospheric Research (NCAR) Thermosphere-Ionosphere-Mesosphere Electrodynamics General Circulation Model (TIME-GCM) is used to assist with this diagnosis. At 480 km GRACE reveals maximum density responses at high southern (winter) latitudes, consistent with recent interpretations in terms of compositional versus temperature effects near the oxygen-helium transition altitude during low solar activity.

Modeling of Thermospheric Neutral Density Variations in Response to Geomagnetic Forcing using GRACE Accelerometer Data

NASA Astrophysics Data System (ADS)

Calabia, A.; Matsuo, T.; Jin, S.

2017-12-01

The upper atmospheric expansion refers to an increase in the temperature and density of Earth's thermosphere due to increased geomagnetic and space weather activities, producing anomalous atmospheric drag on LEO spacecraft. Increased drag decelerates satellites, moving their orbit closer to Earth, decreasing the lifespan of satellites, and making satellite orbit determination difficult. In this study, thermospheric neutral density variations due to geomagnetic forcing are investigated from 10 years (2003-2013) of GRACE's accelerometer-based estimates. In order to isolate the variations produced by geomagnetic forcing, 99.8% of the total variability has been modeled and removed through the parameterization of annual, LST, and solar-flux variations included in the primary Empirical Orthogonal Functions. The residual disturbances of neutral density variations have been investigated further in order to unravel their relationship to several geomagnetic indices and space weather activity indicators. Stronger fluctuations have been found in the southern polar cap, following the dipole-tilt angle variations. While the parameterization of the residual disturbances in terms of Dst index results in the best fit to training data, the use of merging electric field as a predictor leads to the best forecasting performance. An important finding is that modeling of neutral density variations in response geomagnetic forcing can be improved by accounting for the latitude-dependent delay. Our data-driven modeling results are further compared to modeling with TIEGCM.

Combined effects of hydrologic alteration and cyprinid fish in mediating biogeochemical processes in a Mediterranean stream.

PubMed

Rubio-Gracia, Francesc; Almeida, David; Bonet, Berta; Casals, Frederic; Espinosa, Carmen; Flecker, Alexander S; García-Berthou, Emili; Martí, Eugènia; Tuulaikhuu, Baigal-Amar; Vila-Gispert, Anna; Zamora, Lluis; Guasch, Helena

2017-12-01

Flow regimes are important drivers of both stream community and biogeochemical processes. However, the interplay between community and biogeochemical responses under different flow regimes in streams is less understood. In this study, we investigated the structural and functional responses of periphyton and macroinvertebrates to different densities of the Mediterranean barbel (Barbus meridionalis, Cyprinidae) in two stream reaches differing in flow regime. The study was conducted in Llémena Stream, a small calcareous Mediterranean stream with high nutrient levels. We selected a reach with permanent flow (permanent reach) and another subjected to flow regulation (regulated reach) with periods of flow intermittency. At each reach, we used in situ cages to generate 3 levels of fish density. Cages with 10 barbels were used to simulate high fish density (>7indm -2 ); cages with open sides were used as controls (i.e. exposed to actual fish densities of each stream reach) thus having low fish density; and those with no fish were used to simulate the disappearance of fish that occurs with stream drying. Differences in fish density did not cause significant changes in periphyton biomass and macroinvertebrate density. However, phosphate uptake by periphyton was enhanced in treatments lacking fish in the regulated reach with intermittent flow but not in the permanent reach, suggesting that hydrologic alteration hampers the ability of biotic communities to compensate for the absence of fish. This study indicates that fish density can mediate the effects of anthropogenic alterations such as flow intermittence derived from hydrologic regulation on stream benthic communities and associated biogeochemical processes, at least in eutrophic streams. Copyright © 2017. Published by Elsevier B.V.

Application of Raman spectroscopy, surface-enhanced Raman scattering (SERS), and density functional theory for the identification of phenethylamines.

PubMed

Taplin, Francis; O'Donnell, Deanna; Kubic, Thomas; Leona, Marco; Lombardi, John

2013-10-01

We evaluated the normal Raman (NR) and the surface-enhanced Raman scattering (SERS) of three sympathomimetic amines: phenethylamine, ephedrine, and 3,4-methylenedioxymethamphetamine (MDMA). In addition, quantum mechanical calculations-geometry optimization and calculations of the harmonic vibrational frequencies-were performed using the density functional theory (DFT) approach. Vibrational assignments were made by comparing the experimental and calculated spectra. The study found that both NR and SERS provided excellent spectra for the drugs tested. Certain conditions, such as response to various laser wavelengths and background fluorescence of the analyte, could be easily managed using SERS techniques. The DFT-calculated spectra could be correlated with the experimental spectra without the aid of a scaling factor. We also present a set of discriminant bands, useful for distinguishing the three compounds, despite their structural similarities.

Synthesis, characterization and calculated non-linear optical properties of two new chalcones

NASA Astrophysics Data System (ADS)

Singh, Ashok Kumar; Saxena, Gunjan; Prasad, Rajendra; Kumar, Abhinav

2012-06-01

Two new chalcones viz 3-(4-(benzyloxy)phenyl)-1-(2-hydroxyphenyl)prop-2-en-1-one (1) and 3-(4-chlorophenyl)-1-(2-hydroxyphenyl)prop-2-en-1-one (2) have been prepared and characterized by micro analyses, 1H NMR, IR, UV-Vis spectroscopy and single crystal X-ray. The first static hyperpolarizability (β) for both the compounds has been investigated by density functional theory (DFT). Also, the solvent-induced effects on the non-linear optical properties (NLO) were studied by using self-consistent reaction field (SCRF) method. As the solvent polarity increases, the β value increases monotonically. The electronic absorption bands of both 1 and 2 have been assigned by time dependent density functional theory (TD-DFT). Both the compounds displayed better non-linear optical (NLO) responses than the standard p-nitroaniline (pNA).

Pressure-enabled phonon engineering in metals

PubMed Central

Lanzillo, Nicholas A.; Thomas, Jay B.; Watson, Bruce; Washington, Morris; Nayak, Saroj K.

2014-01-01

We present a combined first-principles and experimental study of the electrical resistivity in aluminum and copper samples under pressures up to 2 GPa. The calculations are based on first-principles density functional perturbation theory, whereas the experimental setup uses a solid media piston–cylinder apparatus at room temperature. We find that upon pressurizing each metal, the phonon spectra are blue-shifted and the net electron–phonon interaction is suppressed relative to the unstrained crystal. This reduction in electron–phonon scattering results in a decrease in the electrical resistivity under pressure, which is more pronounced for aluminum than for copper. We show that density functional perturbation theory can be used to accurately predict the pressure response of the electrical resistivity in these metals. This work demonstrates how the phonon spectra in metals can be engineered through pressure to achieve more attractive electrical properties. PMID:24889627

Plastic Responses of a Sessile Prey to Multiple Predators: A Field and Experimental Study

PubMed Central

Hirsch, Philipp Emanuel; Cayon, David; Svanbäck, Richard

2014-01-01

Background Theory predicts that prey facing a combination of predators with different feeding modes have two options: to express a response against the feeding mode of the most dangerous predator, or to express an intermediate response. Intermediate phenotypes protect equally well against several feeding modes, rather than providing specific protection against a single predator. Anti-predator traits that protect against a common feeding mode displayed by all predators should be expressed regardless of predator combination, as there is no need for trade-offs. Principal Findings We studied phenotypic anti-predator responses of zebra mussels to predation threat from a handling-time-limited (crayfish) and a gape-size-limited (roach) predator. Both predators dislodge mussels from the substrate but diverge in their further feeding modes. Mussels increased expression of a non-specific defense trait (attachment strength) against all combinations of predators relative to a control. In response to roach alone, mussels showed a tendency to develop a weaker and more elongated shell. In response to crayfish, mussels developed a harder and rounder shell. When exposed to either a combination of predators or no predator, mussels developed an intermediate phenotype. Mussel growth rate was positively correlated with an elongated weaker shell and negatively correlated with a round strong shell, indicating a trade-off between anti-predator responses. Field observations of prey phenotypes revealed the presence of both anti-predator phenotypes and the trade-off with growth, but intra-specific population density and bottom substrate had a greater influence than predator density. Conclusions Our results show that two different predators can exert both functionally equivalent and inverse selection pressures on a single prey. Our field study suggests that abiotic factors and prey population density should be considered when attempting to explain phenotypic diversity in the wild. PMID:25517986

Interactive effects of a high-quality protein diet and high stocking density on the stress response and some innate immune parameters of Senegalese sole Solea senegalensis.

PubMed

Costas, Benjamín; Aragão, Cláudia; Dias, Jorge; Afonso, António; Conceição, Luís E C

2013-10-01

Amino acids (AA) regulate key metabolic pathways, including some immune responses. Therefore, this study aimed to assess whether an increased availability of dietary AA can mitigate the expected increase in plasma cortisol and metabolites levels due to high stocking density and its subsequent immunosuppression. Senegalese sole (Solea senegalensis) were maintained at low stocking density (LSD; 3.5 kg m(-2)) or high stocking density (HSD; 12 kg m(-2)) for 18 days. Additionally, both treatments were fed a control or a high protein (HP) diet (LSD, LSD HP, HSD and HSD HP). The HP diet slightly increased the levels of digestible indispensable AA, together with tyrosine and cysteine. HSD was effective in inducing a chronic stress response after 18 days of treatment since fish held at HSD presented higher plasma cortisol, glucose and lactate levels. Moreover, this increase in stress indicators translated in a decrease in plasma lysozyme, alternative complement pathway (ACP) and peroxidase activities, suggesting some degree of immunosuppression. Interestingly, while plasma glucose and lactate levels in HSD HP specimens decreased to similar values than LSD fish, plasma lysozyme, ACP and peroxidase activities increased, with even higher values than LSD groups for ACP activity. It is suggested that the HP diet may be used as functional feed since it may represent a metabolic advantage during stressful events and may counteract immunosuppression in sole.

Theoretical and lidar studies of the density response of the mesospheric sodium layer to gravity wave perturbations

NASA Technical Reports Server (NTRS)

Shelton, J. D.; Gardner, C. S.

1981-01-01

The density response of atmospheric layers to gravity waves is developed in two forms, an exact solution and a perturbation series solution. The degree of nonlinearity in the layer density response is described by the series solution whereas the exact solution gives insight into the nature of the responses. Density perturbation in an atmospheric layer are shown to be substantially greater than the atmospheric density perturbation associated with the propagation of a gravity wave. Because of the density gradients present in atmospheric layers, interesting effects were observed such as a phase reversal in the linear layer response which occurs near the layer peak. Once the layer response is understood, the sodium layer can be used as a tracer of atmospheric wave motions. A two dimensional digital signal processing technique was developed. Both spatial and temporal filtering are utilized to enhance the resolution by decreasing shot noise by more han 10 dB. Many of the features associated with a layer density response to gravity waves were observed in high resolution density profiles of the mesospheric sodium layer. These include nonlinearities as well as the phase reversal in the linear layer response.

Form-function analysis of the effect of canopy morphology on leaf self-shading in the seagrass Thalassia testudinum.

PubMed

Enríquez, Susana; Pantoja-Reyes, Norma I

2005-09-01

The variation in seagrass morphology and the magnitude of leaf self-shading within the canopy of Thalassia testudinum, were compared among nine sites in a fringing reef lagoon. We found a significant variation in the growth-form of T. testudinum reflected in a 5.4-fold variation in the attenuation coefficient (K (d)) within the canopy. The largest morphological variation was observed in shoot density. Leaf biomass, leaf area index (LAI), and shoot density were positively associated with canopy-K (d) and with the percentage of surface irradiance received by the top of the seagrass canopy (% Es). These results provide an explanation for the consistent pattern of depth reduction in seagrass leaf biomass and shoot density reported in the literature. Shoot density and shoot size are two descriptors of the growth-form of T. testudinum related to its clonal life-form. Shoot size was not significantly correlated with canopy-K (d), nevertheless, it showed a significant effect on the slope of the relationship between shoot density and canopy-K (d). According to this model, shoot size also contributes to light attenuation within the seagrass canopy by increasing the effect of shoot density. This form-function analysis suggests that light may have a relevant role in the regulation of the optimal plant balance between horizontal (variation in shoot density) and vertical (variation in shoot size) growth of seagrasses. Other environmental factors and interactions also need to be examined to fully understand the mechanistic bases of the morphological responses of seagrasses to the environment.

Optical properties of azobenzene-functionalized self-assembled monolayers: Intermolecular coupling and many-body interactions

NASA Astrophysics Data System (ADS)

Cocchi, Caterina; Moldt, Thomas; Gahl, Cornelius; Weinelt, Martin; Draxl, Claudia

2016-12-01

In a joint theoretical and experimental work, the optical properties of azobenzene-functionalized self-assembled monolayers (SAMs) are studied at different molecular packing densities. Our results, based on density-functional and many-body perturbation theory, as well as on differential reflectance (DR) spectroscopy, shed light on the microscopic mechanisms ruling photo-absorption in these systems. While the optical excitations are intrinsically excitonic in nature, regardless of the molecular concentration, in densely packed SAMs intermolecular coupling and local-field effects are responsible for a sizable weakening of the exciton binding strength. Through a detailed analysis of the character of the electron-hole pairs, we show that distinct excitations involved in the photo-isomerization at low molecular concentrations are dramatically broadened by intermolecular interactions. Spectral shifts in the calculated DR spectra are in good agreement with the experimental results. Our findings represent an important step forward to rationalize the excited-state properties of these complex materials.

Structural, electronic, mechanical, and dynamical properties of graphene oxides: A first principles study

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

Dabhi, Shweta D.; Gupta, Sanjay D.; Jha, Prafulla K., E-mail: prafullaj@yahoo.com

We report the results of a theoretical study on the structural, electronic, mechanical, and vibrational properties of some graphene oxide models (GDO, a-GMO, z-GMO, ep-GMO and mix-GMO) at ambient pressure. The calculations are based on the ab-initio plane-wave pseudo potential density functional theory, within the generalized gradient approximations for the exchange and correlation functional. The calculated values of lattice parameters, bulk modulus, and its first order pressure derivative are in good agreement with other reports. A linear response approach to the density functional theory is used to derive the phonon frequencies. We discuss the contribution of the phonons in themore » dynamical stability of graphene oxides and detailed analysis of zone centre phonon modes in all the above mentioned models. Our study demonstrates a wide range of energy gap available in the considered models of graphene oxide and hence the possibility of their use in nanodevices.« less

Charge Transport Properties of Durene Crystals from First-Principles.

PubMed

Motta, Carlo; Sanvito, Stefano

2014-10-14

We establish a rigorous computational scheme for constructing an effective Hamiltonian to be used for the determination of the charge carrier mobility of pure organic crystals at finite temperature, which accounts for van der Waals interactions, and it includes vibrational contributions from the entire phonon spectrum of the crystal. Such an approach is based on the ab initio framework provided by density functional theory and the construction of a tight-binding effective model via Wannier transformation. The final Hamiltonian includes coupling of the electrons to the crystals phonons, which are also calculated from density functional theory. We apply this methodology to the case of durene, a small π-conjugated molecule, which forms a high-mobility herringbone-stacked crystal. We show that accounting correctly for dispersive forces is fundamental for obtaining a high-quality phonon spectrum, in agreement with experiments. Then, the mobility as a function of temperature is calculated along different crystallographic directions and the phonons most responsible for the scattering are identified.

Time-dependent quantum transport: An efficient method based on Liouville-von-Neumann equation for single-electron density matrix

NASA Astrophysics Data System (ADS)

Xie, Hang; Jiang, Feng; Tian, Heng; Zheng, Xiao; Kwok, Yanho; Chen, Shuguang; Yam, ChiYung; Yan, YiJing; Chen, Guanhua

2012-07-01

Basing on our hierarchical equations of motion for time-dependent quantum transport [X. Zheng, G. H. Chen, Y. Mo, S. K. Koo, H. Tian, C. Y. Yam, and Y. J. Yan, J. Chem. Phys. 133, 114101 (2010), 10.1063/1.3475566], we develop an efficient and accurate numerical algorithm to solve the Liouville-von-Neumann equation. We solve the real-time evolution of the reduced single-electron density matrix at the tight-binding level. Calculations are carried out to simulate the transient current through a linear chain of atoms, with each represented by a single orbital. The self-energy matrix is expanded in terms of multiple Lorentzian functions, and the Fermi distribution function is evaluated via the Padè spectrum decomposition. This Lorentzian-Padè decomposition scheme is employed to simulate the transient current. With sufficient Lorentzian functions used to fit the self-energy matrices, we show that the lead spectral function and the dynamics response can be treated accurately. Compared to the conventional master equation approaches, our method is much more efficient as the computational time scales cubically with the system size and linearly with the simulation time. As a result, the simulations of the transient currents through systems containing up to one hundred of atoms have been carried out. As density functional theory is also an effective one-particle theory, the Lorentzian-Padè decomposition scheme developed here can be generalized for first-principles simulation of realistic systems.

Endothelin-a receptor antagonist treatment improves the periosteal microcirculation after hindlimb ischemia and reperfusion in the rat.

PubMed

Wolfárd, Antal; Császár, József; Gera, László; Petri, András; Simonka, János Aurél; Balogh, Adáa; Boros, Mihály

2002-12-01

To examine the microcirculatory changes in the rat tibial periosteum after hindlimb ischemia and reperfusion and to evaluate the effects of endothelin-A (ET-A) receptor antagonist therapy in this condition. The healing and functioning of vascularized bone autografts depend mainly on the patency of the microcirculation, and the activation of ET-A receptors may be an important component of the tissue response that occurs during ischemia-reoxygenation injuries. Wistar rats were subjected to 1 hour of hindlimb ischemia and 3 hours of reperfusion. The periosteal microcirculation was visualized by intravital fluorescence microscopy. The leukocyte rolling and adherence in the postcapillary venules and the functional capillary density of the periosteum were determined. Two separate groups were treated with the selective ET-A receptor antagonist BQ 610 or the novel ET-A receptor antagonist ETR-p1/fl peptide at the onset of reperfusion. Reperfusion was accompanied by a significant decrease in functional capillary density and by an increase in the primary and secondary leukocyte-endothelial cell interactions. ET-A receptor inhibition reduced the leukocyte rolling and firm adherence and attenuated the decrease in functional capillary density in both treated groups. ET-1 plays a major role in microvascular dysfunction in the periosteum during reperfusion. The ET-1-ET-A receptor system might be an important target for tissue salvage therapy in transplantation surgery.

Morphological and physiological divergences within Quercus ilex support the existence of different ecotypes depending on climatic dryness

PubMed Central

Peguero-Pina, José Javier; Sancho-Knapik, Domingo; Barrón, Eduardo; Camarero, Julio Jesús; Vilagrosa, Alberto; Gil-Pelegrín, Eustaquio

2014-01-01

Background and Aims Several studies show apparently contradictory findings about the functional convergence within the Mediterranean woody flora. In this context, this study evaluates the variability of functional traits within holm oak (Quercus ilex) to elucidate whether provenances corresponding to different morphotypes represent different ecotypes locally adapted to the prevaling stress levels. Methods Several morphological and physiological traits were measured at leaf and shoot levels in 9-year-old seedlings of seven Q. ilex provenances including all recognized morphotypes. Plants were grown in a common garden for 9 years under the same environmental conditions to avoid possible biases due to site-specific characteristics. Key Results Leaf morphometry clearly separates holm oak provenances into ‘ilex’ (more elongated leaves with low vein density) and ‘rotundifolia’ (short and rounded leaves with high vein density) morphotypes. Moreover, these morphotypes represent two consistent and very contrasting functional types in response to dry climates, mainly in terms of leaf area, major vein density, leaf specific conductivity, resistance to drought-induced cavitation and turgor loss point. Conclusions The ‘ilex’ and ‘rotundifolia’ morphotypes correspond to different ecotypes as inferred from their contrasting functional traits. To the best of our knowledge, this is the first time that the combined use of morphological and physiological traits has provided support for the concept of these two holm oak morphotypes being regarded as two different species. PMID:24941998

Excitation spectra of retinal by multiconfiguration pair-density functional theory.

PubMed

Dong, Sijia S; Gagliardi, Laura; Truhlar, Donald G

2018-03-07

Retinal is the chromophore in proteins responsible for vision. The absorption maximum of retinal is sensitive to mutations of the protein. However, it is not easy to predict the absorption spectrum of retinal accurately, and questions remain even after intensive investigation. Retinal poses a challenge for Kohn-Sham density functional theory (KS-DFT) because of the charge transfer character in its excitations, and it poses a challenge for wave function theory because the large size of the molecule makes multiconfigurational perturbation theory methods expensive. In this study, we demonstrate that multiconfiguration pair-density functional theory (MC-PDFT) provides an efficient way to predict the vertical excitation energies of 11-Z retinal, and it reproduces the experimentally determined absorption band widths and peak positions better than complete active space second-order perturbation theory (CASPT2). The consistency between complete active space self-consistent field (CASSCF) and KS-DFT dipole moments is demonstrated to be a useful criterion in selecting the active space. We also found that the nature of the terminal groups and the conformations of retinal play a significant role in the absorption spectrum. By considering a thermal distribution of conformations, we predict an absorption spectrum of retinal that is consistent with the experimental gas-phase spectrum. The location of the absorption peak and the spectral broadening based on MC-PDFT calculations agree better with experiments than those of CASPT2.

Lattice dynamic properties of Rh2XAl (X=Fe and Y) alloys

NASA Astrophysics Data System (ADS)

Al, Selgin; Arikan, Nihat; Demir, Süleyman; Iyigör, Ahmet

2018-02-01

The electronic band structure, elastic and vibrational spectra of Rh2FeAl and Rh2YAl alloys were computed in detail by employing an ab-initio pseudopotential method and a linear-response technique based on the density-functional theory (DFT) scheme within a generalized gradient approximation (GGA). Computed lattice constants, bulk modulus and elastic constants were compared. Rh2YAl exhibited higher ability to resist volume change than Rh2FeAl. The elastic constants, shear modulus, Young modulus, Poisson's ratio, B/G ratio electronic band structure, total and partial density of states, and total magnetic moment of alloys were also presented. Rh2FeAl showed spin up and spin down states whereas Rh2YAl showed none due to being non-magnetic. The calculated total densities of states for both materials suggest that both alloys are metallic in nature. Full phonon spectra of Rh2FeAl and Rh2YA1 alloys in the L21 phase were collected using the ab-initio linear response method. The obtained phonon frequencies were in the positive region indicating that both alloys are dynamically stable.

[Are simple time lags responsible for cyclic variation of population density? : A comparison of laboratory population dynamics of Brachionus calyciflorus pallas (rotatoria) with computer simulations].

PubMed

Halbach, Udo; Burkhardt, Heinz Jürgen

1972-09-01

Laboratory populations of the rotifer Brachionus calyciflorus were cultured at different temperatures (25, 20, 15°C) but otherwise at constant conditions. The population densities showed relatively constant oscillations (Figs. 1 to 3A-C). Amplitudes and frequencies of the oscillations were positively correlated with temperature (Table 1). A test was made, whether the logistic growth function with simple time lag is able to describe the population curves. There are strong similarities between the simulations (Figs. 1-3E) and the real population dynamics if minor adjustments of the empirically determined parameters are made. There-fore it is suggested that time lags are responsible for the observed oscillations. However, the actual time lags probably do not act in the simple manner of the model, because birth and death rates react with different time lags, and both parameters are dependent on individual age and population density. A more complex model, which incorporates these modifications, should lead to a more realistic description of the observed oscillations.

Downmodulation of the Inflammatory Response to Bacterial Infection by γδ T Cells Cytotoxic for Activated Macrophages

PubMed Central

Egan, Paul J.; Carding, Simon R.

2000-01-01

Although γδ T cells are involved in the regulation of inflammation after infection, their precise function is not known. Intraperitoneal infection of T cell receptor (TCR)-δ−/− mice with the intracellular bacterium Listeria monocytogenes resulted in the development of necrotic foci in the livers. In contrast, the peritoneal cavities of infected TCR-δ−/− mice contained an accumulation of low density activated macrophages and a reduced percentage of macrophages undergoing apoptosis. γδ T cell hybridomas derived from mice infected with Listeria were preferentially stimulated by low density macrophages from peritoneal exudates of infected mice. Furthermore, primary splenic γδ T cells isolated from Listeria-infected mice were cytotoxic for low density macrophages in vitro, and cytotoxicity was inhibited in the presence of antibodies to the γδ TCR. These results demonstrate a novel interaction between γδ T cells and activated macrophages in which γδ T cells are stimulated by terminally differentiated macrophages to acquire cytotoxic activity and which, in turn, induce macrophage cell death. This interaction suggests that γδ T cells regulate the inflammatory response to infection with intracellular pathogens by eliminating activated macrophages at the termination of the response. PMID:10859339

Allocation to male vs female floral function varies by currency and responds differentially to density and moisture stress.

PubMed

Brock, M T; Winkelman, R L; Rubin, M J; Edwards, C E; Ewers, B E; Weinig, C

2017-11-01

Allocation of finite resources to separate reproductive functions is predicted to vary across environments and affect fitness. Biomass is the most commonly measured allocation currency; however, in comparison with nutrients it may be less limited and express different environmental and evolutionary responses. Here, we measured carbon, nitrogen, phosphorus, and biomass allocation among floral whorls in recombinant inbred lines of Brassica rapa in multiple environments to characterize the genetic architecture of floral allocation, including its sensitivity to environmental heterogeneity and to choice of currency. Mass, carbon, and nitrogen allocation to female whorls (pistils and sepals) decreased under high density, whereas nitrogen allocation to male organs (stamens) decreased under drought. Phosphorus allocation decreased by half in pistils under drought, while stamen phosphorus was unaffected by environment. While the contents of each currency were positively correlated among whorls, selection to improve fitness through female (or male) function typically favored increased allocation to pistils (or stamens) but decreased allocation to other whorls. Finally, genomic regions underlying correlations among allocation metrics were mapped, and loci related to nitrogen uptake and floral organ development were located within mapped quantitative trait loci. Our candidate gene identification suggests that nutrient uptake may be a limiting step in maintaining male allocation. Taken together, allocation to male vs female function is sensitive to distinct environmental stresses, and the choice of currency affects the interpretation of floral allocation responses to the environment. Further, genetic correlations may counter the evolution of allocation patterns that optimize fitness through female or male function.

Plasmon-induced nonlinear response of silver atomic chains.

PubMed

Yan, Lei; Guan, Mengxue; Meng, Sheng

2018-05-10

Nonlinear response of a linear silver atomic chain upon ultrafast laser excitation has been studied in real time using the time-dependent density functional theory. We observe the presence of nonlinear responses up to the fifth order in tunneling current, which is ascribed to the excitation of high-energy electrons generated by Landau damping of plasmons. The nonlinear effect is enhanced after adsorption of polar molecules such as water due to the enhanced damping rates during plasmon decay. Increasing the length of atomic chains also increases the nonlinear response, favoring higher-order plasmon excitation. These findings offer new insights towards a complete understanding and ultimate control of plasmon-induced nonlinear phenomena to atomic precision.

Charge and Spin Currents in Open-Shell Molecules:  A Unified Description of NMR and EPR Observables.

PubMed

Soncini, Alessandro

2007-11-01

The theory of EPR hyperfine coupling tensors and NMR nuclear magnetic shielding tensors of open-shell molecules in the limit of vanishing spin-orbit coupling (e.g., for organic radicals) is analyzed in terms of spin and charge current density vector fields. The ab initio calculation of the spin and charge current density response has been implemented at the Restricted Open-Shell Hartree-Fock, Unrestricted Hartree-Fock, and unrestricted GGA-DFT level of theory. On the basis of this formalism, we introduce the definition of nuclear hyperfine coupling density, a scalar function of position providing a partition of the EPR observable over the molecular domain. Ab initio maps of spin and charge current density and hyperfine coupling density for small radicals are presented and discussed in order to illustrate the interpretative advantages of the newly introduced approach. Recent NMR experiments providing evidence for the existence of diatropic ring currents in the open-shell singlet pancake-bonded dimer of the neutral phenalenyl radical are directly assessed via the visualization of the induced current density.

Predicting species interactions from edge responses: mongoose predation on hawksbill sea turtle nests in fragmented beach habitat.

PubMed

Leighton, Patrick A; Horrocks, Julia A; Krueger, Barry H; Beggs, Jennifer A; Kramer, Donald L

2008-11-07

Because species respond differently to habitat boundaries and spatial overlap affects encounter rates, edge responses should be strong determinants of spatial patterns of species interactions. In the Caribbean, mongooses (Herpestes javanicus) prey on hawksbill sea turtle (Eretmochelys imbricata) eggs. Turtles nest in both open sand and vegetation patches, with a peak in nest abundance near the boundary between the two microhabitats; mongooses rarely leave vegetation. Using both artificial nests and hawksbill nesting data, we examined how the edge responses of these species predict the spatial patterns of nest mortality. Predation risk was strongly related to mongoose abundance but was not affected by nest density or habitat type. The product of predator and prey edge response functions accurately described the observed pattern of total prey mortality. Hawksbill preference for vegetation edge becomes an ecological trap in the presence of mongooses. This is the first study to predict patterns of predation directly from continuous edge response functions of interacting species, establishing a link between models of edge response and species interactions.

Predicting species interactions from edge responses: mongoose predation on hawksbill sea turtle nests in fragmented beach habitat

PubMed Central

Leighton, Patrick A; Horrocks, Julia A; Krueger, Barry H; Beggs, Jennifer A; Kramer, Donald L

2008-01-01

Because species respond differently to habitat boundaries and spatial overlap affects encounter rates, edge responses should be strong determinants of spatial patterns of species interactions. In the Caribbean, mongooses (Herpestes javanicus) prey on hawksbill sea turtle (Eretmochelys imbricata) eggs. Turtles nest in both open sand and vegetation patches, with a peak in nest abundance near the boundary between the two microhabitats; mongooses rarely leave vegetation. Using both artificial nests and hawksbill nesting data, we examined how the edge responses of these species predict the spatial patterns of nest mortality. Predation risk was strongly related to mongoose abundance but was not affected by nest density or habitat type. The product of predator and prey edge response functions accurately described the observed pattern of total prey mortality. Hawksbill preference for vegetation edge becomes an ecological trap in the presence of mongooses. This is the first study to predict patterns of predation directly from continuous edge response functions of interacting species, establishing a link between models of edge response and species interactions. PMID:18647718

Movement reveals scale dependence in habitat selection of a large ungulate.

PubMed

Northrup, Joseph M; Anderson, Charles R; Hooten, Mevin B; Wittemyer, George

2016-12-01

Ecological processes operate across temporal and spatial scales. Anthropogenic disturbances impact these processes, but examinations of scale dependence in impacts are infrequent. Such examinations can provide important insight to wildlife-human interactions and guide management efforts to reduce impacts. We assessed spatiotemporal scale dependence in habitat selection of mule deer (Odocoileus hemionus) in the Piceance Basin of Colorado, USA, an area of ongoing natural gas development. We employed a newly developed animal movement method to assess habitat selection across scales defined using animal-centric spatiotemporal definitions ranging from the local (defined from five hour movements) to the broad (defined from weekly movements). We extended our analysis to examine variation in scale dependence between night and day and assess functional responses in habitat selection patterns relative to the density of anthropogenic features. Mule deer displayed scale invariance in the direction of their response to energy development features, avoiding well pads and the areas closest to roads at all scales, though with increasing strength of avoidance at coarser scales. Deer displayed scale-dependent responses to most other habitat features, including land cover type and habitat edges. Selection differed between night and day at the finest scales, but homogenized as scale increased. Deer displayed functional responses to development, with deer inhabiting the least developed ranges more strongly avoiding development relative to those with more development in their ranges. Energy development was a primary driver of habitat selection patterns in mule deer, structuring their behaviors across all scales examined. Stronger avoidance at coarser scales suggests that deer behaviorally mediated their interaction with development, but only to a degree. At higher development densities than seen in this area, such mediation may not be possible and thus maintenance of sufficient habitat with lower development densities will be a critical best management practice as development expands globally. © 2016 by the Ecological Society of America.

On the distinction between open and closed economies.

PubMed Central

Timberlake, W; Peden, B F

1987-01-01

Open and closed economies have been assumed to produce opposite relations between responding and the programmed density of reward (the amount of reward divided by its cost). Experimental procedures that are treated as open economies typically dissociate responding and total reward by providing supplemental income outside the experimental session; procedures construed as closed economies do not. In an open economy responding is assumed to be directly related to reward density, whereas in a closed economy responding is assumed to be inversely related to reward density. In contrast to this predicted correlation between response-reward relations and type of economy, behavior regulation theory predicts both direct and inverse relations in both open and closed economies. Specifically, responding should be a bitonic function of reward density regardless of the type of economy and is dependent only on the ratio of the schedule terms rather than on their absolute size. These predictions were tested by four experiments in which pigeons' key pecking produced food on fixed-ratio and variable-interval schedules over a range of reward magnitudes and under several open- and closed-economy procedures. The results better supported the behavior regulation view by showing a general bitonic function between key pecking and food density in all conditions. In most cases, the absolute size of the schedule requirement and the magnitude of reward had no effect; equal ratios of these terms produced approximately equal responding. PMID:3625103

Linking functional response and bioenergetics to estimate juvenile salmon growth in a reservoir food web

USGS Publications Warehouse

Haskell, Craig A.; Beauchamp, David A.; Bollens, Stephen M.

2017-01-01

Juvenile salmon (Oncorhynchus spp.) use of reservoir food webs is understudied. We examined the feeding behavior of subyearling Chinook salmon (O. tshawytscha) and its relation to growth by estimating the functional response of juvenile salmon to changes in the density of Daphnia, an important component of reservoir food webs. We then estimated salmon growth across a broad range of water temperatures and daily rations of two primary prey, Daphnia and juvenile American shad (Alosa sapidissima) using a bioenergetics model. Laboratory feeding experiments yielded a Type-II functional response curve: C = 29.858 P *(4.271 + P)-1 indicating that salmon consumption (C) of Daphnia was not affected until Daphnia densities (P) were < 30 · L-1. Past field studies documented Daphnia densities in lower Columbia River reservoirs of < 3 · L-1 in July but as high as 40 · L-1 in August. Bioenergetics modeling indicated that subyearlings could not achieve positive growth above 22°C regardless of prey type or consumption rate. When feeding on Daphnia, subyearlings could not achieve positive growth above 20°C (water temperatures they commonly encounter in the lower Columbia River during summer). At 16–18°C, subyearlings had to consume about 27,000 Daphnia · day-1 to achieve positive growth. However, when feeding on juvenile American shad, subyearlings had to consume 20 shad · day-1 at 16–18°C, or at least 25 shad · day-1 at 20°C to achieve positive growth. Using empirical consumption rates and water temperatures from summer 2013, subyearlings exhibited negative growth during July (-0.23 to -0.29 g · d-1) and August (-0.05 to -0.07 g · d-1). By switching prey from Daphnia to juvenile shad which have a higher energy density, subyearlings can partially compensate for the effects of higher water temperatures they experience in the lower Columbia River during summer. However, achieving positive growth as piscivores requires subyearlings to feed at higher consumption rates than they exhibited empirically. While our results indicate compromised growth in reservoir habitats, the long-term repercussions to salmon populations in the Columbia River Basin are unknown.

Skin denervation and its clinical significance in late-stage chronic kidney disease.

PubMed

Chao, Chi-Chao; Wu, Vin-Cent; Tan, Chun-Hsiang; Wang, Yi-Mei; Tseng, Ming-Tsung; Wu, Pei-Chen; Lin, Yea-Huey; Lin, Whei-Min; Wu, Kwan-Dun; Hsieh, Sung-Tsang

2011-02-01

To investigate the skin innervation and its clinical significance in late-stage chronic kidney disease (CKD). Case series. National Taiwan University Hospital, Taipei, Taiwan. Forty consecutive nondiabetic patients with late-stage CKD (14 female and 26 male; mean [SD] age, 60.7 [12.3] years), including 2 cases with stage 3 CKD, 6 with stage 4 CKD, and 32 with stage 5 CKD, ie, end-stage kidney disease. Clinical evaluation of neurological deficits, nerve conduction study, autonomic function tests, and a 3-mm-diameter skin biopsy specimen taken from the distal leg. Quantitation of epidermal innervation, parameters of nerve conduction study, R-R interval variability, and sympathetic skin response. Clinically, 21 patients (52.5%) were symptomatic with paresthesia over the limbs or autonomic symptoms. The intraepidermal nerve fiber (IENF) density was markedly reduced in patients with CKD compared with age- and sex-matched controls (mean [SD], 2.8 [2.0] vs 8.6 [2.8] fibers/mm; P < .001). Skin denervation was observed in 27 patients (67.5%). Fifteen patients (37.5%) had abnormalities on nerve conduction studies, and 29 patients (72.5%) had abnormal results on autonomic function tests. By analysis with multiple regression models, the IENF density was negatively correlated with the duration of renal disease (P = .02). Additionally, the R-R interval variability at rest was linearly correlated with the IENF density (P = .02) and the absence of sympathetic skin responses at the soles was associated with reduced IENF density (P = .03). Small-fiber sensory and autonomic neuropathies constitute the major form of neuropathy in late-stage CKD. Furthermore, skin denervation was associated with the duration of renal disease.

Structural and functional cardiac cholinergic deficits in adult neurturin knockout mice.

PubMed

Mabe, Abigail M; Hoover, Donald B

2009-04-01

Previous work provided indirect evidence that the neurotrophic factor neurturin (NRTN) is required for normal cholinergic innervation of the heart. This study used nrtn knockout (KO) and wild-type (WT) mice to determine the effect of nrtn deletion on cardiac cholinergic innervation and function in the adult heart. Immunohistochemistry, confocal microscopy, and quantitative image analysis were used to directly evaluate intrinsic cardiac neuronal development. Atrial acetylcholine (ACh) levels were determined as an indirect index of cholinergic innervation. Cholinergic function was evaluated by measuring negative chronotropic responses to right vagal nerve stimulation in anaesthetized mice and responses of isolated atria to muscarinic agonists. KO hearts contained only 35% the normal number of cholinergic neurons, and the residual cholinergic neurons were 15% smaller than in WT. Cholinergic nerve density at the sinoatrial node was reduced by 87% in KOs, but noradrenergic nerve density was unaffected. Atrial ACh levels were substantially lower in KO mice (0.013 +/- 0.004 vs. 0.050 +/- 0.011 pmol/microg protein; P < 0.02) as expected from cholinergic neuron and nerve fibre deficits. Maximum bradycardia evoked by vagal stimulation was reduced in KO mice (38 +/- 6% vs. 69 +/- 3% decrease at 20 Hz; P < 0.001), and chronotropic responses took longer to develop and fade. In contrast to these deficits, isolated atria from KO mice had normal post-junctional sensitivity to carbachol and bethanechol. These findings demonstrate that NRTN is essential for normal cardiac cholinergic innervation and cholinergic control of heart rate. The presence of residual cardiac cholinergic neurons and vagal bradycardia in KO mice suggests that additional neurotrophic factors may influence this system.

Imidacloprid affects the functional response of predator Podisus nigrispinus (Dallas) (Heteroptera: Pentatomidae) to strains of Spodoptera frugiperda (J.E. Smith) on Bt cotton.

PubMed

Malaquias, J B; Ramalho, F S; Omoto, C; Godoy, W A C; Silveira, R F

2014-03-01

Podisus nigrispinus (Dallas) (Heteroptera: Pentatomidae) is one of the most common asopine species in the neotropical region and its occurrence was reported in several countries of South and Central America, as an important biological control agent for many crops. This study was carried out to identify the imidacloprid impacts on the functional response of predator P. nigrispinus fed on Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae) strain resistant to lambda-cyhalothrin, on Bt cotton expressing Cry1Ac (Bollgard(®)). Spodoptera frugiperda larvae were used in the following conditions: resistant (1) and susceptible (2) strains to lambda-cyhalothrin fed on Bollgard(®) cotton leaves (DP 404 BG); and resistant (3) and susceptible (4) strains to lambda-cyhalothrin fed on non-genetically modified cotton leaves (cultivar DP4049). The predatory behavior of P. nigrispinus was affected by imidacloprid and the type II asymptotic curve was the one that best described the functional response data. Handling time (T h ) of predator females did not differ among treatments in the presence of imidacloprid. The attack rate did decrease, however, due to an increase in the density of larvae offered. Regardless of the treatment (S. frugiperda strain or cotton cultivar), the predation of P. nigrispinus females on S. frugiperda larvae was significantly lower when exposed to imidacloprid, especially at a density of 16 larvae/predator. The predation behavior of P. nigrispinus on S. frugiperda larvae is affected by the insecticide imidacloprid showing that its applications should be used in cotton crop with caution.

Inverting pump-probe spectroscopy for state tomography of excitonic systems.

PubMed

Hoyer, Stephan; Whaley, K Birgitta

2013-04-28

We propose a two-step protocol for inverting ultrafast spectroscopy experiments on a molecular aggregate to extract the time-evolution of the excited state density matrix. The first step is a deconvolution of the experimental signal to determine a pump-dependent response function. The second step inverts this response function to obtain the quantum state of the system, given a model for how the system evolves following the probe interaction. We demonstrate this inversion analytically and numerically for a dimer model system, and evaluate the feasibility of scaling it to larger molecular aggregates such as photosynthetic protein-pigment complexes. Our scheme provides a direct alternative to the approach of determining all Hamiltonian parameters and then simulating excited state dynamics.

Density-functional theory for internal magnetic fields

NASA Astrophysics Data System (ADS)

Tellgren, Erik I.

2018-01-01

A density-functional theory is developed based on the Maxwell-Schrödinger equation with an internal magnetic field in addition to the external electromagnetic potentials. The basic variables of this theory are the electron density and the total magnetic field, which can equivalently be represented as a physical current density. Hence, the theory can be regarded as a physical current density-functional theory and an alternative to the paramagnetic current density-functional theory due to Vignale and Rasolt. The energy functional has strong enough convexity properties to allow a formulation that generalizes Lieb's convex analysis formulation of standard density-functional theory. Several variational principles as well as a Hohenberg-Kohn-like mapping between potentials and ground-state densities follow from the underlying convex structure. Moreover, the energy functional can be regarded as the result of a standard approximation technique (Moreau-Yosida regularization) applied to the conventional Schrödinger ground-state energy, which imposes limits on the maximum curvature of the energy (with respect to the magnetic field) and enables construction of a (Fréchet) differentiable universal density functional.

Validation and application of auxiliary density perturbation theory and non-iterative approximation to coupled-perturbed Kohn-Sham approach for calculation of dipole-quadrupole polarizability

NASA Astrophysics Data System (ADS)

Shedge, Sapana V.; Pal, Sourav; Köster, Andreas M.

2011-07-01

Recently, two non-iterative approaches have been proposed to calculate response properties within density functional theory (DFT). These approaches are auxiliary density perturbation theory (ADPT) and the non-iterative approach to the coupled-perturbed Kohn-Sham (NIA-CPKS) method. Though both methods are non-iterative, they use different techniques to obtain the perturbed Kohn-Sham matrix. In this Letter, for the first time, both of these two independent methods have been used for the calculation of dipole-quadrupole polarizabilities. To validate these methods, three tetrahedral molecules viz., P4,CH4 and adamantane (C10H16) have been used as examples. The comparison with MP2 and CCSD proves the reliability of the methodology.

Uncertainty Analysis of Simulated Hydraulic Fracturing

NASA Astrophysics Data System (ADS)

Chen, M.; Sun, Y.; Fu, P.; Carrigan, C. R.; Lu, Z.

2012-12-01

Artificial hydraulic fracturing is being used widely to stimulate production of oil, natural gas, and geothermal reservoirs with low natural permeability. Optimization of field design and operation is limited by the incomplete characterization of the reservoir, as well as the complexity of hydrological and geomechanical processes that control the fracturing. Thus, there are a variety of uncertainties associated with the pre-existing fracture distribution, rock mechanics, and hydraulic-fracture engineering that require evaluation of their impact on the optimized design. In this study, a multiple-stage scheme was employed to evaluate the uncertainty. We first define the ranges and distributions of 11 input parameters that characterize the natural fracture topology, in situ stress, geomechanical behavior of the rock matrix and joint interfaces, and pumping operation, to cover a wide spectrum of potential conditions expected for a natural reservoir. These parameters were then sampled 1,000 times in an 11-dimensional parameter space constrained by the specified ranges using the Latin-hypercube method. These 1,000 parameter sets were fed into the fracture simulators, and the outputs were used to construct three designed objective functions, i.e. fracture density, opened fracture length and area density. Using PSUADE, three response surfaces (11-dimensional) of the objective functions were developed and global sensitivity was analyzed to identify the most sensitive parameters for the objective functions representing fracture connectivity, which are critical for sweep efficiency of the recovery process. The second-stage high resolution response surfaces were constructed with dimension reduced to the number of the most sensitive parameters. An additional response surface with respect to the objective function of the fractal dimension for fracture distributions was constructed in this stage. Based on these response surfaces, comprehensive uncertainty analyses were conducted among input parameters and objective functions. In addition, reduced-order emulation models resulting from this analysis can be used for optimal control of hydraulic fracturing. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Multiconfiguration Pair-Density Functional Theory Outperforms Kohn-Sham Density Functional Theory and Multireference Perturbation Theory for Ground-State and Excited-State Charge Transfer.

PubMed

Ghosh, Soumen; Sonnenberger, Andrew L; Hoyer, Chad E; Truhlar, Donald G; Gagliardi, Laura

2015-08-11

The correct description of charge transfer in ground and excited states is very important for molecular interactions, photochemistry, electrochemistry, and charge transport, but it is very challenging for Kohn-Sham (KS) density functional theory (DFT). KS-DFT exchange-correlation functionals without nonlocal exchange fail to describe both ground- and excited-state charge transfer properly. We have recently proposed a theory called multiconfiguration pair-density functional theory (MC-PDFT), which is based on a combination of multiconfiguration wave function theory with a new type of density functional called an on-top density functional. Here we have used MC-PDFT to study challenging ground- and excited-state charge-transfer processes by using on-top density functionals obtained by translating KS exchange-correlation functionals. For ground-state charge transfer, MC-PDFT performs better than either the PBE exchange-correlation functional or CASPT2 wave function theory. For excited-state charge transfer, MC-PDFT (unlike KS-DFT) shows qualitatively correct behavior at long-range with great improvement in predicted excitation energies.

Temperature and speed of testing influence on the densification and recovery of polyurethane foams

NASA Astrophysics Data System (ADS)

Apostol, Dragoş Alexandru; Constantinescu, Dan Mihai

2013-02-01

Polyurethane foams with densities of 35, 93, and 200 kg/m3 were tested in compression at three levels of temperatures as: -60 °C, 23 °C, and 80 °C. The influence of speed of testing from 2 mm/min up to 6 m/s (0.0014 to 545 s-1) on the response of the foams is analyzed. Testing is done separately on the rise direction and on the in-plane direction of the foams, and differences in their behavior are commented. With interpolation functions which approximate the plateau and densification region, the specific strain energy is calculated together with the energy efficiency and onset strain of densification. A Nagy-type phenomenological strain-rate-dependent model is proposed to generate engineering stress-strain curves and is validated through comparison with experimental stress-strain curves obtained at different speeds of testing. Starting from a reference experimental curve, two material parameters which are density and temperature dependent are established. Foam recovery for each density of the polyurethane foams is analyzed as a function of direction of testing, temperature, and speed of testing.

F4TCNQ on Cu, Ag, and Au as prototypical example for a strong organic acceptor on coinage metals

NASA Astrophysics Data System (ADS)

Rangger, Gerold M.; Hofmann, Oliver T.; Romaner, Lorenz; Heimel, Georg; Bröker, Benjamin; Blum, Ralf-Peter; Johnson, Robert L.; Koch, Norbert; Zojer, Egbert

2009-04-01

Metal work-function modification with the help of organic acceptors is an efficient tool to significantly enhance the performance of modern state-of-the-art organic molecular electronic devices. Here, the prototypical organic acceptor 2,3,5,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane, F4TCNQ, is characterized on Ag(111), Au(111), and Cu(111) metal surfaces by means of density-functional theory calculations. Particular attention is paid to charge-transfer processes at the metal-organic interface; a subtle balance between charge forward and backward donations in combination with a strong adsorption-induced geometry change are found to be responsible for the observed increase in the system work function. A larger effect is obtained for the metals with larger initial work function. Interestingly, this results in similar charge-injection barriers from the substrate metal into an organic semiconductor deposited on top of the F4TCNQ layer. The impact of the F4TCNQ packing density of the electronic properties of the interface is also addressed. Comparing the calculated energy-level alignments and work-function modifications to experimental data from ultraviolet photoelectron spectroscopy yields good agreement between experiments and simulations.

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.

Stellar mass and velocity functions of galaxies. Backward evolution and the fate of Milky Way siblings

NASA Astrophysics Data System (ADS)

Boissier, S.; Buat, V.; Ilbert, O.

2010-11-01

Context. In recent years, stellar mass functions of both star-forming and quiescent galaxies have been observed at different redshifts in various fields. In addition, star formation rate (SFR) distributions (e.g. in the form of far infrared luminosity functions) were also obtained. Taken together, they offer complementary pieces of information concerning the evolution of galaxies. Aims: We attempt in this paper to check the consistency of the observed stellar mass functions, SFR functions, and the cosmic SFR density with simple backward evolutionary models. Methods: Starting from observed stellar mass functions for star-forming galaxies, we use backwards models to predict the evolution of a number of quantities, such as the SFR function, the cosmic SFR density and the velocity function. Because the velocity is a parameter attached to a galaxy during its history (contrary to the stellar mass), this approach allows us to quantify the number density evolution of galaxies of a given velocity, e.g. of the Milky Way siblings. Results: Observations suggest that the stellar mass function of star-forming galaxies is constant between redshift 0 and 1. To reproduce this result, we must quench star formation in a number of star-forming galaxies. The stellar mass function of these “quenched” galaxies is consistent with available data concerning the increase in the population of quiescent galaxies in the same redshift interval. The stellar mass function of quiescent galaxies is then mainly determined by the distribution of active galaxies that must stop star formation, with a modest mass redistribution during mergers. The cosmic SFR density and the evolution of the SFR functions are recovered relatively well, although they provide some clues to a minor evolution of the stellar mass function of star forming galaxies at the lowest redshifts. We thus consider that we have obtained in a simple way a relatively consistent picture of the evolution of galaxies at intermediate redshifts. If this picture is correct, 50% of the Milky-Way sisters (galaxies with the same velocity as our Galaxy, i.e. 220 km s-1) have quenched their star formation since redshift 1 (and an even higher fraction for higher velocities). We discuss the processes that might be responsible for this transformation.

Self-powered enzyme micropumps

NASA Astrophysics Data System (ADS)

Sengupta, Samudra; Patra, Debabrata; Ortiz-Rivera, Isamar; Agrawal, Arjun; Shklyaev, Sergey; Dey, Krishna K.; Córdova-Figueroa, Ubaldo; Mallouk, Thomas E.; Sen, Ayusman

2014-05-01

Non-mechanical nano- and microscale pumps that function without the aid of an external power source and provide precise control over the flow rate in response to specific signals are needed for the development of new autonomous nano- and microscale systems. Here we show that surface-immobilized enzymes that are independent of adenosine triphosphate function as self-powered micropumps in the presence of their respective substrates. In the four cases studied (catalase, lipase, urease and glucose oxidase), the flow is driven by a gradient in fluid density generated by the enzymatic reaction. The pumping velocity increases with increasing substrate concentration and reaction rate. These rechargeable pumps can be triggered by the presence of specific analytes, which enables the design of enzyme-based devices that act both as sensor and pump. Finally, we show proof-of-concept enzyme-powered devices that autonomously deliver small molecules and proteins in response to specific chemical stimuli, including the release of insulin in response to glucose.

Experimental Modification of Rat Pituitary Growth Hormone Cell Function During and After Spaceflight

NASA Technical Reports Server (NTRS)

Hymer, W. C.; Salada, T.; Nye, P.; Grossman, E. J.; Lane, P. K.; Grindeland, R. E.

1996-01-01

Space-flown rats show a number of flight-induced changes in the structure and function of pituitary Growth Hormone (GH) cells after in vitro postflight testing. To evaluate the possible effects of microgravity on GH cells themselves, freshly dispersed rat anterior pituitary gland cells were seeded into vials containing serum +/- 1 micron HydroCortisone (HC) before flight. Five different cell preparations were used: the entire mixed-cell population of various hormone-producing cell types, cells of density less than 1.071 g/sq cm (band 1), cells of density greater than 1.071 g/sq cm (band 2), and cells prepared from either the dorsal or ventral part of the gland. Relative to ground control samples, bioactive GH released from dense cells during flight was reduced in HC-free medium but was increased in HC-containing medium. Band I and mixed cells usually showed opposite HC-dependent responses. Release of bioactive GH from ventral flight cells was lower; postflight responses to GH-releasing hormone challenge were reduced, and the cytoplasmic area occupied by GH in the dense cells was greater. Collectively, the data show that the chemistry and cellular makeup of the culture system modifies the response of GH cells to microgravity. As such, these cells offer a system to identify gravisensing mechanisms in secretory cells in future microgravity research.

Object-based attentional modulation of biological motion processing: spatiotemporal dynamics using functional magnetic resonance imaging and electroencephalography.

PubMed

Safford, Ashley S; Hussey, Elizabeth A; Parasuraman, Raja; Thompson, James C

2010-07-07

Although it is well documented that the ability to perceive biological motion is mediated by the lateral temporal cortex, whether and when neural activity in this brain region is modulated by attention is unknown. In particular, it is unclear whether the processing of biological motion requires attention or whether such stimuli are processed preattentively. Here, we used functional magnetic resonance imaging, high-density electroencephalography, and cortically constrained source estimation methods to investigate the spatiotemporal effects of attention on the processing of biological motion. Directing attention to tool motion in overlapping movies of biological motion and tool motion suppressed the blood oxygenation level-dependent (BOLD) response of the right superior temporal sulcus (STS)/middle temporal gyrus (MTG), while directing attention to biological motion suppressed the BOLD response of the left inferior temporal sulcus (ITS)/MTG. Similarly, category-based modulation of the cortical current source density estimates from the right STS/MTG and left ITS was observed beginning at approximately 450 ms following stimulus onset. Our results indicate that the cortical processing of biological motion is strongly modulated by attention. These findings argue against preattentive processing of biological motion in the presence of stimuli that compete for attention. Our findings also suggest that the attention-based segregation of motion category-specific responses only emerges relatively late (several hundred milliseconds) in processing.

Instability of superfluid Fermi gases induced by a rotonlike density mode in optical lattices

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

Yunomae, Yoshihiro; Yamamoto, Daisuke; Danshita, Ippei

2009-12-15

We study the stability of superfluid Fermi gases in deep optical lattices in the BCS-Bose-Einstein condensation (BEC) crossover at zero temperature. Within the tight-binding attractive Hubbard model, we calculate the spectrum of the low-energy Anderson-Bogoliubov (AB) mode as well as the single-particle excitations in the presence of superfluid flow in order to determine the critical velocities. To obtain the spectrum of the AB mode, we calculate the density response function in the generalized random-phase approximation applying the Green's function formalism developed by Cote and Griffin to the Hubbard model. We find that the spectrum of the AB mode is separatedmore » from the particle-hole continuum having the characteristic rotonlike minimum at short wavelength due to the strong charge-density-wave fluctuations. The energy of the rotonlike minimum decreases with increasing the lattice velocity and it reaches zero at the critical velocity which is smaller than the pair-breaking velocity. This indicates that the superfluid state is energetically unstable due to the spontaneous emission of the short-wavelength rotonlike excitations of the AB mode instead due to pair breaking. We determine the critical velocities as functions of the interaction strength across the BCS-BEC crossover regime.« less

Effects of Dietary Supplementation with Brazil Nuts on Microvascular Endothelial Function in Hypertensive and Dyslipidemic Patients: A Randomized Crossover Placebo-Controlled Trial.

PubMed

Huguenin, Grazielle V B; Moreira, Annie S B; Siant'Pierre, Tatiana D; Gonçalves, Rodrigo A; Rosa, Glorimar; Oliveira, Glaucia M M; Luiz, Ronir R; Tibirica, Eduardo

2015-11-01

To investigate the effects of dietary supplementation with GBNs on microvascular endothelial function in hypertensive and dyslipidemic patients. Ninety-one patients of both sexes aged 62.1 ± 9.3 years received 13 g/day of GBNs or a placebo for three months with a washout period of one month between treatments. Microvascular endothelial function was assessed using LSCI coupled with iontophoresis of ACh and PORH. We also used skin video capillaroscopy to measure capillary density and recruitment at rest and during PORH. Plasma concentrations of NOx were also measured as a marker of nitric oxide bioavailability. Supplementation with GBNs significantly increased the plasma levels of Se (p < 0.05) and NOx (p < 0.05). However, we did not observe any effects of GBN consumption on microvascular vasodilator responses to ACh or PORH (p > 0.05), and GBNs did not improve capillary density at baseline or recruitment during PORH (p > 0.05). Supplementation with GBNs induced significant increases in the plasma Se concentration and systemic bioavailability of nitric oxide. Nevertheless, GBN supplementation did not lead to any improvement in systemic microvascular reactivity or density in patients with arterial hypertension and dyslipidemia who were undergoing multiple drug therapies. © 2015 John Wiley & Sons Ltd.

Electronic properties of B and Al doped graphane: A hybrid density functional study

NASA Astrophysics Data System (ADS)

Mapasha, R. E.; Igumbor, E.; Andriambelaza, N. F.; Chetty, N.

2018-04-01

Using a hybrid density functional theory approach parametrized by Heyd, Scuseria and Ernzerhof (HSE06 hybrid functional), we study the energetics, structural and electronic properties of a graphane monolayer substitutionally doped with the B (BCH) and Al (AlCH) atoms. The BCH defect can be integrated within a graphane monolayer at a relative low formation energy, without major structural distortions and symmetry breaking. The AlCH defect relaxes outward of the monolayer and breaks the symmetry. The density of states plots indicate that BCH doped graphane monolayer is a wide band gap semiconductor, whereas the AlCH defect introduces the spin dependent mid gap states at the vicinity of the Fermi level, revealing a metallic character with the pronounced magnetic features. We further examine the response of the Al dependent spin states on the multiple charge states doping. We find that the defect formation energy, structural and electronic properties can be altered via charge state modulation. The +1 charge doping opens an energy band gap of 1.75 eV. This value corresponds to the wavelength in the visible spectrum, suggesting an ideal material for solar cell absorbers. Our study fine tunes the graphane band gap through the foreign atom doping as well as via defect charge state modulation.

Statistical analysis of the electrocatalytic activity of Pt nanoparticles supported on novel functionalized reduced graphene oxide-chitosan for methanol electrooxidation

NASA Astrophysics Data System (ADS)

Ekrami-Kakhki, Mehri-Saddat; Abbasi, Sedigheh; Farzaneh, Nahid

2018-01-01

The purpose of this study is to statistically analyze the anodic current density and peak potential of methanol oxidation at Pt nanoparticles supported on functionalized reduced graphene oxide (RGO), using design of experiments methodology. RGO is functionalized with methyl viologen (MV) and chitosan (CH). The novel Pt/MV-RGO-CH catalyst is successfully prepared and characterized with transmission electron microscopy (TEM) image. The electrocatalytic activity of Pt/MV-RGOCH catalyst is experimentally evaluated for methanol oxidation. The effects of methanol concentration and scan rate factors are also investigated experimentally and statistically. The effects of these two main factors and their interactions are investigated, using analysis of variance test, Duncan's multiple range test and response surface method. The results of the analysis of variance show that all the main factors and their interactions have a significant effect on anodic current density and peak potential of methanol oxidation at α = 0.05. The suggested models which encompass significant factors can predict the variation of the anodic current density and peak potential of methanol oxidation. The results of Duncan's multiple range test confirmed that there is a significant difference between the studied levels of the main factors. [Figure not available: see fulltext.

Climate and species functional traits influence maximum live tree stocking in the Lake States, USA

Treesearch

Mark J. Ducey; Christopher W. Woodall; Andrés Bravo-Oviedo

2017-01-01

Quantifying the density of live trees in forest stands and partitioning it between species or other stand components is critical for predicting forest dynamics and responses to management, as well as understanding the impacts of stand composition and structure on productivity. As plant traits such as shade tolerance have been proven to refine understanding of plant...

Introduction to Flight Test Engineering (Introduction aux techniques des essais en vol)

DTIC Science & Technology

2005-07-01

or aircraft parameters • Calculations in the frequency domain ( Fast Fourier Transform) • Data analysis with dedicated software for: • Signal...density Fast Fourier Transform Transfer function analysis Frequency response analysis Etc. PRESENTATION Color/black & white Display screen...envelope by operating the airplane at increasing ranges - representing increasing risk - of engine operation, airspeeds both fast and slow, altitude

Identification of natural frequencies and modal damping ratios of aerospace structures from response data

NASA Technical Reports Server (NTRS)

Michalopoulos, C. D.

1976-01-01

An analysis of one and multidegree of freedom systems with classical damping is presented. Definition and minimization of error functions for each system are discussed. Systems with classical and nonclassical normal modes are studied, and results for first order perturbation are given. An alternative method of matching power spectral densities is provided, and numerical results are reviewed.

Electrical brain activity and response to olanzapine in schizophrenia: a study with LORETA images of P300.

PubMed

Sumiyoshi, Tomiki; Higuchi, Yuko; Kawasaki, Yasuhiro; Matsui, Mie; Kato, Kanade; Yuuki, Hiromi; Arai, Hirofumi; Kurachi, Masayoshi

2006-09-30

The aim of this study was to evaluate the change in the distribution for the P300 generator, as demonstrated by Low Resolution Electromagnetic Tomography (LORETA) images, in patients with schizophrenia during treatment with olanzapine. Data were obtained from five right-handed patients treated with olanzapine for 6 months. Five right-handed normal volunteers also participated in the study. LORETA images of P300 in response to the odd-ball auditory discrimination task revealed a left dominant lateralized high current source density in the temporal lobes in all control subjects. Although this pattern of brain activation was not evident in patients at baseline, 6-month treatment with olanzapine recovered the left dominant pattern of the electrical density in the temporal regions, such as the Heschl gyrus, and improved performance on a test of verbal learning and memory. Scores of the Brief Psychiatric Rating Scale and the Global Assessment of Functioning Scale also improved during treatment. These results provide the first suggestion that enhancement of verbal memory and the functional status by treatment with some antipsychotic drugs may be associated with modulations of the anatomical configuration of electrical brain activity in patients with schizophrenia.

Accelerating molecular property calculations with nonorthonormal Krylov space methods

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

Furche, Filipp; Krull, Brandon T.; Nguyen, Brian D.

Here, we formulate Krylov space methods for large eigenvalue problems and linear equation systems that take advantage of decreasing residual norms to reduce the cost of matrix-vector multiplication. The residuals are used as subspace basis without prior orthonormalization, which leads to generalized eigenvalue problems or linear equation systems on the Krylov space. These nonorthonormal Krylov space (nKs) algorithms are favorable for large matrices with irregular sparsity patterns whose elements are computed on the fly, because fewer operations are necessary as the residual norm decreases as compared to the conventional method, while errors in the desired eigenpairs and solution vectors remainmore » small. We consider real symmetric and symplectic eigenvalue problems as well as linear equation systems and Sylvester equations as they appear in configuration interaction and response theory. The nKs method can be implemented in existing electronic structure codes with minor modifications and yields speed-ups of 1.2-1.8 in typical time-dependent Hartree-Fock and density functional applications without accuracy loss. The algorithm can compute entire linear subspaces simultaneously which benefits electronic spectra and force constant calculations requiring many eigenpairs or solution vectors. The nKs approach is related to difference density methods in electronic ground state calculations, and particularly efficient for integral direct computations of exchange-type contractions. By combination with resolution-of-the-identity methods for Coulomb contractions, three- to fivefold speed-ups of hybrid time-dependent density functional excited state and response calculations are achieved.« less

Accelerating molecular property calculations with nonorthonormal Krylov space methods

DOE PAGES

Furche, Filipp; Krull, Brandon T.; Nguyen, Brian D.; ...

2016-05-03

Here, we formulate Krylov space methods for large eigenvalue problems and linear equation systems that take advantage of decreasing residual norms to reduce the cost of matrix-vector multiplication. The residuals are used as subspace basis without prior orthonormalization, which leads to generalized eigenvalue problems or linear equation systems on the Krylov space. These nonorthonormal Krylov space (nKs) algorithms are favorable for large matrices with irregular sparsity patterns whose elements are computed on the fly, because fewer operations are necessary as the residual norm decreases as compared to the conventional method, while errors in the desired eigenpairs and solution vectors remainmore » small. We consider real symmetric and symplectic eigenvalue problems as well as linear equation systems and Sylvester equations as they appear in configuration interaction and response theory. The nKs method can be implemented in existing electronic structure codes with minor modifications and yields speed-ups of 1.2-1.8 in typical time-dependent Hartree-Fock and density functional applications without accuracy loss. The algorithm can compute entire linear subspaces simultaneously which benefits electronic spectra and force constant calculations requiring many eigenpairs or solution vectors. The nKs approach is related to difference density methods in electronic ground state calculations, and particularly efficient for integral direct computations of exchange-type contractions. By combination with resolution-of-the-identity methods for Coulomb contractions, three- to fivefold speed-ups of hybrid time-dependent density functional excited state and response calculations are achieved.« less

An accurate cost effective DFT approach to study the sensing behaviour of polypyrrole towards nitrate ions in gas and aqueous phases.

PubMed

Wasim, Fatima; Mahmood, Tariq; Ayub, Khurshid

2016-07-28

Density functional theory (DFT) calculations have been performed to study the response of polypyrrole towards nitrate ions in gas and aqueous phases. First, an accurate estimate of interaction energies is obtained by methods calibrated against the gold standard CCSD(T) method. Then, a number of low cost DFT methods are also evaluated for their ability to accurately estimate the binding energies of polymer-nitrate complexes. The low cost methods evaluated here include dispersion corrected potential (DCP), Grimme's D3 correction, counterpoise correction of the B3LYP method, and Minnesota functionals (M05-2X). The interaction energies calculated using the counterpoise (CP) correction and DCP methods at the B3LYP level are in better agreement with the interaction energies calculated using the calibrated methods. The interaction energies of an infinite polymer (polypyrrole) with nitrate ions are calculated by a variety of low cost methods in order to find the associated errors. The electronic and spectroscopic properties of polypyrrole oligomers nPy (where n = 1-9) and nPy-NO3(-) complexes are calculated, and then extrapolated for an infinite polymer through a second degree polynomial fit. Charge analysis, frontier molecular orbital (FMO) analysis and density of state studies also reveal the sensing ability of polypyrrole towards nitrate ions. Interaction energies, charge analysis and density of states analyses illustrate that the response of polypyrrole towards nitrate ions is considerably reduced in the aqueous medium (compared to the gas phase).

Determining Concentration of Nanoparticles from Ellipsometry

NASA Technical Reports Server (NTRS)

Venkatasubbarao, Srivatsa; Kempen, Lothar U.; Chipman, Russell

2008-01-01

A method of using ellipsometry or polarization analysis of light in total internal reflection of a surface to determine the number density of gold nanoparticles on a smooth substrate has been developed. The method can be modified to enable determination of densities of sparse distributions of nanoparticles in general, and is expected to be especially useful for measuring gold-nanoparticle-labeled biomolecules on microarrays. The method is based on theoretical calculations of the ellipsometric responses of gold nanoparticles. Elements of the calculations include the following: For simplicity, the gold nanoparticles are assumed to be spherical and to have the same radius. The distribution of gold nanoparticles is assumed to be a sub-monolayer (that is, sparser than a monolayer). The optical response of the sub-monolayer is modeled by use of a thin-island-film theory, according to which the polarizabilities parallel and perpendicular to the substrate are functions of the wavelength of light, the dielectric functions (permittivities expressed as complex functions of frequency or wavelength) of the gold and the suspending medium (in this case, the suspending medium is air), the fraction of the substrate area covered by the nanoparticles, and the radius of the nanoparticles. For the purpose of the thin-island-film theory, the dielectric function of the gold nanoparticles is modeled as the known dielectric function of bulk gold plus a correction term that is necessitated by the fact that the mean free path length for electrons in gold decreases with decreasing radius, in such a manner as to cause the imaginary part of the dielectric function to increase with decreasing radius (see figure). The correction term is a function of the nanoparticle radius, the wavelength of light, the mean free path and the Fermi speed of electrons in bulk gold, the plasma frequency of gold, and the speed of light in a vacuum. These models are used to calculate ellipsometric responses for various concentrations of gold nanoparticles having an assumed radius. The modeled data indicates distinct spectral features for both the real and the imaginary part of the dielectric function. An ellipsometric measurement would determine this distinct feature and thus can be used to measure nanoparticle concentration. By "ellipsometric responses" is meant the intensities of light measured in various polarization states as functions of the angle of incidence and the polarization states of the incident light. These calculated ellipsometric responses are used as calibration curves: Data from subsequent ellipsometric measurements on real specimens are compared with the calibration curves. The concentration of the nanoparticles on a specimen is assumed to be that of the calibration curve that most closely matches the data pertaining to that specimen.

A note on the accuracy of KS-DFT densities

NASA Astrophysics Data System (ADS)

Ranasinghe, Duminda S.; Perera, Ajith; Bartlett, Rodney J.

2017-11-01

The accuracy of the density of wave function methods and Kohn-Sham (KS) density functionals is studied using moments of the density, ⟨rn ⟩ =∫ ρ (r )rnd τ =∫0∞4 π r2ρ (r ) rnd r ,where n =-1 ,-2,0,1,2 ,and 3 provides information about the short- and long-range behavior of the density. Coupled cluster (CC) singles, doubles, and perturbative triples (CCSD(T)) is considered as the reference density. Three test sets are considered: boron through neon neutral atoms, two and four electron cations, and 3d transition metals. The total density and valence only density are distinguished by dropping appropriate core orbitals. Among density functionals tested, CAMQTP00 and ωB97x show the least deviation for boron through neon neutral atoms. They also show accurate eigenvalues for the HOMO indicating that they should have a more correct long-range behavior for the density. For transition metals, some density functional approximations outperform some wave function methods, suggesting that the KS determinant could be a better starting point for some kinds of correlated calculations. By using generalized many-body perturbation theory (MBPT), the convergence of second-, third-, and fourth-order KS-MBPT for the density is addressed as it converges to the infinite-order coupled cluster result. For the transition metal test set, the deviations in the KS density functional theory methods depend on the amount of exact exchange the functional uses. Functionals with exact exchange close to 25% show smaller deviations from the CCSD(T) density.

Functional response and capture timing in an individual-based model: predation by northern squawfish (Ptychocheilus oregonensis) on juvenile salmonids in the Columbia River

USGS Publications Warehouse

Petersen, James H.; DeAngelis, Donald L.

1992-01-01

The behavior of individual northern squawfish (Ptychocheilus oregonensis) preying on juvenile salmonids was modeled to address questions about capture rate and the timing of prey captures (random versus contagious). Prey density, predator weight, prey weight, temperature, and diel feeding pattern were first incorporated into predation equations analogous to Holling Type 2 and Type 3 functional response models. Type 2 and Type 3 equations fit field data from the Columbia River equally well, and both models predicted predation rates on five of seven independent dates. Selecting a functional response type may be complicated by variable predation rates, analytical methods, and assumptions of the model equations. Using the Type 2 functional response, random versus contagious timing of prey capture was tested using two related models. ln the simpler model, salmon captures were assumed to be controlled by a Poisson renewal process; in the second model, several salmon captures were assumed to occur during brief "feeding bouts", modeled with a compound Poisson process. Salmon captures by individual northern squawfish were clustered through time, rather than random, based on comparison of model simulations and field data. The contagious-feeding result suggests that salmonids may be encountered as patches or schools in the river.

The effect of temperature on the functional response of Phytoseiulus persimilis (Acari: Phytoseiidae).

PubMed

Skirvin, David J; Fenlon, John S

2003-01-01

Environmental variables, such as temperature, are important in determining the efficiency of biological control in ornamental crops. This paper examines the effect of temperature on the functional response of adult female Phytoseiulus persimilis to eggs of the spider mite, Tetranychus urticae. The functional response was determined using a new functional response assay technique with plant stems as an arena, rather than leaf discs. The use of plant stems allows the influence that plant structure has on predation to be incorporated into the assay. Control assays were also used (without predators) to estimate natural losses of prey. The data were analysed using a binomial model, with the use of Abbot's formula to correct for the losses in the controls. A combined equation to describe the effect of temperature and prey density on the predation rate of Phytoseiulus persimilis was derived. The results showed that more prey are eaten as the temperature increases from 15 degrees C to 25 degrees C, but the number of prey eaten then declines at 30 degrees C, although not to the levels seen at 20 degrees C. The implication of these results for biological control in ornamental crops, where the temperature can often exceed 30 degrees C, is discussed.

A new approach for the calculation of response spectral density of a linear stationary random multidegree of freedom system

NASA Astrophysics Data System (ADS)

Sharan, A. M.; Sankar, S.; Sankar, T. S.

1982-08-01

A new approach for the calculation of response spectral density for a linear stationary random multidegree of freedom system is presented. The method is based on modifying the stochastic dynamic equations of the system by using a set of auxiliary variables. The response spectral density matrix obtained by using this new approach contains the spectral densities and the cross-spectral densities of the system generalized displacements and velocities. The new method requires significantly less computation time as compared to the conventional method for calculating response spectral densities. Two numerical examples are presented to compare quantitatively the computation time.

Linearly exact parallel closures for slab geometry

NASA Astrophysics Data System (ADS)

Ji, Jeong-Young; Held, Eric D.; Jhang, Hogun

2013-08-01

Parallel closures are obtained by solving a linearized kinetic equation with a model collision operator using the Fourier transform method. The closures expressed in wave number space are exact for time-dependent linear problems to within the limits of the model collision operator. In the adiabatic, collisionless limit, an inverse Fourier transform is performed to obtain integral (nonlocal) parallel closures in real space; parallel heat flow and viscosity closures for density, temperature, and flow velocity equations replace Braginskii's parallel closure relations, and parallel flow velocity and heat flow closures for density and temperature equations replace Spitzer's parallel transport relations. It is verified that the closures reproduce the exact linear response function of Hammett and Perkins [Phys. Rev. Lett. 64, 3019 (1990)] for Landau damping given a temperature gradient. In contrast to their approximate closures where the vanishing viscosity coefficient numerically gives an exact response, our closures relate the heat flow and nonvanishing viscosity to temperature and flow velocity (gradients).

Sublethal Dosage of Imidacloprid Reduces the Microglomerular Density of Honey Bee Mushroom Bodies

PubMed Central

Peng, Yi-Chan; Yang, En-Cheng

2016-01-01

The dramatic loss of honey bees is a major concern worldwide. Previous studies have indicated that neonicotinoid insecticides cause behavioural abnormalities and have proven that exposure to sublethal doses of imidacloprid during the larval stage decreases the olfactory learning ability of adults. The present study shows the effect of sublethal doses of imidacloprid on the neural development of the honey bee brain by immunolabelling synaptic units in the calyces of mushroom bodies. We found that the density of the synaptic units in the region of the calyces, which are responsible for olfactory and visual functions, decreased after being exposed to a sublethal dose of imidacloprid. This not only links a decrease in olfactory learning ability to abnormal neural connectivity but also provides evidence that imidacloprid damages the development of the nervous system in regions responsible for both olfaction and vision during the larval stage of the honey bee. PMID:26757950

Differential Location and Distribution of Hepatic Immune Cells

PubMed Central

Freitas-Lopes, Maria Alice; Mafra, Kassiana; David, Bruna A.; Carvalho-Gontijo, Raquel; Menezes, Gustavo B.

2017-01-01

The liver is one of the main organs in the body, performing several metabolic and immunological functions that are indispensable to the organism. The liver is strategically positioned in the abdominal cavity between the intestine and the systemic circulation. Due to its location, the liver is continually exposed to nutritional insults, microbiota products from the intestinal tract, and to toxic substances. Hepatocytes are the major functional constituents of the hepatic lobes, and perform most of the liver’s secretory and synthesizing functions, although another important cell population sustains the vitality of the organ: the hepatic immune cells. Liver immune cells play a fundamental role in host immune responses and exquisite mechanisms are necessary to govern the density and the location of the different hepatic leukocytes. Here we discuss the location of these pivotal cells within the different liver compartments, and how their frequency and tissular location can dictate the fate of liver immune responses. PMID:29215603

Segmentation Algorithms for Detection of Targets in IR Imagery (Algorithmes de Segmentation pour la Detection de Cibles sur Images IR),

DTIC Science & Technology

1981-01-01

This fact being established, leptokurtic and platykurtic density functions are defined in terms of deviations from the normal density function. Thus...the usual definitions (Ref. 6) are: Leptokurtic - A density function that is peaked, K > 0, [18] and Platykurtic - A density function that is flat, K...has long Deen accepted that a symmetrical platykurtic density function, with K<O, is characterized by a flatter top and more abrupt terminals than the

Electrochemical Implications of Defects in Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Hall, Jonathan Peter

The electrochemical behavior of carbon nanotubes (CNTs) containing both intrinsic and extrinsically introduced defects has been investigated through the study of bamboo and hollow multi-walled CNT morphologies. The controlled addition of argon, hydrogen, and chlorine ions in addition to atomic hydrogen and magnesium vapor was used for varying the charge and type of extrinsic defects. To quantify changes in the CNTs upon treatment, Raman spectroscopy and electrochemical techniques were employed. It was indicated from Raman spectroscopy, cyclic voltammetry, electrochemical impedance spectroscopy, and chronopotentiometric experiments that the electrochemical response of hollow type CNTs could be tailored more significantly compared to bamboo type CNTs, which have innately high reactive site densities and are less amenable to modification. Total defect density and edge-plane-like defect concentrations monitored through Raman spectroscopy were used to correlate changes in the electrochemical response of the CNT electrodes as a function of treatment. The implementation of CNT electrodes in a prototypical electrolytic capacitor device was then explored and characterized. Dependencies on source current and redox couple concentration were evaluated, as well as changes in the total capacitance as a function of treatment. Cyclability studies were also performed as a function of source current magnitude to evaluate the longevity of the faradaic currents which typically decrease over time in other similar capacitors. This thesis then concludes with an overall summary of the themes and findings of the research presented in this work.

Centella asiatica increases hippocampal synaptic density and improves memory and executive function in aged mice.

PubMed

Gray, Nora E; Zweig, Jonathan A; Caruso, Maya; Martin, Marjoen D; Zhu, Jennifer Y; Quinn, Joseph F; Soumyanath, Amala

2018-06-19

Centella asiatica is a plant used for centuries to enhance memory. We have previously shown that a water extract of Centella asiatica (CAW) attenuates age-related spatial memory deficits in mice and improves neuronal health. Yet the effect of CAW on other cognitive domains remains unexplored as does its mechanism of improving age-related cognitive impairment. This study investigates the effects of CAW on a variety of cognitive tasks as well as on synaptic density and mitochondrial and antioxidant pathways. Twenty-month-old CB6F1 mice were treated with CAW (2 mg/ml) in their drinking water for 2 weeks prior to behavioral testing. Learning, memory, and executive function were assessed using the novel object recognition task (NORT), object location memory task (OLM), and odor discrimination reversal learning (ODRL) test. Tissue was collected for Golgi analysis of spine density as well as assessment of mitochondrial, antioxidant, and synaptic proteins. CAW improved performance in all behavioral tests suggesting effects on hippocampal and cortical dependent memory as well as on prefrontal cortex mediated executive function. There was also an increase in synaptic density in the treated animals, which was accompanied by increased expression of the antioxidant response gene NRF2 as well as the mitochondrial marker porin. These data show that CAW can increase synaptic density as well as antioxidant and mitochondrial proteins and improve multiple facets of age-related cognitive impairment. Because mitochondrial dysfunction and oxidative stress also accompany cognitive impairment in many pathological conditions this suggests a broad therapeutic utility of CAW. © 2018 The Authors. Brain and Behavior published by Wiley Periodicals, Inc.

Analysis of photographic X-ray images. [S-054 telescope on Skylab

NASA Technical Reports Server (NTRS)

Krieger, A. S.

1977-01-01

Some techniques used to extract quantitative data from the information contained in photographic images produced by grazing incidence soft X-ray optical systems are described. The discussion is focussed on the analysis of the data returned by the S-054 X-Ray Spectrographic Telescope Experiment on Skylab. The parameters of the instrument and the procedures used for its calibration are described. The technique used to convert photographic density to focal plane X-ray irradiance is outlined. The deconvolution of the telescope point response function from the image data is discussed. Methods of estimating the temperature, pressure, and number density of coronal plasmas are outlined.

Biochemical, histological and behavioural aspects of visual function during early development of rainbow trout

USGS Publications Warehouse

Carvalho, Paulo S. M.; Noltie, Douglas B.; Tillitt, D.E.

2004-01-01

Retinal structure and concentration of retinoids involved in phototransduction changed during early development of rainbow trout Oncorhynchus mykiss, correlating with improvements in visual function. A test chamber was used to evaluate the presence of optokinetic or optomotor responses and to assess the functionality of the integrated cellular, physiological and biochemical components of the visual system. The results indicated that in rainbow trout optomotor responses start at 10 days post-hatch, and demonstrated for the first time that increases in acuity, sensitivity to low light as well as in motion detection abilities occur from this stage until exogenous feeding starts. The structure of retinal cells such as cone ellipsoids increased in length as photopic visual acuity improved, and rod densities increased concurrently with improvements in scotopic thresholds (2.2 log10 units). An increase in the concentrations of the chromophore all-trans-retinal correlated with improvements of all behavioural measures of visual function during the same developmental phase. ?? 2004 The Fisheries Society of the British Isles.

Efficient Methods of Estimating the Operating Characteristics of Item Response Categories and Challenge to a New Model for the Multiple-Choice Item

DTIC Science & Technology

1981-11-01

i very little effort has been put upon the model validation, which is essential in any scientific research. T’-- -rientation we aim at in the present...better than the former to the target function. This implies that, although the interval of ability e of our interest is even a little smaller than [-3.0...approaches turned out to be similar, with some deviations, i.e., some of them are a little closer to the theoretical density function, and some of

Large isosymmetric reorientation of oxygen octahedra rotation axes in epitaxially strained perovskites.

PubMed

Rondinelli, James M; Coh, Sinisa

2011-06-10

Using first-principles density functional theory calculations, we discover an anomalously large biaxial strain-induced octahedral rotation axis reorientation in orthorhombic perovskites with tendency towards rhombohedral symmetry. The transition between crystallographically equivalent (isosymmetric) structures with different octahedral rotation magnitudes originates from strong strain-octahedral rotation coupling available to perovskites and the energetic hierarchy among competing octahedral tilt patterns. By elucidating these criteria, we suggest many functional perovskites would exhibit the transition in thin film form, thus offering a new landscape in which to tailor highly anisotropic electronic responses.

Light-driven liquid microlenses

NASA Astrophysics Data System (ADS)

Angelini, A.; Pirani, F.; Frascella, F.; Ricciardi, S.; Descrovi, E.

2017-02-01

We propose a liquid polymeric compound based on photo-responsive azo-polymers to be used as light-activated optical element with tunable and reversible functionalities. The interaction of a laser beam locally modifies the liquid density thus producing a refractive index gradient. The laser induced refractive index profiles are observed along the optical axis of the microscope to evaluate the total phase shift induced and along the orthogonal direction to provide the axial distribution of the refractive index variation. The focusing and imaging properties of the liquid lenses as functions of the light intensity are illustrated.

Comparing ab initio density-functional and wave function theories: the impact of correlation on the electronic density and the role of the correlation potential.

PubMed

Grabowski, Ireneusz; Teale, Andrew M; Śmiga, Szymon; Bartlett, Rodney J

2011-09-21

The framework of ab initio density-functional theory (DFT) has been introduced as a way to provide a seamless connection between the Kohn-Sham (KS) formulation of DFT and wave-function based ab initio approaches [R. J. Bartlett, I. Grabowski, S. Hirata, and S. Ivanov, J. Chem. Phys. 122, 034104 (2005)]. Recently, an analysis of the impact of dynamical correlation effects on the density of the neon atom was presented [K. Jankowski, K. Nowakowski, I. Grabowski, and J. Wasilewski, J. Chem. Phys. 130, 164102 (2009)], contrasting the behaviour for a variety of standard density functionals with that of ab initio approaches based on second-order Møller-Plesset (MP2) and coupled cluster theories at the singles-doubles (CCSD) and singles-doubles perturbative triples [CCSD(T)] levels. In the present work, we consider ab initio density functionals based on second-order many-body perturbation theory and coupled cluster perturbation theory in a similar manner, for a range of small atomic and molecular systems. For comparison, we also consider results obtained from MP2, CCSD, and CCSD(T) calculations. In addition to this density based analysis, we determine the KS correlation potentials corresponding to these densities and compare them with those obtained for a range of ab initio density functionals via the optimized effective potential method. The correlation energies, densities, and potentials calculated using ab initio DFT display a similar systematic behaviour to those derived from electronic densities calculated using ab initio wave function theories. In contrast, typical explicit density functionals for the correlation energy, such as VWN5 and LYP, do not show behaviour consistent with this picture of dynamical correlation, although they may provide some degree of correction for already erroneous explicitly density-dependent exchange-only functionals. The results presented here using orbital dependent ab initio density functionals show that they provide a treatment of exchange and correlation contributions within the KS framework that is more consistent with traditional ab initio wave function based methods.

Multiconfiguration pair-density functional theory: barrier heights and main group and transition metal energetics.

PubMed

Carlson, Rebecca K; Li Manni, Giovanni; Sonnenberger, Andrew L; Truhlar, Donald G; Gagliardi, Laura

2015-01-13

Kohn-Sham density functional theory, resting on the representation of the electronic density and kinetic energy by a single Slater determinant, has revolutionized chemistry, but for open-shell systems, the Kohn-Sham Slater determinant has the wrong symmetry properties as compared to an accurate wave function. We have recently proposed a theory, called multiconfiguration pair-density functional theory (MC-PDFT), in which the electronic kinetic energy and classical Coulomb energy are calculated from a multiconfiguration wave function with the correct symmetry properties, and the rest of the energy is calculated from a density functional, called the on-top density functional, that depends on the density and the on-top pair density calculated from this wave function. We also proposed a simple way to approximate the on-top density functional by translation of Kohn-Sham exchange-correlation functionals. The method is much less expensive than other post-SCF methods for calculating the dynamical correlation energy starting with a multiconfiguration self-consistent-field wave function as the reference wave function, and initial tests of the theory were quite encouraging. Here, we provide a broader test of the theory by applying it to bond energies of main-group molecules and transition metal complexes, barrier heights and reaction energies for diverse chemical reactions, proton affinities, and the water dimerization energy. Averaged over 56 data points, the mean unsigned error is 3.2 kcal/mol for MC-PDFT, as compared to 6.9 kcal/mol for Kohn-Sham theory with a comparable density functional. MC-PDFT is more accurate on average than complete active space second-order perturbation theory (CASPT2) for main-group small-molecule bond energies, alkyl bond dissociation energies, transition-metal-ligand bond energies, proton affinities, and the water dimerization energy.

Flexoelectricity in ATiO3 (A = Sr, Ba, Pb) perovskite oxide superlattices from density functional theory

NASA Astrophysics Data System (ADS)

Plymill, Austin; Xu, Haixuan

2018-04-01

Flexoelectric coefficients for several bulk and superlattice perovskite systems are determined using a direct approach from first principles density functional theory calculations. A strong enhancement in the longitudinal flexoelectric coefficient has been observed in the 1SrTiO3/1PbTiO3 superlattice with alternating single atomic layers of SrTiO3 and PbTiO3. It was found that atomistic displacement, charge response under strain, and interfaces affect the flexoelectric properties of perovskite superlattice systems. These factors can be used to tune this effect in dielectrics. It was further found that the calculated Born effective charge for an ion under the influence of strain can differ significantly from the bulk value. These insights can be used to help search for more effective flexoelectric materials to be implemented in electromechanical devices.

Central charge from adiabatic transport of cusp singularities in the quantum Hall effect

NASA Astrophysics Data System (ADS)

Can, Tankut

2017-04-01

We study quantum Hall (QH) states on a punctured Riemann sphere. We compute the Berry curvature under adiabatic motion in the moduli space in the large N limit. The Berry curvature is shown to be finite in the large N limit and controlled by the conformal dimension of the cusp singularity, a local property of the mean density. Utilizing exact sum rules obtained from a Ward identity, we show that for the Laughlin wave function, the dimension of a cusp singularity is given by the central charge, a robust geometric response coefficient in the QHE. Thus, adiabatic transport of curvature singularities can be used to determine the central charge of QH states. We also consider the effects of threaded fluxes and spin-deformed wave functions. Finally, we give a closed expression for all moments of the mean density in the integer QH state on a punctured disk.

Peierls potential of screw dislocations in bcc transition metals: Predictions from density functional theory

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

Weinberger, Christopher R.; Tucker, Garritt J.; Foiles, Stephen M.

2013-02-01

It is well known that screw dislocation motion dominates the plastic deformation in body-centered-cubic metals at low temperatures. The nature of the nonplanar structure of screw dislocations gives rise to high lattice friction, which results in strong temperature and strain rate dependence of plastic flow. Thus the nature of the Peierls potential, which is responsible for the high lattice resistance, is an important physical property of the material. However, current empirical potentials give a complicated picture of the Peierls potential. Here, we investigate the nature of the Peierls potential using density functional theory in the bcc transition metals. The resultsmore » show that the shape of the Peierls potential is sinusoidal for every material investigated. Furthermore, we show that the magnitude of the potential scales strongly with the energy per unit length of the screw dislocation in the material.« less

Nuclear spin relaxation due to chemical shift anisotropy of gas-phase 129Xe.

PubMed

Hanni, Matti; Lantto, Perttu; Vaara, Juha

2011-08-14

Nuclear spin relaxation provides detailed dynamical information on molecular systems and materials. Here, first-principles modeling of the chemical shift anisotropy (CSA) relaxation time for the prototypic monoatomic (129)Xe gas is carried out, both complementing and predicting the results of NMR measurements. Our approach is based on molecular dynamics simulations combined with pre-parametrized ab initio binary nuclear shielding tensors, an "NMR force field". By using the Redfield relaxation formalism, the simulated CSA time correlation functions lead to spectral density functions that, for the first time, quantitatively determine the experimental spin-lattice relaxation times T(1). The quality requirements on both the Xe-Xe interaction potential and binary shielding tensor are investigated in the context of CSA T(1). Persistent dimers Xe(2) are found to be responsible for the CSA relaxation mechanism in the low-density limit of the gas, completely in line with the earlier experimental findings.

A study of the chiro-optical properties of Carvone

NASA Astrophysics Data System (ADS)

Lambert, Jason

2011-10-01

The intrinsic optical rotatory dispersion (IORD) and circular dichroism (CD) of the conformationally flexible carvone molecule has been investigated in 17 solvents and compared with results from calculations for the ``free'' (gas phase) molecule. The G3 method was used to determine the relative energies of the six conformers. The ORD of (R)-(-)-carvone at 589 nm was calculated using coupled cluster and density-functional methods, including temperature-dependent vibrational corrections. Vibrational corrections are significant and are primarily associated with normal modes involving the stereogenic carbon atom and the carbonyl group, whose n->&*circ; excitation plays a significant role in the chiroptical response of carvone. However, without the vibrational correction the calculated ORD is of opposite sign to that of the experiment for the CCSD and B3LYP methods. Calculations performed in solution using the PCM model were also opposite in sign to of the experiment when using the B3LYP density functional.

Time-dependent broken-symmetry density functional theory simulation of the optical response of entangled paramagnetic defects: Color centers in lithium fluoride

NASA Astrophysics Data System (ADS)

Janesko, Benjamin G.

2018-02-01

Parameter-free atomistic simulations of entangled solid-state paramagnetic defects may aid in the rational design of devices for quantum information science. This work applies time-dependent density functional theory (TDDFT) embedded-cluster simulations to a prototype entangled-defect system, namely two adjacent singlet-coupled F color centers in lithium fluoride. TDDFT calculations accurately reproduce the experimental visible absorption of both isolated and coupled F centers. The most accurate results are obtained by combining spin symmetry breaking to simulate strong correlation, a large fraction of exact (Hartree-Fock-like) exchange to minimize the defect electrons' self-interaction error, and a standard semilocal approximation for dynamical correlations between the defect electrons and the surrounding ionic lattice. These results motivate application of two-reference correlated ab initio approximations to the M-center, and application of TDDFT in parameter-free simulations of more complex entangled paramagnetic defect architectures.

Simulating Valence-to-Core X-ray Emission Spectroscopy of Transition Metal Complexes with Time-Dependent Density Functional Theory.

PubMed

Zhang, Yu; Mukamel, Shaul; Khalil, Munira; Govind, Niranjan

2015-12-08

Valence-to-core (VtC) X-ray emission spectroscopy (XES) has emerged as a powerful technique for the structural characterization of complex organometallic compounds in realistic environments. Since the spectrum represents electronic transitions from the ligand molecular orbitals to the core holes of the metal centers, the approach is more chemically sensitive to the metal-ligand bonding character compared with conventional X-ray absorption techniques. In this paper we study how linear-response time-dependent density functional theory (LR-TDDFT) can be harnessed to simulate K-edge VtC X-ray emission spectra reliably. LR-TDDFT allows one to go beyond the single-particle picture that has been extensively used to simulate VtC-XES. We consider seven low- and high-spin model complexes involving chromium, manganese, and iron transition metal centers. Our results are in good agreement with experiment.

Dynamic Optical Tuning of Interlayer Interactions in the Transition Metal Dichalcogenides

DOE PAGES

Mannebach, Ehren M.; Nyby, Clara; Ernst, Friederike; ...

2017-11-09

Modulation of weak interlayer interactions between quasi-two-dimensional atomic planes in the transition metal dichalcogenides (TMDCs) provides avenues for tuning their functional properties. Here we show that above-gap optical excitation in the TMDCs leads to an unexpected large-amplitude, ultrafast compressive force between the two-dimensional layers, as probed by in situ measurements of the atomic layer spacing at femtosecond time resolution. We show that this compressive response arises from a dynamic modulation of the interlayer van der Waals interaction and that this represents the dominant light-induced stress at low excitation densities. A simple analytic model predicts the magnitude and carrier density dependencemore » of the measured strains. Furthermore, this work establishes a new method for dynamic, nonequilibrium tuning of correlation-driven dispersive interactions and of the optomechanical functionality of TMDC quasi-two-dimensional materials.« less

An ab initio molecular dynamics and density functional theory study of the formation of phosphate chains from metathiophosphates.

PubMed

Mosey, Nicholas J; Woo, Tom K

2006-09-04

The reactions that occur between metathiophosphate (MTP) molecules are identified and examined through ab initio molecular dynamics simulations and static quantum chemical calculations at the density functional level of theory. The simulations show that certain types of MTPs can react to yield phosphate chains, while others only dimerize. These differences are rationalized in terms of reaction energies and the electronic structures of these molecules. In the reaction leading to the formation of phosphate chains, the reactive center, a tri-coordinate phosphorus atom, is continually regenerated. A polymerization mechanism linking MTPs to phosphate chains is developed on the basis of these results. This information sheds light on the underlying processes that may be responsible for the formation of phosphates under high-temperature conditions and may prove useful in the development of protocols for the rational synthesis of complex phosphate structures.

Predicting elastic properties of β-HMX from first-principles calculations.

PubMed

Peng, Qing; Rahul; Wang, Guangyu; Liu, Gui-Rong; Grimme, Stefan; De, Suvranu

2015-05-07

We investigate the performance of van der Waals (vdW) functions in predicting the elastic constants of β cyclotetramethylene tetranitramine (HMX) energetic molecular crystals using density functional theory (DFT) calculations. We confirm that the accuracy of the elastic constants is significantly improved using the vdW corrections with environment-dependent C6 together with PBE and revised PBE exchange-correlation functionals. The elastic constants obtained using PBE-D3(0) calculations yield the most accurate mechanical response of β-HMX when compared with experimental stress-strain data. Our results suggest that PBE-D3 calculations are reliable in predicting the elastic constants of this material.

TD-CI simulation of the electronic optical response of molecules in intense fields II: comparison of DFT functionals and EOM-CCSD.

PubMed

Sonk, Jason A; Schlegel, H Bernhard

2011-10-27

Time-dependent configuration interaction (TD-CI) simulations can be used to simulate molecules in intense laser fields. TD-CI calculations use the excitation energies and transition dipoles calculated in the absence of a field. The EOM-CCSD method provides a good estimate of the field-free excited states but is rather expensive. Linear-response time-dependent density functional theory (TD-DFT) is an inexpensive alternative for computing the field-free excitation energies and transition dipoles needed for TD-CI simulations. Linear-response TD-DFT calculations were carried out with standard functionals (B3LYP, BH&HLYP, HSE2PBE (HSE03), BLYP, PBE, PW91, and TPSS) and long-range corrected functionals (LC-ωPBE, ωB97XD, CAM-B3LYP, LC-BLYP, LC-PBE, LC-PW91, and LC-TPSS). These calculations used the 6-31G(d,p) basis set augmented with three sets of diffuse sp functions on each heavy atom. Butadiene was employed as a test case, and 500 excited states were calculated with each functional. Standard functionals yield average excitation energies that are significantly lower than the EOM-CC, while long-range corrected functionals tend to produce average excitation energies slightly higher. Long-range corrected functionals also yield transition dipoles that are somewhat larger than EOM-CC on average. The TD-CI simulations were carried out with a three-cycle Gaussian pulse (ω = 0.06 au, 760 nm) with intensities up to 1.26 × 10(14) W cm(-2) directed along the vector connecting the end carbons. The nonlinear response as indicated by the residual populations of the excited states after the pulse is far too large with standard functionals, primarily because the excitation energies are too low. The LC-ωPBE, LC-PBE, LC-PW91, and LC-TPSS long-range corrected functionals produce responses comparable to EOM-CC.

Blocking PirB up-regulates spines and functional synapses to unlock visual cortical plasticity and facilitate recovery from amblyopia

PubMed Central

Bochner, David N.; Sapp, Richard W.; Adelson, Jaimie D.; Zhang, Siyu; Lee, Hanmi; Djurisic, Maja; Syken, Josh; Dan, Yang; Shatz, Carla J.

2015-01-01

During critical periods of development, the brain easily changes in response to environmental stimuli, but this neural plasticity declines by adulthood. By acutely disrupting paired immunoglobulin-like receptor B(PirB) function at specific ages, we show that PirB actively represses neural plasticity throughout life. We disrupted PirB function either by genetically introducing a conditional PirB allele into mice or by minipump infusion of a soluble PirB ectodomain (sPirB) into mouse visual cortex. We found that neural plasticity, as measured by depriving mice of vision in one eye and testing ocular dominance, was enhanced by this treatment both during the critical period and when PirB function was disrupted in adulthood. Acute blockade of PirB triggered the formation of new functional synapses, as indicated by increases in miniature excitatory postsynaptic current (mEPSC) frequency and spine density on dendrites of layer 5 pyramidal neurons. In addition, recovery from amblyopia— the decline in visual acuity and spine density resulting from long-term monocular deprivation— was possible after a 1-week infusion of sPirB after the deprivation period. Thus, neural plasticity in adult visual cortex is actively repressed and can be enhanced by blocking PirB function. PMID:25320232

Linear response to long wavelength fluctuations using curvature simulations

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

Baldauf, Tobias; Zaldarriaga, Matias; Seljak, Uroš

2016-09-01

We study the local response to long wavelength fluctuations in cosmological N -body simulations, focusing on the matter and halo power spectra, halo abundance and non-linear transformations of the density field. The long wavelength mode is implemented using an effective curved cosmology and a mapping of time and distances. The method provides an alternative, more direct, way to measure the isotropic halo biases. Limiting ourselves to the linear case, we find generally good agreement between the biases obtained from the curvature method and the traditional power spectrum method at the level of a few percent. We also study the responsemore » of halo counts to changes in the variance of the field and find that the slope of the relation between the responses to density and variance differs from the naïve derivation assuming a universal mass function by approximately 8–20%. This has implications for measurements of the amplitude of local non-Gaussianity using scale dependent bias. We also analyze the halo power spectrum and halo-dark matter cross-spectrum response to long wavelength fluctuations and derive second order halo bias from it, as well as the super-sample variance contribution to the galaxy power spectrum covariance matrix.« less

Screening of the aerodynamic and biophysical properties of barley malt

NASA Astrophysics Data System (ADS)

Ghodsvali, Alireza; Farzaneh, Vahid; Bakhshabadi, Hamid; Zare, Zahra; Karami, Zahra; Mokhtarian, Mohsen; Carvalho, Isabel. S.

2016-10-01

An understanding of the aerodynamic and biophysical properties of barley malt is necessary for the appropriate design of equipment for the handling, shipping, dehydration, grading, sorting and warehousing of this strategic crop. Malting is a complex biotechnological process that includes steeping; germination and finally, the dehydration of cereal grains under controlled temperature and humidity conditions. In this investigation, the biophysical properties of barley malt were predicted using two models of artificial neural networks as well as response surface methodology. Stepping time and germination time were selected as the independent variables and 1 000 kernel weight, kernel density and terminal velocity were selected as the dependent variables (responses). The obtained outcomes showed that the artificial neural network model, with a logarithmic sigmoid activation function, presents more precise results than the response surface model in the prediction of the aerodynamic and biophysical properties of produced barley malt. This model presented the best result with 8 nodes in the hidden layer and significant correlation coefficient values of 0.783, 0.767 and 0.991 were obtained for responses one thousand kernel weight, kernel density, and terminal velocity, respectively. The outcomes indicated that this novel technique could be successfully applied in quantitative and qualitative monitoring within the malting process.

Structure factor of blends of solvent-free nanoparticle-organic hybrid materials: density-functional theory and small angle X-ray scattering.

PubMed

Yu, Hsiu-Yu; Srivastava, Samanvaya; Archer, Lynden A; Koch, Donald L

2014-12-07

We investigate the static structure factor S(q) of solvent-free nanoparticle-organic hybrid materials consisting of silica nanocores and space-filling polyethylene glycol coronas using a density-functional theory and small angle X-ray scattering measurements. The theory considers a bidisperse suspension of hard spheres with different radii and tethered bead-spring oligomers with different grafting densities to approximate the polydispersity effects in experiments. The experimental systems studied include pure samples with different silica core volume fractions and the associated mean corona grafting densities, and blends with different mixing ratios of the pure samples, in order to introduce varying polydispersity of corona grafting density. Our scattering experiments and theory show that, compared to the hard-sphere suspension with the same core volume fraction, S(q) for pure samples exhibit both substantially smaller values at small q and stronger particle correlations corresponding to a larger effective hard core at large q, indicating that the tethered incompressible oligomers enforce a more uniform particle distribution, and the densely grafted brush gives rise to an additional exclusionary effect between the nanoparticles. According to the theory, polydispersity in the oligomer grafting density controls the deviation of S(q) from the monodisperse system at smaller q, and the interplay of the enhanced effective core size and the entropic attraction among the particles is responsible for complex variations in the particle correlations at larger q. The successful comparison between the predictions and the measurements for the blends further suggests that S(q) can be used to assess the uniformity of grafting density in polymer-grafted nanoparticle materials.

Relationship between masticatory function and internal structure of the mandible based on computed tomography findings.

PubMed

Sato, Hidemasa; Kawamura, Akira; Yamaguchi, Masaru; Kasai, Kazutaka

2005-12-01

The purposes of this study were to investigate bone mineral density as a part of bone construction in human skulls and to examine the relationship between dentofacial morphology and masticatory function by using computed tomography (CT) findings. Changes in bone mineral density in the mandible because of loss of masticatory function were tested in rats by experimentally producing an environment that inhibited mastication by the molars. Data for the human study were obtained from 27 modern male Japanese skulls (mean age, 28 years) from the University of Tokyo. Cortical bone thickness (CBT) and CT value (CV) were measured by each CT scan of the first and molars. For the animal study, a metal cap was inserted between the maxillary and mandibular incisors to prevent the molars from biting in 6-week-old male Wistar rats. The rats were killed after 2, 4, or 6 weeks, and bone mineral density was measured in cancellous and cortical bone equivalent to the first molar region by using peripheral quantitative computed tomography. In the human skull study, significant negative correlations were observed between CV in the regions of the buccal side of the second molar and the angle between the Frankfort horizontal and mandibular planes. Significant negative correlations were also observed between the gonial angle and CV in the buccal and basal sides. In the animal study, cancellous bone mineral density began to decline 4 weeks after the start of the experiment in the masticatory hypofunction group compared with the control group. By week 6, cancellous bone density had declined by 11.6% on the buccal side, 16.7% on the lingual side, 12.3% at the bifurcation of the root, and 38.1% at the root apex. Cortical bone density declined by 8% to 12% on the lingual side. The results support our hypothesis that a functional adaptive response by the mandible to mechanical stress resulting from mastication occurs not only in the muscle insertion area, but also in mandibular alveolar bone in the molar region.

Quantum Kramers model: Corrections to the linear response theory for continuous bath spectrum

NASA Astrophysics Data System (ADS)

Rips, Ilya

2017-01-01

Decay of the metastable state is analyzed within the quantum Kramers model in the weak-to-intermediate dissipation regime. The decay kinetics in this regime is determined by energy exchange between the unstable mode and the stable modes of thermal bath. In our previous paper [Phys. Rev. A 42, 4427 (1990), 10.1103/PhysRevA.42.4427], Grabert's perturbative approach to well dynamics in the case of the discrete bath [Phys. Rev. Lett. 61, 1683 (1988), 10.1103/PhysRevLett.61.1683] has been extended to account for the second order terms in the classical equations of motion (EOM) for the stable modes. Account of the secular terms reduces EOM for the stable modes to those of the forced oscillator with the time-dependent frequency (TDF oscillator). Analytic expression for the characteristic function of energy loss of the unstable mode has been derived in terms of the generating function of the transition probabilities for the quantum forced TDF oscillator. In this paper, the approach is further developed and applied to the case of the continuous frequency spectrum of the bath. The spectral density functions of the bath of stable modes are expressed in terms of the dissipative properties (the friction function) of the original bath. They simplify considerably for the one-dimensional systems, when the density of phonon states is constant. Explicit expressions for the fourth order corrections to the linear response theory result for the characteristic function of the energy loss and its cumulants are obtained for the particular case of the cubic potential with Ohmic (Markovian) dissipation. The range of validity of the perturbative approach in this case is determined (γ /ωb<0.26 ), which includes the turnover region. The dominant correction to the linear response theory result is associated with the "work function" and leads to reduction of the average energy loss and its dispersion. This reduction increases with the increasing dissipation strength (up to ˜10 % ) within the range of validity of the approach. We have also calculated corrections to the depopulation factor and the escape rate for the quantum and for the classical Kramers models. Results for the classical escape rate are in very good agreement with the numerical simulations for high barriers. The results can serve as an additional proof of the robustness and accuracy of the linear response theory.