Two complementary molecular energy decomposition schemes: the Mayer and Ziegler-Rauk methods in comparison

In the present paper we discuss and compare two different energy decomposition schemes: Mayer's Hartree-Fock energy decomposition into diatomic and monoatomic contributions [Chem. Phys. Lett. 382, 265 (2003)], and the Ziegler-Rauk dissociation energy decomposition [Inorg. Chem. 18, 1558 (1979)]. The Ziegler-Rauk scheme is based on a separation of a molecule into fragments, while Mayer's scheme can be used in the cases where a fragmentation of the system in clearly separable parts is not possible. In the Mayer scheme, the density of a free atom is deformed to give the one-atom Mulliken density that subsequently interacts to give rise to the diatomic interaction energy. We give a detailed analysis of the diatomic energy contributions in the Mayer scheme and a close look onto the one-atom Mulliken densities. The Mulliken density ρA has a single large maximum around the nuclear position of the atom A, but exhibits slightly negative values in the vicinity of neighboring atoms. The main connecting point between both analysis schemes is the electrostatic energy. Both decomposition schemes utilize the same electrostatic energy expression, but differ in how fragment densities are defined. In the Mayer scheme, the electrostatic component originates from the interaction of the Mulliken densities, while in the Ziegler-Rauk scheme, the undisturbed fragment densities interact. The values of the electrostatic energy resulting from the two schemes differ significantly but typically have the same order of magnitude. Both methods are useful and complementary since Mayer's decomposition focuses on the energy of the finally formed molecule, whereas the Ziegler-Rauk scheme describes the bond formation starting from undeformed fragment densities

Slopes of Avian Species-Area Relationships, Human Population Density, and Environmental Factors

There is increasing interest in how humans influence spatial patterns in biodiversity. One of the most frequently noted and marked of these patterns is the increase in species richness with area, the species–area relationship (SAR). SARs are used for a number of conservation purposes, including predicting extinction rates, setting conservation targets, and identifying biodiversity hotspots. Such applications can be improved by a detailed understanding of the factors promoting spatial variation in the slope of SARs, which is currently the subject of a vigorous debate. Moreover, very few studies have considered the anthropogenic influences on the slopes of SARs; this is particularly surprising given that in much of the world areas with high human population density are typically those with a high number of species, which generates conservation conflicts. Here we determine correlates of spatial variation in the slopes of species–area relationships, using the British avifauna as a case study. Whilst we focus on human population density, a widely used index of human activities, we also take into account (1) the rate of increase in habitat heterogeneity with increasing area, which is frequently proposed to drive SARs, (2) environmental energy availability, which may influence SARs by affecting species occupancy patterns, and (3) species richness. We consider environmental variables measured at both local (10 km × 10 km) and regional (290 km × 290 km) spatial grains, but find that the former consistently provides a better fit to the data. In our case study, the effect of species richness on the slope SARs appears to be scale dependent, being negative at local scales but positive at regional scales. In univariate tests, the slope of the SAR correlates negatively with human population density and environmental energy availability, and positively with the rate of increase in habitat heterogeneity. We conducted two sets of multiple regression analyses, with and without species richness as a predictor. When species richness is included it exerts a dominant effect, but when it is excluded temperature has the dominant effect on the slope of the SAR, and the effects of other predictors are marginal.

A case of four-coordinate silver(I) adopting a high energy planar geometry. Experiment and theory

The ligands PhL and MeL are obtained by condensing 2-formylpyridine with benzil dihydrazone and diacetyl dihydrazone, respectively, in 2: 1 molar proportion. With silver( I), PhL yields a double-stranded dinuclear cationic helicate 1 in which the metal is tetrahedral but MeL gives a cationic one-dimensional polymeric complex 2 where silver( I) is distorted square planar and the ligand backbone is nearly planar. In both complexes, metal: ligand ratio is 1: 1. Ab initio calculations on the ligands at the HF/6-31+G* level reveal that while PhL strongly prefers a helical conformation, MeL has a natural inclination to remain in a planar conformation. Density functional theory calculations on model silver( I) complexes show that formation of the linear polymer in the case of MeL is also an important factor in imposing the planar geometry of Ag(I) in 2.

Regression based D-optimality experimental design for sparse kernel density estimation

This paper derives an efficient algorithm for constructing sparse kernel density (SKD) estimates. The algorithm first selects a very small subset of significant kernels using an orthogonal forward regression (OFR) procedure based on the D-optimality experimental design criterion. The weights of the resulting sparse kernel model are then calculated using a modified multiplicative nonnegative quadratic programming algorithm. Unlike most of the SKD estimators, the proposed D-optimality regression approach is an unsupervised construction algorithm and it does not require an empirical desired response for the kernel selection task. The strength of the D-optimality OFR is owing to the fact that the algorithm automatically selects a small subset of the most significant kernels related to the largest eigenvalues of the kernel design matrix, which counts for the most energy of the kernel training data, and this also guarantees the most accurate kernel weight estimate. The proposed method is also computationally attractive, in comparison with many existing SKD construction algorithms. Extensive numerical investigation demonstrates the ability of this regression-based approach to efficiently construct a very sparse kernel density estimate with excellent test accuracy, and our results show that the proposed method compares favourably with other existing sparse methods, in terms of test accuracy, model sparsity and complexity, for constructing kernel density estimates.

Low-lying excited states and primary photoproducts of [Os-3(CO)(10)-(s-cis-L)] (L = cyclohexa-1,3-diene, buta-1,3-diene)] clusters studied by picosecond time-resolved UV/Vis and IR spectroscopy and by density functional theory

Combined picosecond transient absorption and time-resolved infrared studies were performed, aimed at characterising low-lying excited states of the cluster [Os-3(CO)(10)(s-cis-L)] (L= cyclohexa-1,3-diene, 1) and monitoring the formation of its photoproducts. Theoretical (DFT and TD-DFT) calculations on the closely related cluster with L=buta-1,3-diene (2') have revealed that the low-lying electronic transitions of these [Os-3(CO)(10)(s-cis-1,3-diene)] clusters have a predominant sigma(core)pi*(CO) character. From the lowest sigmapi* excited state, cluster 1 undergoes fast Os-Os(1,3-diene) bond cleavage (tau=3.3 ps) resulting in the formation of a coordinatively unsaturated primary photoproduct (1a) with a single CO bridge. A new insight into the structure of the transient has been obtained by DFT calculations. The cleaved Os-Os(1,3-diene) bond is bridged by the donor 1,3-diene ligand, compensating for the electron deficiency at the neighbouring Os centre. Because of the unequal distribution of the electron density in transient la, a second CO bridge is formed in 20 ps in the photoproduct [Os-3(CO)(8)(mu-CO)(2)- (cyclohexa-1,3-diene)] (1b). The latter compound, absorbing strongly around 630 nm, mainly regenerates the parent cluster with a lifetime of about 100 ns in hexane. Its structure, as suggested by the DFT calculations, again contains the 1,3-diene ligand coordinated in a bridging fashion. Photoproduct 1b can therefore be assigned as a high-energy coordination isomer of the parent cluster with all Os-Os bonds bridged.

Kinetic energy analysis of the response of the Atlantic meridional overturning circulation to CO2-forced climate change

Atmosphere–ocean general circulation models (AOGCMs) predict a weakening of the Atlantic meridional overturning circulation (AMOC) in response to anthropogenic forcing of climate, but there is a large model uncertainty in the magnitude of the predicted change. The weakening of the AMOC is generally understood to be the result of increased buoyancy input to the north Atlantic in a warmer climate, leading to reduced convection and deep water formation. Consistent with this idea, model analyses have shown empirical relationships between the AMOC and the meridional density gradient, but this link is not direct because the large-scale ocean circulation is essentially geostrophic, making currents and pressure gradients orthogonal. Analysis of the budget of kinetic energy (KE) instead of momentum has the advantage of excluding the dominant geostrophic balance. Diagnosis of the KE balance of the HadCM3 AOGCM and its low-resolution version FAMOUS shows that KE is supplied to the ocean by the wind and dissipated by viscous forces in the global mean of the steady-state control climate, and the circulation does work against the pressure-gradient force, mainly in the Southern Ocean. In the Atlantic Ocean, however, the pressure-gradient force does work on the circulation, especially in the high-latitude regions of deep water formation. During CO2-forced climate change, we demonstrate a very good temporal correlation between the AMOC strength and the rate of KE generation by the pressure-gradient force in 50–70°N of the Atlantic Ocean in each of nine contemporary AOGCMs, supporting a buoyancy-driven interpretation of AMOC changes. To account for this, we describe a conceptual model, which offers an explanation of why AOGCMs with stronger overturning in the control climate tend to have a larger weakening under CO2 increase.

Kinetic energy analysis of the response of the Atlantic meridional overturning circulation to CO2-forced climate change

Atmosphere–ocean general circulation models (AOGCMs) predict a weakening of the Atlantic meridional overturning circulation (AMOC) in response to anthropogenic forcing of climate, but there is a large model uncertainty in the magnitude of the predicted change. The weakening of the AMOC is generally understood to be the result of increased buoyancy input to the north Atlantic in a warmer climate, leading to reduced convection and deep water formation. Consistent with this idea, model analyses have shown empirical relationships between the AMOC and the meridional density gradient, but this link is not direct because the large-scale ocean circulation is essentially geostrophic, making currents and pressure gradients orthogonal. Analysis of the budget of kinetic energy (KE) instead of momentum has the advantage of excluding the dominant geostrophic balance. Diagnosis of the KE balance of the HadCM3 AOGCM and its low-resolution version FAMOUS shows that KE is supplied to the ocean by the wind and dissipated by viscous forces in the global mean of the steady-state control climate, and the circulation does work against the pressure-gradient force, mainly in the Southern Ocean. In the Atlantic Ocean, however, the pressure-gradient force does work on the circulation, especially in the high-latitude regions of deep water formation. During CO2-forced climate change, we demonstrate a very good temporal correlation between the AMOC strength and the rate of KE generation by the pressure-gradient force in 50–70°N of the Atlantic Ocean in each of nine contemporary AOGCMs, supporting a buoyancy-driven interpretation of AMOC changes. To account for this, we describe a conceptual model, which offers an explanation of why AOGCMs with stronger overturning in the control climate tend to have a larger weakening under CO2 increase

Statistical evaluation of the early-stage development of Jatropha energy plantations in Northeastern Mexico

A systematic evaluation of agricultural factors affecting the adaptation of the tropical oil plant Jatropha curcas L. to the semi-arid subtropical climate in Northeastern Mexico has been conducted. The factors studied include plant density and topology, as well as fungi and virus abundances. A multiple regression analysis shows that total fruit production can be well predicted by the area per plant and the total presence of fungi. Four common herbicides and a mechanical weed control measure were established at a dedicated test array and their impact on plant productivity was assessed.

Development of the Surface Urban Energy and Water balance Scheme (SUEWS) for cold climate cities

The Surface Urban Energy and Water Balance Scheme (SUEWS) is developed to include snow. The processes addressed include accumulation of snow on the different urban surface types: snow albedo and density aging, snow melting and re-freezing of meltwater. Individual model parameters are assessed and independently evaluated using long-term observations in the two cold climate cities of Helsinki and Montreal. Eddy covariance sensible and latent heat fluxes and snow depth observations are available for two sites in Montreal and one in Helsinki. Surface runoff from two catchments (24 and 45 ha) in Helsinki and snow properties (albedo and density) from two sites in Montreal are also analysed. As multiple observation sites with different land-cover characteristics are available in both cities, model development is conducted independent of evaluation. The developed model simulates snowmelt related runoff well (within 19% and 3% for the two catchments in Helsinki when there is snow on the ground), with the springtime peak estimated correctly. However, the observed runoff peaks tend to be smoother than the simulated ones, likely due to the water holding capacity of the catchments and the missing time lag between the catchment and the observation point in the model. For all three sites the model simulates the timing of the snow accumulation and melt events well, but underestimates the total snow depth by 18–20% in Helsinki and 29–33% in Montreal. The model is able to reproduce the diurnal pattern of net radiation and turbulent fluxes of sensible and latent heat during cold snow, melting snow and snow-free periods. The largest model uncertainties are related to the timing of the melting period and the parameterization of the snowmelt. The results show that the enhanced model can simulate correctly the exchange of energy and water in cold climate cities at sites with varying surface cover.

An energy budget agent-based model of earthworm populations and its application to study the effects of pesticides

Earthworms are important organisms in soil communities and so are used as model organisms in environmental risk assessments of chemicals. However current risk assessments of soil invertebrates are based on short-term laboratory studies, of limited ecological relevance, supplemented if necessary by site-specific field trials, which sometimes are challenging to apply across the whole agricultural landscape. Here, we investigate whether population responses to environmental stressors and pesticide exposure can be accurately predicted by combining energy budget and agent-based models (ABMs), based on knowledge of how individuals respond to their local circumstances. A simple energy budget model was implemented within each earthworm Eisenia fetida in the ABM, based on a priori parameter estimates. From broadly accepted physiological principles, simple algorithms specify how energy acquisition and expenditure drive life cycle processes. Each individual allocates energy between maintenance, growth and/or reproduction under varying conditions of food density, soil temperature and soil moisture. When simulating published experiments, good model fits were obtained to experimental data on individual growth, reproduction and starvation. Using the energy budget model as a platform we developed methods to identify which of the physiological parameters in the energy budget model (rates of ingestion, maintenance, growth or reproduction) are primarily affected by pesticide applications, producing four hypotheses about how toxicity acts. We tested these hypotheses by comparing model outputs with published toxicity data on the effects of copper oxychloride and chlorpyrifos on E. fetida. Both growth and reproduction were directly affected in experiments in which sufficient food was provided, whilst maintenance was targeted under food limitation. Although we only incorporate toxic effects at the individual level we show how ABMs can readily extrapolate to larger scales by providing good model fits to field population data. The ability of the presented model to fit the available field and laboratory data for E. fetida demonstrates the promise of the agent-based approach in ecology, by showing how biological knowledge can be used to make ecological inferences. Further work is required to extend the approach to populations of more ecologically relevant species studied at the field scale. Such a model could help extrapolate from laboratory to field conditions and from one set of field conditions to another or from species to species.

Statistical-dynamical downscaling for wind energy potentials: evaluation and applications to decadal hindcasts and climate change projections

A statistical–dynamical downscaling (SDD) approach for the regionalization of wind energy output (Eout) over Europe with special focus on Germany is proposed. SDD uses an extended circulation weather type (CWT) analysis on global daily mean sea level pressure fields with the central point being located over Germany. Seventy-seven weather classes based on the associated CWT and the intensity of the geostrophic flow are identified. Representatives of these classes are dynamically downscaled with the regional climate model COSMO-CLM. By using weather class frequencies of different data sets, the simulated representatives are recombined to probability density functions (PDFs) of near-surface wind speed and finally to Eout of a sample wind turbine for present and future climate. This is performed for reanalysis, decadal hindcasts and long-term future projections. For evaluation purposes, results of SDD are compared to wind observations and to simulated Eout of purely dynamical downscaling (DD) methods. For the present climate, SDD is able to simulate realistic PDFs of 10-m wind speed for most stations in Germany. The resulting spatial Eout patterns are similar to DD-simulated Eout. In terms of decadal hindcasts, results of SDD are similar to DD-simulated Eout over Germany, Poland, Czech Republic, and Benelux, for which high correlations between annual Eout time series of SDD and DD are detected for selected hindcasts. Lower correlation is found for other European countries. It is demonstrated that SDD can be used to downscale the full ensemble of the Earth System Model of the Max Planck Institute (MPI-ESM) decadal prediction system. Long-term climate change projections in Special Report on Emission Scenarios of ECHAM5/MPI-OM as obtained by SDD agree well to the results of other studies using DD methods, with increasing Eout over northern Europe and a negative trend over southern Europe. Despite some biases, it is concluded that SDD is an adequate tool to assess regional wind energy changes in large model ensembles.

The effect of a single supernova explosion on the cuspy density profile of a small-mass dark matter halo

Some observations of galaxies, and in particular dwarf galaxies, indicate a presence of cored density profiles in apparent contradiction with cusp profiles predicted by dark matter N-body simulations. We constructed an analytical model, using particle distribution functions (DFs), to show how a supernova (SN) explosion can transform a cusp density profile in a small-mass dark matter halo into a cored one. Considering the fact that an SN efficiently removes matter from the centre of the first haloes, we study the effect of mass removal through an SN perturbation in the DFs. We find that the transformation from a cusp into a cored profile occurs even for changes as small as 0.5 per cent of the total energy of the halo, which can be produced by the expulsion of matter caused by a single SN explosion.

The effects of stocking density in physiological parameters and growth of the endangered teleost species piabanha, Brycon insignis (Steindachner, 1877)

This study investigated the effects of stocking density on the growth and fatty acid (FA) of Brycon insignis metabolism. Fingerlings (360) were distributed into eight ponds at two stocking densities (105 and 210 g/m(3)). The analysis of growth showed that the condition factor (K) and the coefficient of variation (CV) for body mass were not affected by stocking density. However, final body mass and length, specific growth rate (SGR), and weight gain (WG) were higher in the low stocking density group, which also presented a higher feed efficiency (FE) and survival (S). By contrast, muscle protein levels were higher in the high stocking density group. The plasma and muscle lipid content were not affected by stocking density, but fish reared at lower stocking density presented higher lipid concentration in the liver, with no differences in hepatosomatic index values. Even with the differences observed in metabolic and growth parameters, plasma cortisol was not affected by stocking density. The FA profile in the muscle and liver neutral fraction were not affected by stocking density, but the FA in the polar fractions differed between the two stocking densities. In the liver, total polyunsaturated fatty acids (PUFA) and PUFA n - 3 increased in higher stocking density, mainly due to an increase in docosahexaenoic acid (DHA). In addition, PUFA n - 6 were also increased in the higher stocking density group, mainly due to an increase in arachidonic acid (AA) and docosadienoic acid (22:2n - 6). In the muscle polar fraction, the saturated fatty acids (SFA) and monounsaturated fatty acids (MUFA) decreased in the animals from the higher stocking density group, and this reduction was compensated by an increase in PUFA n - 3 and PUFA n - 6, mainly the FA with 20-22 carbons (20:4n - 6: 22:4:n - 6; 22:5n - 6, 22:5n - 3, and 22:6n - 3). A different profile was observed for the C18 PUFAs, mainly 18:2n - 6 and 18:4n - 6, which were higher in the lower density stocking group. The data suggest that when living in high stocking density, B. insignis differentially utilizes the hepatic lipids as energy source and remodels the membrane fatty acids, with higher amounts of DHA in the polar muscle fraction compensated for by a decrease in MUFA. The zootechnical and physiological indices reveal that the lower stocking density group achieve overall better performance. (C) 2010 Elsevier B.V. All rights reserved.

Many-body energy decomposition of hydrogen-bonded glycine clusters in gas-phase

A detailed analysis of the many-body contribution to the interaction energies of the gas-phase hydrogen-bonded glycine clusters, (Gly)(N), N = 1-4 is presented. The energetics of the hydrogen-bonded dimer, trimer and tetramer complexes have been analyzed using density-functional theory. The magnitude of the two-through four-body energy terms have been calculated and compared. The relaxation energy and the two-body energy terms are the principal contributors to the total binding energy. Four-body contribution is negligible. However, the three-body contribution is found to be sizable and the formation of the cyclic glycine trimer presents geometric strains that make it less favorable. (C) 2010 Elsevier B.V. All rights reserved.

Effects of Side-Chain and Electron Exchange Correlation on the Band Structure of Perylene Diimide Liquid Crystals: A Density Functional Study

The structural and electronic properties of perylene diimide liquid crystal PPEEB are studied using ab initio methods based on the density functional theory (I)FT). Using available experimental crystallographic data as a guide, we propose a detailed structural model for the packing of solid PPEEB. We find that due to the localized nature of the band edge wave function, theoretical approaches beyond the standard method, such as hybrid functional (PBE0), are required to correctly characterize the band structure of this material. Moreover, unlike previous assumptions, we observe the formation of hydrogen bonds between the side chains of different molecules, which leads to a dispersion of the energy levels. This result indicates that the side chains of the molecular crystal not only are responsible for its structural conformation but also can be used for tuning the electronic and optical properties of these materials.