Three dimensional picture of the local structure of 1,4-Polybutadiene from a complete atomistic model and neutron scattering data

An efficient method of combining neutron diffraction data over an extended Q range with detailed atomistic models is presented. A quantitative and qualitative mapping of the organization of the chain conformation in both glass and liquid phase has been performed. The proposed structural refinement method is based on the exploitation of the intrachain features of the diffraction pattern by the use of internal coordinates for bond lengths, valence angles and torsion rotations. Models are built stochastically by assignment of these internal coordinates from probability distributions with limited variable parameters. Variation of these parameters is used in the construction of models that minimize the differences between the observed and calculated structure factors. A series of neutron scattering data of 1,4-polybutadiene at the region 20320 K is presented. Analysis of the experimental data yield bond lengths for C-C and C=C of 1.54 and 1.35 Å respectively. Valence angles of the backbone were found to be at 112 and 122.8 for the CCC and CC=C respectively. Three torsion angles corresponding to the double bond and the adjacent R and β bonds were found to occupy cis and trans, s(, trans and g( and trans states, respectively. We compare our results with theoretical predictions, computer simulations, RIS models, and previously reported experimental results.

A complete atomistic model of molten polyethylene from neutron scattering data: a new methodology for polymer structure

A new approach to the study of the local organization in amorphous polymer materials is presented. The method couples neutron diffraction experiments that explore the structure on the spatial scale 1–20 Å with the reverse Monte Carlo fitting procedure to predict structures that accurately represent the experimental scattering results over the whole momentum transfer range explored. Molecular mechanics and molecular dynamics techniques are also used to produce atomistic models independently from any experimental input, thereby providing a test of the viability of the reverse Monte Carlo method in generating realistic models for amorphous polymeric systems. An analysis of the obtained models in terms of single chain properties and of orientational correlations between chain segments is presented. We show the viability of the method with data from molten polyethylene. The analysis derives a model with average C-C and C-H bond lengths of 1.55 Å and 1.1 Å respectively, average backbone valence angle of 112, a torsional angle distribution characterized by a fraction of trans conformers of 0.67 and, finally, a weak interchain orientational correlation at around 4 Å.

A detailed single chain model for molten poly(tetrafluoroethylene) from a novel structure refinement technique on neutron scattering data

We present a new methodology that couples neutron diffraction experiments over a wide Q range with single chain modelling in order to explore, in a quantitative manner, the intrachain organization of non-crystalline polymers. The technique is based on the assignment of parameters describing the chemical, geometric and conformational characteristics of the polymeric chain, and on the variation of these parameters to minimize the difference between the predicted and experimental diffraction patterns. The method is successfully applied to the study of molten poly(tetrafluoroethylene) at two different temperatures, and provides unambiguous information on the configuration of the chain and its degree of flexibility. From analysis of the experimental data a model is derived with CC and CF bond lengths of 1.58 and 1.36 Å, respectively, a backbone valence angle of 110° and a torsional angle distribution which is characterized by four isometric states, namely a split trans state at ± 18°, giving rise to a helical chain conformation, and two gauche states at ± 112°. The probability of trans conformers is 0.86 at T = 350°C, which decreases slightly to 0.84 at T = 400°C. Correspondingly, the chain segments are characterized by long all-trans sequences with random changes in sign, rather anisotropic in nature, which give rise to a rather stiff chain. We compare the results of this quantitative analysis of the experimental scattering data with the theoretical predictions of both force fields and molecular orbital conformation energy calculations.

A linear model for the structure of turbulence beneath surface water waves

The structure of turbulence in the ocean surface layer is investigated using a simplified semi-analytical model based on rapid-distortion theory. In this model, which is linear with respect to the turbulence, the flow comprises a mean Eulerian shear current, the Stokes drift of an irrotational surface wave, which accounts for the irreversible effect of the waves on the turbulence, and the turbulence itself, whose time evolution is calculated. By analysing the equations of motion used in the model, which are linearised versions of the Craik–Leibovich equations containing a ‘vortex force’, it is found that a flow including mean shear and a Stokes drift is formally equivalent to a flow including mean shear and rotation. In particular, Craik and Leibovich’s condition for the linear instability of the first kind of flow is equivalent to Bradshaw’s condition for the linear instability of the second. However, the present study goes beyond linear stability analyses by considering flow disturbances of finite amplitude, which allows calculating turbulence statistics and addressing cases where the linear stability is neutral. Results from the model show that the turbulence displays a structure with a continuous variation of the anisotropy and elongation, ranging from streaky structures, for distortion by shear only, to streamwise vortices resembling Langmuir circulations, for distortion by Stokes drift only. The TKE grows faster for distortion by a shear and a Stokes drift gradient with the same sign (a situation relevant to wind waves), but the turbulence is more isotropic in that case (which is linearly unstable to Langmuir circulations).

Correction of atmospheric delay effects in radar interferometry using a nested mesoscale atmospheric model

The temporal variability of the atmosphere through which radio waves pass in the technique of differential radar interferometry can seriously limit the accuracy with which the method can measure surface motion. A forward, nested mesoscale model of the atmosphere can be used to simulate the variable water content along the radar path and the resultant phase delays. Using this approach we demonstrate how to correct an interferogram of Mount Etna in Sicily associated with an eruption in 2004-5. The regional mesoscale model (Unified Model) used to simulate the atmosphere at higher resolutions consists of four nested domains increasing in resolution (12, 4, 1, 0.3 km), sitting within the analysis version of a global numerical model that is used to initiate the simulation. Using the high resolution 3D model output we compute the surface pressure, temperature and the water vapour, liquid and solid water contents, enabling the dominant hydrostatic and wet delays to be calculated at specific times corresponding to the acquisition of the radar data. We can also simulate the second-order delay effects due to liquid water and ice.

The structure of the optimal income tax in the quasi-linear model

Existing numerical characterizations of the optimal income tax have been based on a limited number of model specifications. As a result, they do not reveal which properties are general. We determine the optimal tax in the quasi-linear model under weaker assumptions than have previously been used; in particular, we remove the assumption of a lower bound on the utility of zero consumption and the need to permit negative labor incomes. A Monte Carlo analysis is then conducted in which economies are selected at random and the optimal tax function constructed. The results show that in a significant proportion of economies the marginal tax rate rises at low skills and falls at high. The average tax rate is equally likely to rise or fall with skill at low skill levels, rises in the majority of cases in the centre of the skill range, and falls at high skills. These results are consistent across all the specifications we test. We then extend the analysis to show that these results also hold for Cobb-Douglas utility.

An evaluation of the spatiotemporal structure of large-scale European drought within the HiGEM climate model

We compare the characteristics of synthetic European droughts generated by the HiGEM1 coupled climate model run with present day atmospheric composition with observed drought events extracted from the CRU TS3 data set. The results demonstrate consistency in both the rate of drought occurrence and the spatiotemporal structure of the events. Estimates of the probability density functions for event area, duration and severity are shown to be similar with confidence > 90%. Encouragingly, HiGEM is shown to replicate the extreme tails of the observed distributions and thus the most damaging European drought events. The soil moisture state is shown to play an important role in drought development. Once a large-scale drought has been initiated it is found to be 50% more likely to continue if the local soil moisture is below the 40th percentile. In response to increased concentrations of atmospheric CO2, the modelled droughts are found to increase in duration, area and severity. The drought response can be largely attributed to temperature driven changes in relative humidity. 1 HiGEM is based on the latest climate configuration of the Met Office Hadley Centre Unified Model (HadGEM1) with the horizontal resolution increased to 1.25 x 0.83 degrees in longitude and latitude in the atmosphere and 1/3 x 1/3 degrees in the ocean.

The vertical structure of oceanic Rossby waves: a comparison of high-resolution model data to theoretical vertical structures

Tests of the new Rossby wave theories that have been developed over the past decade to account for discrepancies between theoretical wave speeds and those observed by satellite altimeters have focused primarily on the surface signature of such waves. It appears, however, that the surface signature of the waves acts only as a rather weak constraint, and that information on the vertical structure of the waves is required to better discriminate between competing theories. Due to the lack of 3-D observations, this paper uses high-resolution model data to construct realistic vertical structures of Rossby waves and compares these to structures predicted by theory. The meridional velocity of a section at 24° S in the Atlantic Ocean is pre-processed using the Radon transform to select the dominant westward signal. Normalized profiles are then constructed using three complementary methods based respectively on: (1) averaging vertical profiles of velocity, (2) diagnosing the amplitude of the Radon transform of the westward propagating signal at different depths, and (3) EOF analysis. These profiles are compared to profiles calculated using four different Rossby wave theories: standard linear theory (SLT), SLT plus mean flow, SLT plus topographic effects, and theory including mean flow and topographic effects. Our results support the classical theoretical assumption that westward propagating signals have a well-defined vertical modal structure associated with a phase speed independent of depth, in contrast with the conclusions of a recent study using the same model but for different locations in the North Atlantic. The model structures are in general surface intensified, with a sign reversal at depth in some regions, notably occurring at shallower depths in the East Atlantic. SLT provides a good fit to the model structures in the top 300 m, but grossly overestimates the sign reversal at depth. The addition of mean flow slightly improves the latter issue, but is too surface intensified. SLT plus topography rectifies the overestimation of the sign reversal, but overestimates the amplitude of the structure for much of the layer above the sign reversal. Combining the effects of mean flow and topography provided the best fit for the mean model profiles, although small errors at the surface and mid-depths are carried over from the individual effects of mean flow and topography respectively. Across the section the best fitting theory varies between SLT plus topography and topography with mean flow, with, in general, SLT plus topography performing better in the east where the sign reversal is less pronounced. None of the theories could accurately reproduce the deeper sign reversals in the west. All theories performed badly at the boundaries. The generalization of this method to other latitudes, oceans, models and baroclinic modes would provide greater insight into the variability in the ocean, while better observational data would allow verification of the model findings.

Systematic model forecast error in Rossby wave structure

Diabatic processes can alter Rossby wave structure; consequently errors arising from model processes propagate downstream. However, the chaotic spread of forecasts from initial condition uncertainty renders it difficult to trace back from root mean square forecast errors to model errors. Here diagnostics unaffected by phase errors are used, enabling investigation of systematic errors in Rossby waves in winter-season forecasts from three operational centers. Tropopause sharpness adjacent to ridges decreases with forecast lead time. It depends strongly on model resolution, even though models are examined on a common grid. Rossby wave amplitude reduces with lead time up to about five days, consistent with under-representation of diabatic modification and transport of air from the lower troposphere into upper-tropospheric ridges, and with too weak humidity gradients across the tropopause. However, amplitude also decreases when resolution is decreased. Further work is necessary to isolate the contribution from errors in the representation of diabatic processes.

Vertical structure and physical processes of the Madden-Julian oscillation: exploring key model physics in climate simulations

Aimed at reducing deficiencies in representing the Madden-Julian oscillation (MJO) in general circulation models (GCMs), a global model evaluation project on vertical structure and physical processes of the MJO was coordinated. In this paper, results from the climate simulation component of this project are reported. It is shown that the MJO remains a great challenge in these latest generation GCMs. The systematic eastward propagation of the MJO is only well simulated in about one-fourth of the total participating models. The observed vertical westward tilt with altitude of the MJO is well simulated in good MJO models, but not in the poor ones. Damped Kelvin wave responses to the east of convection in the lower troposphere could be responsible for the missing MJO preconditioning process in these poor MJO models. Several process-oriented diagnostics were conducted to discriminate key processes for realistic MJO simulations. While large-scale rainfall partition and low-level mean zonal winds over the Indo-Pacific in a model are not found to be closely associated with its MJO skill, two metrics, including the low-level relative humidity difference between high and low rain events and seasonal mean gross moist stability, exhibit statistically significant correlations with the MJO performance. It is further indicated that increased cloud-radiative feedback tends to be associated with reduced amplitude of intraseasonal variability, which is incompatible with the radiative instability theory previously proposed for the MJO. Results in this study confirm that inclusion of air-sea interaction can lead to significant improvement in simulating the MJO.

The representation of the West-African Monsoon vertical cloud structure in the Met Office Unified Model: an evaluation with CloudSat

Weather and climate model simulations of the West African Monsoon (WAM) have generally poor representation of the rainfall distribution and monsoon circulation because key processes, such as clouds and convection, are poorly characterized. The vertical distribution of cloud and precipitation during the WAM are evaluated in Met Office Unified Model simulations against CloudSat observations. Simulations were run at 40-km and 12-km horizontal grid length using a convection parameterization scheme and at 12-km, 4-km, and 1.5-km grid length with the convection scheme effectively switched off, to study the impact of model resolution and convection parameterization scheme on the organisation of tropical convection. Radar reflectivity is forward-modelled from the model cloud fields using the CloudSat simulator to present a like-with-like comparison with the CloudSat radar observations. The representation of cloud and precipitation at 12-km horizontal grid length improves dramatically when the convection parameterization is switched off, primarily because of a reduction in daytime (moist) convection. Further improvement is obtained when reducing model grid length to 4 km or 1.5 km, especially in the representation of thin anvil and mid-level cloud, but three issues remain in all model configurations. Firstly, all simulations underestimate the fraction of anvils with cloud top height above 12 km, which can be attributed to too low ice water contents in the model compared to satellite retrievals. Secondly, the model consistently detrains mid-level cloud too close to the freezing level, compared to higher altitudes in CloudSat observations. Finally, there is too much low-level cloud cover in all simulations and this bias was not improved when adjusting the rainfall parameters in the microphysics scheme. To improve model simulations of the WAM, more detailed and in-situ observations of the dynamics and microphysics targeting these non-precipitating cloud types are required.

Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level

Abstract Background: The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North+East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe. Results: A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST=0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST=0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars. Conclusions: The variation found at group and sub-group levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.

The nested assembly of individual-resource networks

P>1. Much of the current understanding of ecological systems is based on theory that does not explicitly take into account individual variation within natural populations. However, individuals may show substantial variation in resource use. This variation in turn may be translated into topological properties of networks that depict interactions among individuals and the food resources they consume (individual-resource networks). 2. Different models derived from optimal diet theory (ODT) predict highly distinct patterns of trophic interactions at the individual level that should translate into distinct network topologies. As a consequence, individual-resource networks can be useful tools in revealing the incidence of different patterns of resource use by individuals and suggesting their mechanistic basis. 3. In the present study, using data from several dietary studies, we assembled individual-resource networks of 10 vertebrate species, previously reported to show interindividual diet variation, and used a network-based approach to investigate their structure. 4. We found significant nestedness, but no modularity, in all empirical networks, indicating that (i) these populations are composed of both opportunistic and selective individuals and (ii) the diets of the latter are ordered as predictable subsets of the diets of the more opportunistic individuals. 5. Nested patterns are a common feature of species networks, and our results extend its generality to trophic interactions at the individual level. This pattern is consistent with a recently proposed ODT model, in which individuals show similar rank preferences but differ in their acceptance rate for alternative resources. Our findings therefore suggest a common mechanism underlying interindividual variation in resource use in disparate taxa.

Towards an assessment of character interdependence in avian RNA phylogenetics: A general secondary structure model for the avian mitochondrial 16S rRNA

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Synthesis, Structure, and Phosphatase-Like Activity of a New Trinuclear Gd Complex with the Unsymmetrical Ligand H(3)L As a Model for Nucleases

The new trinuclear gadolinium complex [Gd(3)L(2)(NO(3))(2)(H(2)O)(4)]NO(3)center dot 8H(2)O (1) with the unsymmetrical ligand 2-[N-bis-(2-pyridylmethyl)aminomethyl]-4-methyl-6-[N-bis(2-hydroxy-2-oxoethyl)aminomethyl] phenol (H(3)L) was synthesized and characterized. The new ligand H(3)L was obtained in good yield. Complex I crystallizes in an orthorhombic cell, space group Pcab. Kinetic studies show that complex 1 is highly active in the hydrolysis of the substrate 2,4-bis(dinitrophenyl)phosphate (K(m) = 4.09 mM, V(max) = 2.68 x 10(-2) mM s(-1), and k(cat) = V(max)/[1] = 0.67 s(-1)). Through a potentiometric study and determination of the kinetic behavior of 1 in acetonitrile/water solution, the species present in solution could be identified, and a trinuclear monohydroxo species appears to be the most prominent catalyst under mild conditions. Complex 1 displays high efficiency in DNA hydrolytic cleavage, and complete kinetic studies were carried out (K(m) = 4.57 x 10(-4) M, K(cat)` = 3.42 h(-1), and k(cat)`/K(m) = 7.48 x 10(3) M(-1) h(-1)). Studies with a radical scavenger (dimethyl sulfoxide, DMSO) showed that it did not inhibit the activity, indicating the hydrolytic action of 1 in the cleavage of DNA, and studies on the incubation of distamycin with plasmid DNA suggest that 1 is regio-specific, interacting with the minor groove of DNA.