2-D R-matrix propagation: A large scale electron scattering simulation dominated by the multiplication of dynamically changing matrices

We examine the computational aspects of propagating a global R-matrix, R, across sub-regions in a 2-D plane. This problem originates in the large scale simulation of electron collisions with atoms and ions at intermediate energies. The propagation is dominated by matrix multiplications which are complicated because of the dynamic nature of R, which changes the designations of its rows and columns and grows in size as the propagation proceeds. The use of PBLAS to solve this problem on distributed memory HPC machines is the main focus of the paper.

Can the dynamical impact of the stratosphere on the troposphere be described by large-scale adjustment to the stratospheric PV distribution?

Recent numerical experiments have demonstrated that the state of the stratosphere has a dynamical impact on the state of the troposphere. To account for such an effect, a number of mechanisms have been proposed in the literature, all of which amount to a large-scale adjustment of the troposphere to potential vorticity (PV) anomalies in the stratosphere. This paper analyses whether a simple PV adjustment suffices to explain the actual dynamical response of the troposphere to the state of the stratosphere, the actual response being determined by ensembles of numerical experiments run with an atmospheric general-circulation model. For this purpose, a new PV inverter is developed. It is shown that the simple PV adjustment hypothesis is inadequate. PV anomalies in the stratosphere induce, by inversion, flow anomalies in the troposphere that do not coincide spatially with the tropospheric changes determined by the numerical experiments. Moreover, the tropospheric anomalies induced by PV inversion are on a larger scale than the changes found in the numerical experiments, which are linked to the Atlantic and Pacific storm-tracks. These findings imply that the impact of the stratospheric state on the troposphere is manifested through the impact on individual synoptic-scale systems and their self-organization in the storm-tracks. Changes in these weather systems in the troposphere are not merely synoptic-scale noise on a larger scale tropospheric response, but an integral part of the mechanism by which the state of the stratosphere impacts that of the troposphere.

Large-scale functional expression of WT and truncated human adenosine A(2A) receptor in Pichia pastoris bioreactor cultures

Background: The large-scale production of G-protein coupled receptors (GPCRs) for functional and structural studies remains a challenge. Recent successes have been made in the expression of a range of GPCRs using Pichia pastoris as an expression host. P. pastoris has a number of advantages over other expression systems including ability to post-translationally modify expressed proteins, relative low cost for production and ability to grow to very high cell densities. Several previous studies have described the expression of GPCRs in P. pastoris using shaker flasks, which allow culturing of small volumes (500 ml) with moderate cell densities (OD600 similar to 15). The use of bioreactors, which allow straightforward culturing of large volumes, together with optimal control of growth parameters including pH and dissolved oxygen to maximise cell densities and expression of the target receptors, are an attractive alternative. The aim of this study was to compare the levels of expression of the human Adenosine 2A receptor (A(2A)R) in P. pastoris under control of a methanol-inducible promoter in both flask and bioreactor cultures. Results: Bioreactor cultures yielded an approximately five times increase in cell density (OD600 similar to 75) compared to flask cultures prior to induction and a doubling in functional expression level per mg of membrane protein, representing a significant optimisation. Furthermore, analysis of a C-terminally truncated A2AR, terminating at residue V334 yielded the highest levels (200 pmol/mg) so far reported for expression of this receptor in P. pastoris. This truncated form of the receptor was also revealed to be resistant to C-terminal degradation in contrast to the WT A(2A)R, and therefore more suitable for further functional and structural studies. Conclusion: Large-scale expression of the A(2A)R in P. pastoris bioreactor cultures results in significant increases in functional expression compared to traditional flask cultures.

Results of PMIP2 coupled simulations of the mid-Holocene and Last Glacial Maximum, Part 1: experiments and large-scale features

A set of coupled ocean-atmosphere simulations using state of the art climate models is now available for the Last Glacial Maximum and the Mid-Holocene through the second phase of the Paleoclimate Modeling Intercomparison Project (PMIP2). This study presents the large-scale features of the simulated climates and compares the new model results to those of the atmospheric models from the first phase of the PMIP, for which sea surface temperature was prescribed or computed using simple slab ocean formulations. We consider the large-scale features of the climate change, pointing out some of the major differences between the different sets of experiments. We show in particular that systematic differences between PMIP1 and PMIP2 simulations are due to the interactive ocean, such as the amplification of the African monsoon at the Mid-Holocene or the change in precipitation in mid-latitudes at the LGM. Also the PMIP2 simulations are in general in better agreement with data than PMIP1 simulations.

Inferring the structure of the solar corona and inner heliosphere during the Maunder minimum using global thermodynamic magnetohydrodynamic simulations

Observations of the Sun’s corona during the space era have led to a picture of relatively constant, but cyclically varying solar output and structure. Longer-term, more indirect measurements, such as from 10Be, coupled by other albeit less reliable contemporaneous reports, however, suggest periods of significant departure from this standard. The Maunder Minimum was one such epoch where: (1) sunspots effectively disappeared for long intervals during a 70 yr period; (2) eclipse observations suggested the distinct lack of a visible K-corona but possible appearance of the F-corona; (3) reports of aurora were notably reduced; and (4) cosmic ray intensities at Earth were inferred to be substantially higher. Using a global thermodynamic MHD model, we have constructed a range of possible coronal configurations for the Maunder Minimum period and compared their predictions with these limited observational constraints. We conclude that the most likely state of the corona during—at least—the later portion of the Maunder Minimum was not merely that of the 2008/2009 solar minimum, as has been suggested recently, but rather a state devoid of any large-scale structure, driven by a photospheric field composed of only ephemeral regions, and likely substantially reduced in strength. Moreover, we suggest that the Sun evolved from a 2008/2009-like configuration at the start of the Maunder Minimum toward an ephemeral-only configuration by the end of it, supporting a prediction that we may be on the cusp of a new grand solar minimum.

Climate perspective on the large-scale circulation associated with the transition of the first South Atlantic hurricane

The landfall of Cyclone Catarina on the Brazilian coast in March 2004 became known as the first documented hurricane in the South Atlantic Ocean, promoting a new view oil how large-scale features can contribute to tropical transition. The aim of this paper is to put the large-scale circulation associated with Catarina`s transition in climate perspective. This is discussed in the light of a robust pattern of spatial correlations between thermodynamic and dynamic variables of importance for hurricane formation. A discussion on how transition mechanisms respond to the present-day circulation is presented. These associations help in understanding why Catarina was formed in a region previously thought to be hurricane-free. Catarina developed over a large-scale area of thermodynamically favourable air/sea temperature contrast. This aspect explains the paradox that such a rare system developed when the sea surface temperature was slightly below average. But, although thermodynamics played an important role, it is apparent that Catarina would not have formed without the key dynamic interplay triggered by a high latitude blocking. The blocking was associated with an extreme positive phase of the Southern Annular Mode (SAM) both hemispherically and locally, and the nearby area where Catarina developed is found to be more cyclonic during the positive phase of the SAM. A conceptual model is developed and a `South Atlantic index` is introduced as a useful diagnostic of potential conditions leading to tropical transition in the area, where large-scale indices indicate trends towards more favourable atmospheric conditions for tropical cyclone formation. Copyright (c) 2008 Royal Meteorological Society

Performance and economic indicators of a large scale fish farming in Mato Grosso, Brazil

Performance and economic indicators of a large scale fish farm that produces round fish, located in Mato Grosso State, Brazil, were evaluated. The 130.8 ha-water surface area was distributed in 30 ponds. Average total production costs and the following economic indicators were calculated: gross income (GI), gross margin (GM), gross margin index (GMI), profitability index (PI) and profit (P) for the farm as a whole and for ten ponds individually. Production performance indicators were also obtained, such as: production cycle (PC), apparent feed conversion (FC), average biomass storage (ABS), survival index (SI) and final average weight (FAW). The average costs to produce an average 2.971 kg.ha-1 per year were: R$ 2.43, R$ 0.72 and R$ 3.15 as average variable, fixed and total costs, respectively. Gross margin and profit per year per hectare of water surface were R$ 2,316.91 and R$ 180.98, respectively. The individual evaluation of the ponds showed that the best pond performance was obtained for PI 38%, FC 1.7, ABS 0.980 kg.m-2, TS 56%, FAW 1.873 kg with PC of 12.3 months. The worst PI was obtained for the pond that displayed losses of 138%, FC 2.6, ABS 0.110 kg.m-2, SI 16% and FAW 1.811 kg. However, large scale production of round-fish in farms is economically feasible. The studied farm displays favorable conditions to improve performance and economic indicators, but it is necessary to reproduce the breeding techniques and performance indicators achieved in few ponds to the entire farm.

The full Fisher matrix for galaxy surveys

Starting from the Fisher matrix for counts in cells, we derive the full Fisher matrix for surveys of multiple tracers of large-scale structure. The key step is the classical approximation, which allows us to write the inverse of the covariance of the galaxy counts in terms of the naive matrix inverse of the covariance in a mixed position-space and Fourier-space basis. We then compute the Fisher matrix for the power spectrum in bins of the 3D wavenumber , the Fisher matrix for functions of position (or redshift z) such as the linear bias of the tracers and/or the growth function and the cross-terms of the Fisher matrix that expresses the correlations between estimations of the power spectrum and estimations of the bias. When the bias and growth function are fully specified, and the Fourier-space bins are large enough that the covariance between them can be neglected, the Fisher matrix for the power spectrum reduces to the widely used result that was first derived by Feldman, Kaiser & Peacock. Assuming isotropy, a fully analytical calculation of the Fisher matrix in the classical approximation can be performed in the case of a constant-density, volume-limited survey.

Investigation of the Impacts of Large-Scale Wind Power Penetration on the Angle and Voltage Stability of Power Systems

The complexity of power systems has increased in recent years due to the operation of existing transmission lines closer to their limits, using flexible AC transmission system (FACTS) devices, and also due to the increased penetration of new types of generators that have more intermittent characteristics and lower inertial response, such as wind generators. This changing nature of a power system has considerable effect on its dynamic behaviors resulting in power swings, dynamic interactions between different power system devices, and less synchronized coupling. This paper presents some analyses of this changing nature of power systems and their dynamic behaviors to identify critical issues that limit the large-scale integration of wind generators and FACTS devices. In addition, this paper addresses some general concerns toward high compensations in different grid topologies. The studies in this paper are conducted on the New England and New York power system model under both small and large disturbances. From the analyses, it can be concluded that high compensation can reduce the security limits under certain operating conditions, and the modes related to operating slip and shaft stiffness are critical as they may limit the large-scale integration of wind generation.

Development of parallelizable flood inundation models for large scale analysis

Flood disasters are a major cause of fatalities and economic losses, and several studies indicate that global flood risk is currently increasing. In order to reduce and mitigate the impact of river flood disasters, the current trend is to integrate existing structural defences with non structural measures. This calls for a wider application of advanced hydraulic models for flood hazard and risk mapping, engineering design, and flood forecasting systems. Within this framework, two different hydraulic models for large scale analysis of flood events have been developed. The two models, named CA2D and IFD-GGA, adopt an integrated approach based on the diffusive shallow water equations and a simplified finite volume scheme. The models are also designed for massive code parallelization, which has a key importance in reducing run times in large scale and high-detail applications. The two models were first applied to several numerical cases, to test the reliability and accuracy of different model versions. Then, the most effective versions were applied to different real flood events and flood scenarios. The IFD-GGA model showed serious problems that prevented further applications. On the contrary, the CA2D model proved to be fast and robust, and able to reproduce 1D and 2D flow processes in terms of water depth and velocity. In most applications the accuracy of model results was good and adequate to large scale analysis. Where complex flow processes occurred local errors were observed, due to the model approximations. However, they did not compromise the correct representation of overall flow processes. In conclusion, the CA model can be a valuable tool for the simulation of a wide range of flood event types, including lowland and flash flood events.

Constraints on neutrino mass fraction using Redshift Space Distortions

Redshift Space Distortions (RSD) are an apparent anisotropy in the distribution of galaxies due to their peculiar motion. These features are imprinted in the correlation function of galaxies, which describes how these structures distribute around each other. RSD can be represented by a distortions parameter $\beta$, which is strictly related to the growth of cosmic structures. For this reason, measurements of RSD can be exploited to give constraints on the cosmological parameters, such us for example the neutrino mass. Neutrinos are neutral subatomic particles that come with three flavours, the electron, the muon and the tau neutrino. Their mass differences can be measured in the oscillation experiments. Information on the absolute scale of neutrino mass can come from cosmology, since neutrinos leave a characteristic imprint on the large scale structure of the universe. The aim of this thesis is to provide constraints on the accuracy with which neutrino mass can be estimated when expoiting measurements of RSD. In particular we want to describe how the error on the neutrino mass estimate depends on three fundamental parameters of a galaxy redshift survey: the density of the catalogue, the bias of the sample considered and the volume observed. In doing this we make use of the BASICC Simulation from which we extract a series of dark matter halo catalogues, characterized by different value of bias, density and volume. This mock data are analysed via a Markov Chain Monte Carlo procedure, in order to estimate the neutrino mass fraction, using the software package CosmoMC, which has been conveniently modified. In this way we are able to extract a fitting formula describing our measurements, which can be used to forecast the precision reachable in future surveys like Euclid, using this kind of observations.

Bispectrum of cosmological models with massive neutrinos

Uno dei più importanti campi di ricerca che coinvolge gli astrofisici è la comprensione della Struttura a Grande Scala dell'universo. I principi della Formazione delle Strutture sono ormai ben saldi, e costituiscono la base del cosiddetto "Modello Cosmologico Standard". Fino agli inizi degli anni 2000, la teoria che spiegava con successo le proprietà statistiche dell'universo era la cosiddetta "Teoria Perturbativa Standard". Attraverso simulazioni numeriche e osservazioni di qualità migliore, si è evidenziato il limite di quest'ultima teoria nel descrivere il comportamento dello spettro di potenza su scale oltre il regime lineare. Ciò spinse i teorici a trovare un nuovo approccio perturbativo, in grado di estendere la validità dei risultati analitici. In questa Tesi si discutono le teorie "Renormalized Perturbation Theory"e"Multipoint Propagator". Queste nuove teorie perturbative sono la base teorica del codice BisTeCca, un codice numerico originale che permette il calcolo dello spettro di potenza a 2 loop e del bispettro a 1 loop in ordine perturbativo. Come esempio applicativo, abbiamo utilizzato BisTeCca per l'analisi dei bispettri in modelli di universo oltre la cosmologia standard LambdaCDM, introducendo una componente di neutrini massicci. Si mostrano infine gli effetti su spettro di potenza e bispettro, ottenuti col nostro codice BisTeCca, e si confrontano modelli di universo con diverse masse di neutrini.

Performance and economic indicators of a large scale fish farming in Mato Grosso, Brazil

Performance and economic indicators of a large scale fish farm that produces round fish, located in Mato Grosso State, Brazil, were evaluated. The 130.8 ha-water surface area was distributed in 30 ponds. Average total production costs and the following economic indicators were calculated: gross income (GI), gross margin (GM), gross margin index (GMI), profitability index (PI) and profit (P) for the farm as a whole and for ten ponds individually. Production performance indicators were also obtained, such as: production cycle (PC), apparent feed conversion (FC), average biomass storage (ABS), survival index (SI) and final average weight (FAW). The average costs to produce an average 2.971 kg.ha-1 per year were: R$ 2.43, R$ 0.72 and R$ 3.15 as average variable, fixed and total costs, respectively. Gross margin and profit per year per hectare of water surface were R$ 2,316.91 and R$ 180.98, respectively. The individual evaluation of the ponds showed that the best pond performance was obtained for PI 38%, FC 1.7, ABS 0.980 kg.m-2, TS 56%, FAW 1.873 kg with PC of 12.3 months. The worst PI was obtained for the pond that displayed losses of 138%, FC 2.6, ABS 0.110 kg.m-2, SI 16% and FAW 1.811 kg. However, large scale production of round-fish in farms is economically feasible. The studied farm displays favorable conditions to improve performance and economic indicators, but it is necessary to reproduce the breeding techniques and performance indicators achieved in few ponds to the entire farm.