Interaction between wave and coastal structure: Validation of two lagrangian numerical models with experimental results marine 2011

Numerical modeling of the interaction among waves and coastal structures is a challenge due to the many nonlinear phenomena involved, such as, wave propagation, wave transformation with water depth, interaction among incident and reflected waves, run-up / run-down and wave overtopping. Numerical models based on Lagrangian formulation, like SPH (Smoothed Particle Hydrodynamics), allow simulating complex free surface flows. The validation of these numerical models is essential, but comparing numerical results with experimental data is not an easy task. In the present paper, two SPH numerical models, SPHysics LNEC and SPH UNESP, are validated comparing the numerical results of waves interacting with a vertical breakwater, with data obtained in physical model tests made in one of the LNEC's flume. To achieve this validation, the experimental set-up is determined to be compatible with the Characteristics of the numerical models. Therefore, the flume dimensions are exactly the same for numerical and physical model and incident wave characteristics are identical, which allows determining the accuracy of the numerical models, particularly regarding two complex phenomena: wave-breaking and impact loads on the breakwater. It is shown that partial renormalization, i.e. renormalization applied only for particles near the structure, seems to be a promising compromise and an original method that allows simultaneously propagating waves, without diffusion, and modeling accurately the pressure field near the structure.

Thermochemical equilibrium modeling of biomass downdraft gasifier: Stoichiometric models

The aim of this work is to develop stoichiometric equilibrium models that permit the study of parameters effect in the gasification process of a particular feedstock. In total four models were tested in order to determine the syngas composition. One of these four models, called M2, was based on the theoretical equilibrium constants modified by two correction factors determined using published experimental data. The other two models, M3 and M4 were based in correlations, while model M4 was based in correlations to determine the equilibrium constants, model M3 was based in correlations that relate the H-2, CO and CO2 content on the synthesis gas. Model M2 proved to be the more accurate and versatile among these four models, and also showed better results than some previously published models. Also a case study for the gasification of a blend of hardwood chips and glycerol at 80% and 20% respectively, was performed considering equivalence ratios form 0.3 to 0.5, moisture contents from 0%-20% and oxygen percentages in the gasification agent of 100%, 60% and 21%. (C) 2013 Elsevier Ltd. All rights reserved.

Egg production curve fitting using nonlinear models for selected and nonselected lines of White Leghorn hens

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

Low-Resolution Molecular Models Reveal the Oligomeric State of the PPAR and the Conformational Organization of Its Domains in Solution

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

Comments about some species abundance patterns: classic, neutral, and niche partitioning models

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Age constraints and fine tuning in variable-mass particle models

VAMP (variable-mass particle) scenarios, in which the mass of the cold dark matter particles is a function of the scalar field responsible for the present acceleration of the Universe, have been proposed as a solution to the cosmic coincidence problem, since in the attractor regime both dark energy and dark matter scale in the same way. We find that only a narrow region in parameter space leads to models with viable values for the Hubble constant and dark energy density today. In the allowed region, the dark energy density starts to dominate around the present epoch and consequently such models cannot solve the coincidence problem. We show that the age of the Universe in this scenario is considerably higher than the age for noncoupled dark energy models, and conclude that more precise independent measurements of the age of the Universe would be useful in distinguishing between coupled and noncoupled dark energy models.

T-duality of axial and vector dyonic integrable models

A general construction of affine nonabelian (NA)-Toda models in terms of the axial and vector gauged two loop WZNW model is discussed. They represent integrable perturbations of the conformal sigma -models (with tachyons included) describing (charged) black hole type string backgrounds. We study the off-critical T-duality between certain families of axial and vector type integrable models for the case of affine NA-Toda theories with one global U(1) symmetry. In particular we find the Lie algebraic condition defining a subclass of T-selfdual torsionless NA-Toda models and their zero curvature representation. (C) 2001 Academic Press.

Short and long period optimization of drug doses in the treatment of AIDS

Técnicas de otimização numérica são úteis na solução de problemas de determinação da melhor entrada para sistemas descritos por modelos matemáticos e cujos objetivos podem ser expressos de uma maneira quantitativa. Este trabalho aborda o problema de otimizar as dosagens dos medicamentos no tratamento da AIDS em termos de um balanço entre a resposta terapêutica e os efeitos colaterais. Um modelo matemático para descrever a dinâmica do vírus HIV e células CD4 é utilizado para calcular a dosagem ótima do medicamento no tratamento a curto prazo de pacientes com AIDS por um método de otimização direta utilizando uma função custo do tipo Bolza. Os parâmetros do modelo foram ajustados com dados reais obtidos da literatura. Com o objetivo de simplificar os procedimentos numéricos, a lei de controle foi expressa em termos de uma expansão em séries que, após truncamento, permite obter controles sub-ótimos. Quando os pacientes atingem um estado clínico satisfatório, a técnica do Regulador Linear Quadrático (RLQ) é utilizada para determinar a dosagem permanente de longo período para os medicamentos. As dosagens calculadas utilizando a técnica RLQ , tendem a ser menores do que a equivalente terapia de dose constante em termos do expressivo aumento na contagem das células T+ CD4 e da redução da densidade de vírus livre durante um intervalo fixo de tempo.

Test systems and mathematical models for transmission network expansion planning

The data of four networks that can be used in carrying out comparative studies with methods for transmission network expansion planning are given. These networks are of various types and different levels of complexity. The main mathematical formulations used in transmission expansion studies-transportation models, hybrid models, DC power flow models, and disjunctive models are also summarised and compared. The main algorithm families are reviewed-both analytical, combinatorial and heuristic approaches. Optimal solutions are not yet known for some of the four networks when more accurate models (e.g. The DC model) are used to represent the power flow equations-the state of the art with regard to this is also summarised. This should serve as a challenge to authors searching for new, more efficient methods.

Distribution Transformer Modeling for Application in Three-Phase Power Flow Algorithm

In this paper, it is presented a methodology for three-phase distribution transformer modeling, considering several types of transformer configuration, to be used in algorithms of power flow in three-phase radial distribution networks. The paper provides a detailed discussion about the models and the results from an implementation of the power flow algorithm. The results, taken from three different networks, are presented for several transformer configurations and for voltage regulators as well.

Robust linear mixed models with normal/independent distributions and Bayesian MCMC implementation

Linear mixed effects models have been widely used in analysis of data where responses are clustered around some random effects, so it is not reasonable to assume independence between observations in the same cluster. In most biological applications, it is assumed that the distributions of the random effects and of the residuals are Gaussian. This makes inferences vulnerable to the presence of outliers. Here, linear mixed effects models with normal/independent residual distributions for robust inferences are described. Specific distributions examined include univariate and multivariate versions of the Student-t, the slash and the contaminated normal. A Bayesian framework is adopted and Markov chain Monte Carlo is used to carry out the posterior analysis. The procedures are illustrated using birth weight data on rats in a texicological experiment. Results from the Gaussian and robust models are contrasted, and it is shown how the implementation can be used for outlier detection. The thick-tailed distributions provide an appealing robust alternative to the Gaussian process in linear mixed models, and they are easily implemented using data augmentation and MCMC techniques.

Molecular modeling databases: A new way in the search of protein targets for drug development

DBMODELING is a relational database of annotated comparative protein structure models and their metabolic, pathway characterization. It is focused on enzymes identified in the genomes of Mycobacterium tuberculosis and Xylella fastidiosa. The main goal of the present database is to provide structural models to be used in docking simulations and drug design. However, since the accuracy of structural models is highly dependent on sequence identity between template and target, it is necessary to make clear to the user that only models which show high structural quality should be used in such efforts. Molecular modeling of these genomes generated a database, in which all structural models were built using alignments presenting more than 30% of sequence identity, generating models with medium and high accuracy. All models in the database are publicly accessible at http://www.biocristalografia.df.ibilce.unesp.br/tools. DBMODELING user interface provides users friendly menus, so that all information can be printed in one stop from any web browser. Furthermore, DBMODELING also provides a docking interface, which allows the user to carry out geometric docking simulation, against the molecular models available in the database. There are three other important homology model databases: MODBASE, SWISSMODEL, and GTOP. The main applications of these databases are described in the present article. © 2007 Bentham Science Publishers Ltd.

The structural origin and biological function of pH-sensitivity in firefly luciferases

Firefly luciferases are called pH-sensitive because their bioluminescence spectra display a typical red-shift at acidic pH, higher temperatures, and in the presence of heavy metal cations, whereas other beetle luciferases (click beetles and railroadworms) do not, and for this reason they are called pH-insensitive. Despite many studies on firefly luciferases, the origin of pH-sensitivity is far from being understood. This subject is revised in view of recent results. Some substitutions of amino-acid residues influencing pH-sensitivity in firefly luciferases have been identified. Sequence comparison, site-directed mutagenesis and modeling studies have shown a set of residues differing between pH-sensitive and pH-insensitive luciferases which affect bioluminescence colors. Some substitutions dramatically affecting bioluminescence colors in both groups of luciferases are clustered in the loop between residues 223-235 (Photinus pyralis sequence). A network of hydrogen bonds and salt bridges involving the residues N229-S284-E311-R337 was found to be important for affecting bioluminescence colors. It is suggested that these structural elements may affect the benzothiazolyl side of the luciferin-binding site affecting bioluminescence colors. Experimental evidence suggest that the residual red light emission in pH-sensitive luciferases could be a vestige that may have biological importance in some firefly species. Furthermore, the potential utility of pH-sensitivity for intracellular biosensing applications is considered. © The Royal Society of Chemistry and Owner Societies.

The accuracy potential of Galileo E5/E1 pseudoranges for surveying and mapping

In the paper we discuss the potential of the new Galileo signals for pseudorange based surveying and mapping in open areas under optimal reception conditions (open sky scenarios) and suboptimal ones (multipath created by moderate to thick tree coverage). The paper reviews the main features of the Galileo E5 AltBOC and E1 CBOC signals; describes the simulation strategy, models and algorithms to generate realistic E5 and E1 pseudoranges with and without multipath sources; describes the ionosphere modeling strategy, models and algorithms and discusses and presents the expected positioning accuracy and precision results. According to the simulations performed, pseudoranges can be extracted from the Galileo E5 AltBOC signals with tracking errors (1-σ level) ranging from 0.02 m (open sky scenarios) to 0.08 m (tree covered scenarios) whereas for the Galileo E1 CBOC signals the tracking errors range between 0.25 m to 2.00 m respectively. With these tracking errors and with the explicit estimation of the ionosphere parameters, simulations indicate real-time open sky cm-level horizontal positioning precisions and dm-level vertical ones and dm-level accuracies for both the horizontal and vertical position components.

Isolation, homology modeling and renal effects of a C-type natriuretic peptide from the venom of the Brazilian yellow scorpion (Tityus serrulatus)

Mammalian natriuretic peptides (NPs) have been extensively investigated for use as therapeutic agents in the treatment of cardiovascular diseases. Here, we describe the isolation, sequencing and tridimensional homology modeling of the first C-type natriuretic peptide isolated from scorpion venom. In addition, its effects on the renal function of rats and on the mRNA expression of natriuretic peptide receptors in the kidneys are delineated. Fractionation of Tityusserrulatus venom using chromatographic techniques yielded a peptide with a molecular mass of 2190.64Da, which exhibited the pattern of disulfide bridges that is characteristic of a C-type NP (TsNP, T. serrulatus Natriuretic Peptide). In the isolated perfused rat kidney assay, treatment with two concentrations of TsNP (0.03 and 0.1μg/mL) increased the perfusion pressure, glomerular filtration rate and urinary flow. After 60min of treatment at both concentrations, the percentages of sodium, potassium and chloride transport were decreased, and the urinary cGMP concentration was elevated. Natriuretic peptide receptor-A (NPR-A) mRNA expression was down regulated in the kidneys treated with both concentrations of TsNP, whereas NPR-B, NPR-C and CG-C mRNAs were up regulated at the 0.1μg/mL concentration. In conclusion, this work describes the isolation and modeling of the first natriuretic peptide isolated from scorpion venom. In addition, examinations of the renal actions of TsNP indicate that its effects may be related to the activation of NPR-B, NPR-C and GC-C. © 2013 Elsevier Ltd.