Modeling and simulation of severe slugging with mass transfer effects

A mathematical model and numerical simulations are presented to investigate the dynamics of gas, oil and water flow in a pipeline-riser system. The pipeline is modeled as a lumped parameter system and considers two switchable states: one in which the gas is able to penetrate into the riser and another in which there is a liquid accumulation front, preventing the gas from penetrating the riser. The riser model considers a distributed parameter system, in which movable nodes are used to evaluate local conditions along the subsystem. Mass transfer effects are modeled by using a black oil approximation. The model predicts the liquid penetration length in the pipeline and the liquid level in the riser, so it is possible to determine which type of severe slugging occurs in the system. The method of characteristics is used to simplify the differentiation of the resulting hyperbolic system of equations. The equations are discretized and integrated using an implicit method with a predictor-corrector scheme for the treatment of the nonlinearities. Simulations corresponding to severe slugging conditions are presented and compared to results obtained with OLGA computer code, showing a very good agreement. A description of the types of severe slugging for the three-phase flow of gas, oil and water in a pipeline-riser system with mass transfer effects are presented, as well as a stability map. (C) 2011 Elsevier Ltd. All rights reserved.

Her2p molecular modeling, mutant analysis and intramitochondrial localization

Bacterial GatCAB amidotransferases are responsible for the transamidation of mischarged glutamyl-tRNA(Gln) into glutaminyl-tRNA(Gln). Mitochondria matrix also has a multienzymatic complex necessary for the transamidation of glutamyl-tRNA(Gln). Gtf1p, Her2p and Pet112p are the constituents of mitochondrial GatFAB amidotransferase complex. Her2p is subunit A of GatFAB complex, while Gtf1p is subunit F, a connector protein between Pet112p (subunit B) and Her2p. Here we evaluate through molecular modeling and amino acid correlation analysis the HER2 protein family. Localization studies indicated that Her2p is predominantly localized in the mitochondrial outer membrane, but it is also located in the mitochondrial matrix where together with Pet112p and Gtf1p constitutes the GatFAB complex. Finally, HER2 random mutagenesis unveiled important residues that provide thermo stability for the complex and are differently suppressed by overexpression of GTF1 or PET112. For instance, her2/ts11 mutant showed its fermentative growth impaired, and poorly rescued by GTF1 indicating that Her2p unknown function in the mitochondria outer membrane affects cell viability.

Feature-oriented regional modeling and simulations (FORMS) for the western South Atlantic: Southeastern Brazil region

The multi-scale synoptic circulation system in the southeastern Brazil (SEBRA) region is presented using a feature-oriented approach. Prevalent synoptic circulation structures, or ""features,"" are identified from previous observational studies. These features include the southward-flowing Brazil Current (BC), the eddies off Cabo Sao Tome (CST - 22 degrees S) and off Cabo Frio (CF - 23 degrees S), and the upwelling region off CF and CST. Their synoptic water-mass (T-S) structures are characterized and parameterized to develop temperature-salinity (T-S) feature models. Following [Gangopadhyay, A., Robinson, A.R., Haley, PJ., Leslie, W.J., Lozano, C.j., Bisagni, J., Yu, Z., 2003. Feature-oriented regional modeling and simulation (forms) in the gulf of maine and georges bank. Cont. Shelf Res. 23 (3-4), 317-353] methodology, a synoptic initialization scheme for feature-oriented regional modeling and simulation (FORMS) of the circulation in this region is then developed. First, the temperature and salinity feature-model profiles are placed on a regional circulation template and objectively analyzed with available background climatology in the deep region. These initialization fields are then used for dynamical simulations via the Princeton Ocean Model (POM). A few first applications of this methodology are presented in this paper. These include the BC meandering, the BC-eddy interaction and the meander-eddy-upwelling system (MEUS) simulations. Preliminary validation results include realistic wave-growth and eddy formation and sustained upwelling. Our future plan includes the application of these feature models with satellite, in-situ data and advanced data-assimilation schemes for nowcasting and forecasting the SEBRA region. (c) 2008 Elsevier Ltd. All rights reserved.

ESTIMATING REACTION CONSTANTS BY AB INITIO MOLECULAR MODELING: A STUDY ON THE OXIDATION OF PHENOL TO CATECHOL AND HYDROQUINONE IN ADVANCED OXIDATION PROCESSES

Molecular modeling is growing as a research tool in Chemical Engineering studies, as can be seen by a simple research on the latest publications in the field. Molecular investigations retrieve information on properties often accessible only by expensive and time-consuming experimental techniques, such as those involved in the study of radical-based chain reactions. In this work, different quantum chemical techniques were used to study phenol oxidation by hydroxyl radicals in Advanced Oxidation Processes used for wastewater treatment. The results obtained by applying a DFT-based model showed good agreement with experimental values available, as well as qualitative insights into the mechanism of the overall reaction chain. Solvation models were also tried, but were found to be limited for this reaction system within the considered theoretical level without further parameterization.

Synthesis, Biological Evaluation, And Molecular Modeling of Chalcone Derivatives As Potent Inhibitors of Mycobacterium tuberculosis Protein Tyrosine Phosphatases (PtpA and PtpB)

Tuberculosis (TB) is a major infectious disease caused by Mycobacterium tuberculosis (Mtb). According to the World Health Organization (WHO), about 1.8 million people die from TB and 10 million new cases are recorded each year. Recently, a new series of naphthylchalcones has been identified as inhibitors of Mtb protein tyrosine phosphatases (PTPs). In this work, 100 chalcones were designed, synthesized, and investigated for their inhibitory properties against MtbPtps. Structure-activity relationships (SAR) were developed, leading to the discovery of new potent inhibitors with IC50 values in the low-micromolar range. Kinetic studies revealed competitive inhibition and high selectivity toward the Mtb enzymes. Molecular modeling investigations were carried out with the aim of revealing the most relevant structural requirements underlying the binding affinity and selectivity of this series of inhibitors as potential anti-TB drugs.

Estimating reaction constants by ab initio molecular modeling: a study on the oxidation of phenol to catechol and hydroquinone in advanced oxidation processes

Molecular modeling is growing as a research tool in Chemical Engineering studies, as can be seen by a simple research on the latest publications in the field. Molecular investigations retrieve information on properties often accessible only by expensive and time-consuming experimental techniques, such as those involved in the study of radical-based chain reactions. In this work, different quantum chemical techniques were used to study phenol oxidation by hydroxyl radicals in Advanced Oxidation Processes used for wastewater treatment. The results obtained by applying a DFT-based model showed good agreement with experimental values available, as well as qualitative insights into the mechanism of the overall reaction chain. Solvation models were also tried, but were found to be limited for this reaction system within the considered theoretical level without further parameterization.

Polymeric micelles and molecular modeling applied to the development of radiopharmaceuticals

Micelles composed of amphiphilic copolymers linked to a radioactive element are used in nuclear medicine predominantly as a diagnostic application. A relevant advantage of polymeric micelles in aqueous solution is their resulting particle size, which can vary from 10 to 100 nm in diameter. In this review, polymeric micelles labeled with radioisotopes including technetium (99mTc) and indium (111In), and their clinical applications for several diagnostic techniques, such as single photon emission computed tomography (SPECT), gamma-scintigraphy, and nuclear magnetic resonance (NMR), were discussed. Also, micelle use primarily for the diagnosis of lymphatic ducts and sentinel lymph nodes received special attention. Notably, the employment of these diagnostic techniques can be considered a significant tool for functionally exploring body systems as well as investigating molecular pathways involved in the disease process. The use of molecular modeling methodologies and computer-aided drug design strategies can also yield valuable information for the rational design and development of novel radiopharmaceuticals.

Inhibitors of Trypanosoma brucei trypanothione reductase: comparative molecular field analysis modeling and structural basis for selective inhibition

Background: Sleeping sickness is a major cause of death in Africa. Since no secure treatment is available, the development of novel therapeutic agents is urgent. In this context, the enzyme trypanothione reductase (TR) is a prominent molecular target that has been investigated in drug design for sleeping sickness. Results: In this study, comparative molecular field analysis models were generated for a series of Trypanosoma brucei TR inhibitors. Statistically significant results were obtained and the models were applied to predict the activity of external test sets, with good correlation between predicted and experimental results. We have also investigated the structural requirements for the selective inhibition of the parasite's enzyme over the human glutathione reductase. Conclusion: The quantitative structure-activity relationship models provided valuable information regarding the essential molecular requirements for the inhibitory activity upon the target protein, providing important insights into the design of more potent and selective TR inhibitors.

Mathematical modeling and analysis of the particle interactions in the direct filtration using the colloidal theory

This work used the colloidal theory to describe forces and energy interactions of colloidal complexes in the water and those formed during filtration run in direct filtration. Many interactions of particle energy profiles between colloidal surfaces for three geometries are presented here in: spherical, plate and cylindrical; and four surface interactions arrangements: two cylinders, two spheres, two plates and a sphere and a plate. Two different situations were analyzed, before and after electrostatic destabilization by action of the alum sulfate as coagulant in water studies samples prepared with kaolin. In the case were used mathematical modeling by extended DLVO theory (from the names: Derjarguin-Landau-Verwey-Overbeek) or XDLVO, which include traditional approach of the electric double layer (EDL), surfaces attraction forces or London-van der Waals (LvdW), esteric forces and hydrophobic forces, additionally considering another forces in colloidal system, like molecular repulsion or Born Repulsion and Acid-Base (AB) chemical function forces from Lewis.

Molecular barcode and morphological analyses reveal the taxonomic and biogeographical status of the striped-legged hermit crab species Clibanarius sclopetarius (Herbst, 1796) and Clibanarius vittatus (Bosc, 1802) (Decapoda: Diogenidae)

The taxonomic status of the species Clibanarius sclopetarius (Herbst, 1796) and Clibanarius vittatus (Bosc, 1802), which have sympatric biogeographical distributions restricted to the western Atlantic Ocean, is based only on differences in the colour pattern of the walking legs of adults. Their morphological similarity led to the suggestion that they be synonymised. In order to investigate this hypothesis, we included species of Clibanarius Dana, 1892 in a molecular phylogenetic analysis of partial sequences of the mitochondrial 16S rDNA gene and the COI barcode region. In addition, we combined the molecular results with morphological observations obtained from several samples of these two species. The genetic divergences of the 16S rDNA and COI sequences between C. sclopetarius and C. vittatus ranged from 4.5 to 5.9% and 9.4 to 11.9%, which did not justify their synonymisation. Differences in the telson morphology, chela ornamentation, and coloration of the eyestalks and antennal peduncle provided support for the separation of the two species. Another interesting result was a considerable genetic difference found between populations of C. vittatus from Brazil and the Gulf of Mexico, which may indicate the existence of two homonymous species.

Molecular phylogeny and morphometric analyses reveal deep divergence between Amazonia and Atlantic Forest species of Dendrophryniscus

Dendrophryniscus is an early diverging clade of bufonids represented by few small-bodied species distributed in Amazonia and the Atlantic Forest. We used mitochondrial (414 bp of 12S, 575 bp of 16S genes) and nuclear DNA (785 bp of RAG-1) to investigate phylogenetic relationships and the timing of diversification within the genus. These molecular data were gathered from 23 specimens from 19 populations, including eight out of the 10 nominal species of the genus as well as Rhinella boulengeri. Analyses also included sequences of representatives of 18 other bufonid genera that were publically available. We also examined morphological characters to analyze differences within Dendrophryniscus. We found deep genetic divergence between an Amazonian and an Atlantic Forest clade, dating back to Eocene. Morphological data corroborate this distinction. We thus propose to assign the Amazonian species to a new genus, Amazonella. The species currently named R. boulengeri, which has been previously assigned to the genus Rhamphophryne, is shown to be closely related to Dendrophryniscus species. Our findings illustrate cryptic trends in bufonid morphological evolution, and point to a deep history of persistence and diversification within the Amazonian and Atlantic rainforests. We discuss our results in light of available paleoecological data and the biogeographic patterns observed in other similarly distributed groups. (C) 2011 Elsevier Inc. All rights reserved.

Spiroplasma in Drosophila melanogaster Populations: Prevalence, Male-Killing, Molecular Identification, and No Association with Wolbachia

Spiroplasma endosymbionts are maternally transmitted bacteria that may kill infected sons resulting in the production of female-biased broods. The prevalence of male killers varies considerably both between and within species. Here, we evaluate the spatial and temporal status of male-killing and non-male-killing Spiroplasma infection in three Brazilian populations of Drosophila melanogaster, nearly a decade after the first occurrence report for this species. The incidence of the male-killing Spiroplasma ranged from close to 0 to 17.7 % (so far the highest estimate for a Drosophila species) with a suggestion of temporal decline in a population. We also found non-male-killing Spiroplasma coexisting in one population at lower prevalence (3-5 %), and we did not detect it in the other two. This may be taken as a suggestion of a spreading advantage conferred by the male-killing strategy. Sequencing two loci, we identified the phylogenetic position of Spiroplasma strains from the three localities, showing that all strains group closely in the poulsonii clade. Due to intensive sampling effort, we were able to test the association between Spiroplasma infections and another widespread endosymbiont, Wolbachia, whose prevalence ranged from 81.8 to 100 %. The prevalence of Wolbachia did not differ between Spiroplasma-infected and uninfected strains in our largest sample nor were the prevalences of the two endosymbionts associated across localities.

Molecular chemistry and the missing mass problem in planetary nebulae

Context. Detections of molecular lines, mainly from H-2 and CO, reveal molecular material in planetary nebulae. Observations of a variety of molecules suggest that the molecular composition in these objects differs from that found in interstellar clouds or in circumstellar envelopes. The success of the models, which are mostly devoted to explain molecular densities in specific planetary nebulae, is still partial however. Aims. The present study aims at identifying the influence of stellar and nebular properties on the molecular composition of planetary nebulae by means of chemical models. A comparison of theoretical results with those derived from the observations may provide clues to the conditions that favor the presence of a particular molecule. Methods. A self-consistent photoionization numerical code was adapted to simulate cold molecular regions beyond the ionized zone. The code was used to obtain a grid of models and the resulting column densities are compared with those inferred from observations. Results. Our models show that the inclusion of an incident flux of X-rays is required to explain the molecular composition derived for planetary nebulae. We also obtain a more accurate relation for the N(CO)/N(H-2) ratio in these objects. Molecular masses obtained by previous works in the literature were then recalculated, showing that these masses can be underestimated by up to three orders of magnitude. We conclude that the problem of the missing mass in planetary nebulae can be solved by a more accurate calculation of the molecular mass.

Serologic and molecular diagnostic and bioassay in mice for detection of Toxoplasma gondii in free ranges chickens from Pantanal of Mato Grosso do Sul

Holsback L., Pena H.F.J., Ragozo A., Lopes E. G., Gennari S. M. & Soares R. M. 2012. Serologic and molecular diagnostic and bioassay in mice for detection of Toxoplasma gondii in free range chickens from Pantanal of Mato Grosso do Sul. Pesquisa Veterinaria Brasileira 32(8): 721-726. Setor de Veterinaria e Producao Animal, Universidade Estadual do Norte do Parana, Campus Luiz Meneghel, Rodovia BR 369 Km 54, Bandeirantes, PR 86360-000, Brazil. E-mail: lhsfertonani@uenp.edu.br The aim of this study was to investigate the occurrence of Toxoplasma gondii and compare the results obtained in the Modified Agglutination Test (MAT), Polimerase Chain Reaction (PCR) and bioassay in mice. In order to accomplish this, 40 free-range chickens from eight farms in neighboring areas to the Pantanal in Nhecolandia, Mato Grosso do Sul, were euthanized and blood samples, brain and heart were collected. The occurrence of anti-T. gondii antibodies found in chickens was 67.5% (27 samples), considering as a cutoff point the dilution 1:5. Among the samples analyzed, 7 (25.9%) were positive in the dilution 1: 5, 3 (11.1%) in 1: 10, 2 (7.4%) in 1: 20, 3 (11.1%) in 1: 320, 1 (3.7%) in 1: 640, 3 (11.1%) in 1: 1280, 2 (7.4%) in 1: 2560, 4 (14.8%) in 1: 5120 and 2 (7.4%) in 1: 10.240. From the mixture of tissue samples (brain and heart) from the chickens analyzed, 16 (40%) presented electrophoretic bands compatible with T. gondii by PCR (gene B1). In the comparison of techniques, 59.26% positivity in PCR was revealed among animals that were seropositive in MAT (cutoff 1: 5). From 141 inoculated mice, six (4.44%) died of acute toxoplasmosis between 15 and 23 days after inoculation. Surviving mice were sacrificed at 74 days after inoculation, and a total of 28 cysts were found in the brains of 10 distinct groups. From the seropositive hens, 27 bioassays were performed and 11 (40.7%) isolates were obtained. A greater number of isolations happened in mice that were inoculated with tissues from chickens that had high titers for anti-T. gondii antibodies. Chronic infection in mice was observed in nine groups (33.3%) from five different properties. Among the surviving mice, 25.6% were positive for T. gondii in MAT (1: 25). From mice positive in PCR, 87.5% were also positive in MAT. Among the PCR-negative mice, 5.2% were positive for T. gondii in MAT. It can be concluded through this study that the occurrence of infecton by T. gondii in the rural properties studied was high, that PCR directed to gene B1 does not confirm the viability of the parasite, but it can be used as a screening method for the selection of chickens infected by T. gondii, that the animals with titer greater than 10 must be prioritized for the selection of animals for bioassay, since for them, the chances of isolating the parasite are greater and that seroconversion in experimentally infected mice is not a good indicator for isolating the agent.

Modeling and Identification of an Open-frame Underwater Vehicle: The Yaw Motion Dynamics

A semi-autonomous unmanned underwater vehicle (UUV), named LAURS, is being developed at the Laboratory of Sensors and Actuators at the University of Sao Paulo. The vehicle has been designed to provide inspection and intervention capabilities in specific missions of deep water oil fields. In this work, a method of modeling and identification of yaw motion dynamic system model of an open-frame underwater vehicle is presented. Using an on-board low cost magnetic compass sensor the method is based on the utilization of an uncoupled 1-DOF (degree of freedom) dynamic system equation and the application of the integral method which is the classical least squares algorithm applied to the integral form of the dynamic system equations. Experimental trials with the actual vehicle have been performed in a test tank and diving pool. During these experiments, thrusters responsible for yaw motion are driven by sinusoidal voltage signal profiles. An assessment of the feasibility of the method reveals that estimated dynamic system models are more reliable when considering slow and small sinusoidal voltage signal profiles, i.e. with larger periods and with relatively small amplitude and offset.