Showing papers by "State University of Campinas published in 2009"

PACKMOL: a package for building initial configurations for molecular dynamics simulations.

Abstract: Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system's overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules must keep safe pairwise distances. Obtaining such a molecular arrangement can be considered a packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules must be greater than some specified tolerance. We have developed a code able to pack millions of atoms, grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straightforward. In addition, different atoms belonging to the same molecule may also be restricted to different spatial regions, in such a way that more ordered molecular arrangements can be built, as micelles, lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies from a few seconds to a few minutes in a personal computer. The input files are simple and currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and can be downloaded from http://www.ime.unicamp.br/~martinez/packmol/.

Comprehensive Approach to Modeling and Simulation of Photovoltaic Arrays

Abstract: This paper proposes a method of modeling and simulation of photovoltaic arrays. The main objective is to find the parameters of the nonlinear I-V equation by adjusting the curve at three points: open circuit, maximum power, and short circuit. Given these three points, which are provided by all commercial array data sheets, the method finds the best I-V equation for the single-diode photovoltaic (PV) model including the effect of the series and parallel resistances, and warranties that the maximum power of the model matches with the maximum power of the real array. With the parameters of the adjusted I-V equation, one can build a PV circuit model with any circuit simulator by using basic math blocks. The modeling method and the proposed circuit model are useful for power electronics designers who need a simple, fast, accurate, and easy-to-use modeling method for using in simulations of PV systems. In the first pages, the reader will find a tutorial on PV devices and will understand the parameters that compose the single-diode PV model. The modeling method is then introduced and presented in details. The model is validated with experimental data of commercial PV arrays.

Saturated fatty acids produce an inflammatory response predominantly through the activation of TLR4 signaling in hypothalamus: implications for the pathogenesis of obesity.

Abstract: In animal models of diet-induced obesity, the activation of an inflammatory response in the hypothalamus produces molecular and functional resistance to the anorexigenic hormones insulin and leptin. The primary events triggered by dietary fats that ultimately lead to hypothalamic cytokine expression and inflammatory signaling are unknown. Here, we test the hypothesis that dietary fats act through the activation of toll-like receptors 2/4 and endoplasmic reticulum stress to induce cytokine expression in the hypothalamus of rodents. According to our results, long-chain saturated fatty acids activate predominantly toll-like receptor 4 signaling, which determines not only the induction of local cytokine expression but also promotes endoplasmic reticulum stress. Rats fed on a monounsaturated fat-rich diet do not develop hypothalamic leptin resistance, whereas toll-like receptor 4 loss-of-function mutation and immunopharmacological inhibition of toll-like receptor 4 protects mice from diet-induced obesity. Thus, toll-like receptor 4 acts as a predominant molecular target for saturated fatty acids in the hypothalamus, triggering the intracellular signaling network that induces an inflammatory response, and determines the resistance to anorexigenic signals.

Systematic measurements of identified particle spectra in pp, d+Au, and Au+Au collisions at the star detector.

Abstract: Identified charged-particle spectra of pi(+/-), K(+/-), p, and (p) over bar at midrapidity (vertical bar y vertical bar < 0.1) measured by the dE/dx method in the STAR (solenoidal tracker at the BNL Relativistic Heavy Ion Collider) time projection chamber are reported for pp and d + Au collisions at root s(NN) = 200 GeV and for Au + Au collisions at 62.4, 130, and 200 GeV. Average transverse momenta, total particle production, particle yield ratios, strangeness, and baryon production rates are investigated as a function of the collision system and centrality. The transverse momentum spectra are found to be flatter for heavy particles than for light particles in all collision systems; the effect is more prominent for more central collisions. The extracted average transverse momentum of each particle species follows a trend determined by the total charged-particle multiplicity density. The Bjorken energy density estimate is at least several GeV/fm(3) for a formation time less than 1 fm/c. A significantly larger net-baryon density and a stronger increase of the net-baryon density with centrality are found in Au + Au collisions at 62.4 GeV than at the two higher energies. Antibaryon production relative to total particle multiplicity is found to be constant over centrality, but increases with the collision energy. Strangeness production relative to total particle multiplicity is similar at the three measured RHIC energies. Relative strangeness production increases quickly with centrality in peripheral Au + Au collisions, to a value about 50% above the pp value, and remains rather constant in more central collisions. Bulk freeze-out properties are extracted from thermal equilibrium model and hydrodynamics-motivated blast-wave model fits to the data. Resonance decays are found to have little effect on the extracted kinetic freeze-out parameters because of the transverse momentum range of our measurements. The extracted chemical freeze-out temperature is constant, independent of collision system or centrality; its value is close to the predicted phase-transition temperature, suggesting that chemical freeze-out happens in the vicinity of hadronization and the chemical freeze-out temperature is universal despite the vastly different initial conditions in the collision systems. The extracted kinetic freeze-out temperature, while similar to the chemical freeze-out temperature in pp, d + Au, and peripheral Au + Au collisions, drops significantly with centrality in Au + Au collisions, whereas the extracted transverse radial flow velocity increases rapidly with centrality. There appears to be a prolonged period of particle elastic scatterings from chemical to kinetic freeze-out in central Au + Au collisions. The bulk properties extracted at chemical and kinetic freeze-out are observed to evolve smoothly over the measured energy range, collision systems, and collision centralities.

Modeling and circuit-based simulation of photovoltaic arrays

Abstract: This paper presents an easy and accurate method of modeling photovoltaic arrays. The method is used to obtain the parameters of the array model using information from the datasheet. The photovoltaic array model can be simulated with any circuit simulator. The equations of the model are presented in details and the model is validated with experimental data. Finally, simulation examples are presented. This paper is useful for power electronics designers and researchers who need an effective and straightforward way to model and simulate photovoltaic arrays.

LIPSIN: line speed publish/subscribe inter-networking

Abstract: A large fraction of today's Internet applications are internally publish/subscribe in nature; the current architecture makes it cumbersome and inept to support them. In essence, supporting efficient publish/subscribe requires data-oriented naming, efficient multicast, and in-network caching. Deployment of native IP-based multicast has failed, and overlay-based multicast systems are inherently inefficient. We surmise that scalable and efficient publish/subscribe will require substantial architectural changes, such as moving from endpoint-oriented systems to information-centric architectures.In this paper, we propose a novel multicast forwarding fabric, suitable for large-scale topic-based publish/subscribe. Due to very simple forwarding decisions and small forwarding tables, the fabric may be more energy efficient than the currently used ones. To understand the limitations and potential, we provide efficiency and scalability analysis via simulations and early measurements from our two implementations. We show that the system scales up to metropolitan WAN sizes, and we discuss how to interconnect separate networks.

Robustness of quantum discord to sudden death

Abstract: We calculate the dissipative dynamics of two-qubit quantum discord under Markovian environments. We analyze various dissipative channels such as dephasing, depolarizing, and generalized amplitude damping, assuming independent perturbation, in which each qubit is coupled to its own channel. Choosing initial conditions that manifest the so-called sudden death of entanglement, we compare the dynamics of entanglement with that of quantum discord. We show that in all cases where entanglement suddenly disappears, quantum discord vanishes only in the asymptotic limit, behaving similarly to individual decoherence of the qubits, even at finite temperatures. Hence, quantum discord is more robust than the entanglement against decoherence so that quantum algorithms based only on quantum discord correlations may be more robust than those based on entanglement.

Azimuthal charged-particle correlations and possible local strong parity violation

Abstract: Parity-odd domains, corresponding to nontrivial topological solutions of the QCD vacuum, might be created during relativistic heavy-ion collisions. These domains are predicted to lead to charge separation of quarks along the system's orbital momentum axis. We investigate a three-particle azimuthal correlator which is a P even observable, but directly sensitive to the charge separation effect. We report measurements of charged hadrons near center-of-mass rapidity with this observable in Au+Au and Cu+Cu collisions at s(NN)=200 GeV using the STAR detector. A signal consistent with several expectations from the theory is detected. We discuss possible contributions from other effects that are not related to parity violation.

Assessing the effects of temperature on the population of Aedes aegypti, the vector of dengue.

Abstract: Dengue is a vector-borne disease transmitted by the mosquito Aedes aegypti. The incidence of dengue disease shows a clear dependence on seasonal variation. How does the temperature affect the incidence? We addressed this question indirectly by estimating the size of the A. aegypti population for different temperatures applying population dynamics theory. In order to achieve this objective we designed temperature-controlled experiments to assess the entomological parameters regarding the mosquito's life-cycle at different temperatures. By obtaining the mortality, transition and oviposition rates for different stages of the life-cycle of the mosquito we were able to calculate the basic offspring number Q(0), which is the capacity of vector reproduction and ultimately gives the size of the vector population.

Nymphalid butterflies diversify following near demise at the Cretaceous/Tertiary boundary

Abstract: The butterfly family Nymphalidae contains some of the most important non-drosophilid insect model systems for evolutionary and ecological studies, yet the evolutionary history of the group has remained shrouded in mystery. We have inferred a robust phylogenetic hypothesis based on sequences of 10 genes and 235 morphological characters for exemplars of 400 of the 540 valid nymphalid genera representing all major lineages of the family. By dating the branching events, we infer that Nymphalidae originated in the Cretaceous at 90 Ma, but that the ancestors of 10–12 lineages survived the end-Cretaceous catastrophe in the Neotropical and Oriental regions. Patterns of diversification suggest extinction of lineages at the Cretaceous/Tertiary boundary (65 Ma) and subsequent elevated speciation rates in the Tertiary.

Nisin biotechnological production and application: a review

Abstract: Nisin is a natural antimicrobial peptide produced by strains of Lactococcus lactis subsp. lactis that effectively inhibits Gram-positive and Gram-negative bacteria and also the outgrowth of spores of Bacilli and Clostridia. Additionally it has been used as a biopreservative and a potential agent in pharmaceutical, veterinary and health care products. This review focuses on the nisin production in batch cultures utilizing milk skimmed and milk whey as an inexpensive medium for cultivation of L. lactis, aiming to reduce the process cost. At the same time, the exploitation of milk whey as a bacterial substrate can be considered economically advantageous method to help diminish environment pollution problems.

Sensitivity of Patient Outcomes to Pharmacist Interventions. Part I: Systematic Review and Meta-Analysis in Diabetes Management

Abstract: Background:Pharmacists participate in managing diabetes therapy. Despite many reviews, few have quantified the impact of pharmacists' interventions.Objectives:TO identity outcomes sensitive to pharmacists' interventions and quantify their impact through critical literature review.Methods:All original research describing the impact of pharmacists' interventions in the management of diabetic pharmacotherapy was sought in International Pharmaceutical Abstracts, MEDLINE, Embase, Cochrane Register, and Cumulative Index to Nursing & Allied Health Literature from inception through 2006. Two independent reviewers identified articles, compared results, and settled differences through consensus. The Downs-Black scale was used to assess quality. Data included intervention type, patient numbers, demographics, study characteristics, instruments used, data compared, and outcomes reported. A random-effects meta-analysis combined amenable results.Results:Of 302 articles identified, 108 involved pharmacists' interventions...

High-fat diet induces apoptosis of hypothalamic neurons.

Abstract: Consumption of dietary fats is amongst the most important environmental factors leading to obesity. In rodents, the consumption of fat-rich diets blunts leptin and insulin anorexigenic signaling in the hypothalamus by a mechanism dependent on the in situ activation of inflammation. Since inflammatory signal transduction can lead to the activation of apoptotic signaling pathways, we evaluated the effect of high-fat feeding on the induction of apoptosis of hypothalamic cells. Here, we show that consumption of dietary fats induce apoptosis of neurons and a reduction of synaptic inputs in the arcuate nucleus and lateral hypothalamus. This effect is dependent upon diet composition, and not on caloric intake, since pair-feeding is not sufficient to reduce the expression of apoptotic markers. The presence of an intact TLR4 receptor, protects cells from further apoptotic signals. In diet-induced inflammation of the hypothalamus, TLR4 exerts a dual function, on one side activating pro-inflammatory pathways that play a central role in the development of resistance to leptin and insulin, and on the other side restraining further damage by controlling the apoptotic activity.

Flavonoids with gastroprotective activity.

Abstract: Peptic ulcers are a common disorder of the entire gastrointestinal tract that occurs mainly in the stomach and the proximal duodenum. This disease is multifactorial and its treatment faces great difficulties due to the limited effectiveness and severe side effects of the currently available drugs. The use of natural products for the prevention and treatment of different pathologies is continuously expanding throughout the world. This is particularly true with regards to flavonoids, which represent a highly diverse class of secondary metabolites with potentially beneficial human health effects that is widely distributed in the plant kingdom and currently consumed in large amounts in the diet. They display several pharmacological properties in the gastroprotective area, acting as anti-secretory, cytoprotective and antioxidant agents. Besides their action as gastroprotectives, flavonoids also act in healing of gastric ulcers and additionally these polyphenolic compounds can be new alternatives for suppression or modulation of peptic ulcers associated with H. pylori. In this review, we have summarized the literature on ninety-five flavonoids with varying degrees of antiulcerogenic activity, confirming that flavonoids have a therapeutic potential for the more effective treatment of peptic ulcers.

Production of bioethanol and other bio-based materials from sugarcane bagasse: Integration to conventional bioethanol production process

Abstract: Ethanol may be produced using sugarcane bagasse as raw material through the Organosolv process with dilute acid hydrolysis, thus increasing ethanol production with the same cultivated sugarcane area. In this work simulations of bioethanol production from sugarcane juice and bagasse are carried out using software UniSim Design. A typical large scale production plant is considered: 1000 m 3 /day of ethanol is produced using sugarcane juice as raw material. A three-step hydrolysis process (pre-hydrolysis of hemicellulose, Organosolv delignification and cellulose hydrolysis) of surplus sugarcane bagasse is considered. Pinch analysis is used to determine the minimum hot utility obtained with thermal integration of the plant, in order to find out the maximum availability of bagasse that can be used in the hydrolysis process, taking into consideration the use of 50% of generated sugarcane trash as fuel for electricity and steam production. Two different cases were analyzed for the product purification step: conventional and doubleeffect distillation systems. It was found that the double-effect distillation system allows 90% of generated bagasse to be used as raw material in the hydrolysis plant, which accounts for an increase of 26% in bioethanol production, considering exclusively the fermentation of hexoses obtained from the cellulosic fraction.

ANN-based soft-sensor for real-time process monitoring and control of an industrial polymerization process

Abstract: This paper presents the development and the industrial implementation of a virtual sensor (soft-sensor) in the polyethylene terephthalate (PET) production process. This soft-sensor, based on a feed-forward artificial neural network (ANN), was primarily used to provide on-line estimates of the PET viscosity, which is necessary for process control purposes. The ANN-based soft-sensor (ANN-SS) was also used for providing redundant measurements of the viscosity that could be compared to the results obtained from the process viscometer. It was shown that the proposed ANN-SS was able to adequately infer the polymer viscosity, in such a way so as this soft-sensor could be used in the real-time process control strategy. The proposed control system has successfully been applied in servo and regulatory problems, thus allowing an effective and feasible operation of the industrial plant.

Supervised pattern classification based on optimum-path forest

Abstract: We present a supervised classification method which represents each class by one or more optimum-path trees rooted at some key samples, called prototypes. The training samples are nodes of a complete graph, whose arcs are weighted by the distances between the feature vectors of their nodes. Prototypes are identified in all classes and the minimization of a connectivity function by dynamic programming assigns to each training sample a minimum-cost path from its most strongly connected prototype. This competition among prototypes partitions the graph into an optimum-path forest rooted at them. The class of the samples in an optimum-path tree is assumed to be the same of its root. A test sample is classified similarly, by identifying which tree would contain it, if the sample were part of the training set. By choice of the graph model and connectivity function, one can devise other optimum-path forest classifiers. We present one of them, which is fast, simple, multiclass, parameter independent, does not make any assumption about the shapes of the classes, and can handle some degree of overlapping between classes. We also propose a general algorithm to learn from errors on an evaluation set without increasing the training set, and show the advantages of our method with respect to SVM, ANN-MLP, and k-NN classifiers in several experiments with datasets of various types. © 2009 Wiley Periodicals, Inc. Int J Imaging Syst Technol, 19, 120–131, 2009. A preliminary version of the paper was presented at the 12th International Workshop on Combinatorial Image Analysis (Papa et al.,2008a).

Basic validation procedures for regression models in QSAR and QSPR studies: theory and application

Abstract: Four quantitative structure-activity relationships (QSAR) and quantitative structure-property relationship (QSPR) data sets were selected from the literature and used to build regression models with 75, 56, 50 and 15 training samples. The models were validated by leave-one-out crossvalidation, leave-N-out crossvalidation (LNO), external validation, y-randomization and bootstrapping. Validations have shown that the size of the training sets is the crucial factor in determining model performance, which deteriorates as the data set becomes smaller. Models from very small data sets suffer from the impossibility of being thoroughly validated, failure and atypical behavior in certain validations (chance correlation, lack of robustness to resampling and LNO), regardless of their good performance in leave-one-out crossvalidation, fitting and even in external validation. A simple determination of the critical Nin LNO has been introduced by using the limit of 0.1 for oscillations in Q2, quantified as the variation range in single LNO and two standard deviations in multiple LNO. It has been demonstrated that it is sufficient to perform 10 -25 y-randomization and bootstrap runs for a typical model validation. The bootstrap schemes based on hierarchical cluster analysis give more reliable and reasonable results than bootstraps relying only on randomization of the complete data set. Data quality in terms of statistical significance of descriptor -yrelationships is the second important factor for model performance.Variable selection that does not eliminate insignificant descriptor - yrelationships may lead to situations in which they are not detected during model validation, especially when dealing with large data sets.

Probiotic cheese: health benefits, technological and stability aspects

Abstract: This review presents the technological hurdles involved in the development and stability of probiotic cheeses. Firstly, the potential of cheese as a food probiotic carrier is discussed, emphasizing its advantages, when compared to fermented milks and yogurts. Fresh cheese and ripened cheeses are also discussed, and questions concerning the viability of probiotic cultures in these foods are considered. Overall, the manufacture of probiotic cheese should have minimum changes when compared to traditional products. In addition, the physico-chemical parameters that influence the quality of these products must be measured, aiming at process optimization.

Effect of light cycles (night/day) on CO2 fixation and biomass production by microalgae in photobioreactors

Abstract: The objective of this study was to evaluate the effect of the photoperiod on the biomass production and carbon dioxide fixation rates using a photosynthetic culture of the cyanobacterium Aphanothece microscopica Nageli in bubble column photobioreactors. The cultures were carried out at temperatures of 35 °C, air enriched with carbon dioxide at concentrations of 15% and photon flux density of 150 μmol m −2 s −1 . The light cycles evaluated were 0:24, 2:22, 4:20, 6:18, 8:16, 10:14, 12:12, 14:10, 16:8, 18:6, 20:4, 22:2 and 24:0 (night:day), respectively. The results obtained indicated that the duration of the light periods was a determinant factor in the performance of the photobioreactors. A linear reduction in biomass production and carbon dioxide fixation with reductions in the duration of the light period was evident, with the exception of the 12:12 (night:day) cycles. Reductions of up to 99.69% in the carbon-fixation rates as compared with cultures under continuous illumination were obtained.

New insights into dye-sensitized solar cells with polymer electrolytes

Abstract: Polymer electrolytes or gel polymer electrolytes are interesting alternatives to substitute liquid electrolytes in dye-sensitized solar cells (DSSC). The interest in this research field is growing continuously, reflected in the increase in the number of papers published each year concerning these materials. This feature article presents a brief review of the history and development of polymer electrolytes aiming at applications in DSSC. Recent improvements achieved by modifications of the composition and by introduction of additives such as inorganic nanofillers, organic molecules and ionic liquids are described. The stabilities of DSSC assembled with these materials are also discussed and further improvements that can be introduced to maximize performance of the solar cell, such as photoelectrode modification, will also be presented.

Genome structure of a Saccharomyces cerevisiae strain widely used in bioethanol production

Abstract: Bioethanol is a biofuel produced mainly from the fermentation of carbohydrates derived from agricultural feedstocks by the yeast Saccharomyces cerevisiae. One of the most widely adopted strains is PE-2, a heterothallic diploid naturally adapted to the sugar cane fermentation process used in Brazil. Here we report the molecular genetic analysis of a PE-2 derived diploid (JAY270), and the complete genome sequence of a haploid derivative (JAY291). The JAY270 genome is highly heterozygous (approximately 2 SNPs/kb) and has several structural polymorphisms between homologous chromosomes. These chromosomal rearrangements are confined to the peripheral regions of the chromosomes, with breakpoints within repetitive DNA sequences. Despite its complex karyotype, this diploid, when sporulated, had a high frequency of viable spores. Hybrid diploids formed by outcrossing with the laboratory strain S288c also displayed good spore viability. Thus, the rearrangements that exist near the ends of chromosomes do not impair meiosis, as they do not span regions that contain essential genes. This observation is consistent with a model in which the peripheral regions of chromosomes represent plastic domains of the genome that are free to recombine ectopically and experiment with alternative structures. We also explored features of the JAY270 and JAY291 genomes that help explain their high adaptation to industrial environments, exhibiting desirable phenotypes such as high ethanol and cell mass production and high temperature and oxidative stress tolerance. The genomic manipulation of such strains could enable the creation of a new generation of industrial organisms, ideally suited for use as delivery vehicles for future bioenergy technologies.