Docking and molecular dynamics simulation of quinone compounds with trypanocidal activity

In this work, two different docking programs were used, AutoDock and FlexX, which use different types of scoring functions and searching methods. The docking poses of all quinone compounds studied stayed in the same region in the trypanothione reductase. This region is a hydrophobic pocket near to Phe396, Pro398 and Leu399 amino acid residues. The compounds studied displays a higher affinity in trypanothione reductase (TR) than glutathione reductase (GR), since only two out of 28 quinone compounds presented more favorable docking energy in the site of human enzyme. The interaction of quinone compounds with the TR enzyme is in agreement with other studies, which showed different binding sites from the ones formed by cysteines 52 and 58. To verify the results obtained by docking, we carried out a molecular dynamics simulation with the compounds that presented the highest and lowest docking energies. The results showed that the root mean square deviation (RMSD) between the initial and final pose were very small. In addition, the hydrogen bond pattern was conserved along the simulation. In the parasite enzyme, the amino acid residues Leu399, Met400 and Lys402 are replaced in the human enzyme by Met406, Tyr407 and Ala409, respectively. In view of the fact that Leu399 is an amino acid of the Z site, this difference could be explored to design selective inhibitors of TR.

Coherence dynamics of two-mode condensates in asymmetric potentials

Detection of weak forces with an accuracy beyond the standard quantum limit holds promise both for fundamental research and for technological applications. Schemes involving ultracold atoms for such measurements are now considered to be prime candidates for increased sensitivity. In this paper we use a combination of analytical and numerical techniques to investigate the possible subshot-noise estimation of applied force fields through detection of coherence dynamics of Bose-condensed atoms in asymmetric double-well traps. Following a semiclassical description of the system dynamics and fringe visibility, we present numerical simulations of the full quantum dynamics that demonstrate the dynamical production of phase squeezing beyond the standard quantum limit. Nonlinear interactions are found to limit the achievable amount to a finite value determined by the external weak force.

Using system dynamics for collaborative design : a case study

Background  In order to facilitate the collaborative design, system dynamics (SD) with a group modelling approach was used in the early stages of planning a new stroke unit. During six workshops a SD model was created in a multiprofessional group. Aim To explore to which extent and how the use of system dynamics contributed to the collaborative design process. Method A case study was conducted using several data sources. Results SD supported a collaborative design, by facilitating an explicit description of stroke care process, a dialogue and a joint understanding. The construction of the model obliged the group to conceptualise the stroke care and experimentation with the model gave the opportunity to reflect on care. Conclusion SD facilitated the collaborative design process and should be integrated in the early stages of the design process as a quality improvement tool.

Exchange rate dynamics in Brazil

The paper aims to investigate on empirical and theoretical grounds the Brazilian exchange rate dynamics under floating exchange rates. The empirical analysis examines the short and long term behavior of the exchange rate, interest rate (domestic and foreign) and country risk using econometric techniques such as variance decomposition, Granger causality, cointegration tests, error correction models, and a GARCH model to estimate the exchange rate volatility. The empirical findings suggest that one can argue in favor of a certain degree of endogeneity of the exchange rate and that flexible rates have not been able to insulate the Brazilian economy in the same patterns predicted by literature due to its own specificities (managed floating with the use of international reserves and domestic interest rates set according to inflation target) and to externally determined variables such as the country risk. Another important outcome is the lack of a closer association of domestic and foreign interest rates since the new exchange regime has been adopted. That is, from January 1999 to May 2004, the US monetary policy has no significant impact on the Brazilian exchange rate dynamics, which has been essentially endogenous primarily when we consider the fiscal dominance expressed by the probability of default.

Essays on price dynamics

Esta tese tem como objetivo principal aproximar a evidencia empirica existente sobre os agregados macroeconomicos com as novas evidencias empiricas baseadas nos micro dados de precos ao consumidor, tendo como base os modelos padroes de rigidez de preco utilizados na literatura de politica monetaria. Para isso, esta tese utiliza a base de dados individuais de precos ao consumidor no Brasil fornecida pela Fundacao Getulio Vargas. Especificamente, esta tese foca em tres temas principais: a existencia de variac˜oes temporararias de precos, a heterogeneidade na rigidez de precos entre firmas de um mesmo setor e o formato das func˜oes hazard. Os resultados mostram que: existe de fato uma correlac˜ao entre as variaveis referentes as mudancas temporararias de precos e os agregados macroeconomicos; a heterogeneidade na rigidez de precos entre firmas de um mesmo setor apresenta efeitos significativos sobre a dinamica dos agregados macroeconomicos; e por fim, o formato mais geral da func˜ao hazard proposta nesta tese possibilita novas dinamicas dos agregados macroeconomicos.

Dynamics of micro-entrepeneurial activities

This paper generates and organizes stylized facts related to the dynamics of selfemployment activities in Brazil. The final purpose is to help the design of policies to assist micro-entrepreneurial units. The 'first part of the paper uses as a main tool of analysis transitional data constructed from household surveys. The longitudinal information used covers three transition horizons: 1-month, 12-month and 5-year periods. Quantitative flows analysis assesses the main origins, destinies and various types of risks assumed by microentrepreneurial activities. Complementarily, logistic regressions provides evidence on the main characteristics and resources of micro-entrepreneurial units. In particular, we use the movements from self-employment to employer activities as measures of entrepreneurial success. We also use these transitions as measures of employment creation intensity within the self-employed segment.The second part of the paper explores various data sources. First, we attempt to analyze the life-cycle trajectories and determinants of self-employment. We use cohort data constructed from PME and qualitative data on financial and work history factors related to the opening of small bussiness from the informal firms survey implemented during 1994. Second, we apply a standart Mincerian wage equation approach to self-employment profits. This exerci se attempts to capture the correlation patterns between micro-entrepreneurial performance and a variety of firms leveI variables present in the 1994 Informal Survey. Finally, we use a a survey on the poor enterpreneurs of Rocinha favela as a laboratory to study poor entrepreneurs resources and behavior.In sum, the main questions pursued in the paper are: i) who are the Brazilian selfemployed?; ii) in particular: what is relative importance among the self-employed of subsistence activities versus those activities with growth and capital accumulation potential?; iii) what are the main static and dynamic determinants ofmicro-entrepreneurial success?; iv) what is the degree ofrisk associated with micro-entrepreneurial activities in Brazil?; v) What is the life-cycle profile of self-employment?; vi) what are the main constraints on poor entrepreneurs activities?.

DYNAMICS AT INFINITY of A CUBIC CHUA'S SYSTEM

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Multi-Agent Simulation of Urban Social Dynamics for Spatial Load Forecasting

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Modelling the dynamics of dengue real epidemics

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Evolutionary dynamics of heterochromatin in the genome of Dichotomius beetles based on chromosomal analysis

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

Use of forest fragments by blue-winged macaws (Primolius maracana) within a fragmented landscape

Parrots are the most threatened group of birds in the world, mainly because of the reduction and fragmentation of their natural habitats. However, few studies have investigated the dynamics of parrot populations in disturbed landscapes on a broad scale. In this paper, we studied the ecological interactions of the vulnerable blue-winged macaw (Primolius maracana) in a fragmented landscape surrounding a large protected park in southeastern Brazil. We sampled 36 forest fragments that varied in size, characteristics, degree of isolation and type of surrounding matrix in order to assess the importance of habitat features on the maintenance of these birds. Blue-winged macaws were recorded in 70% of the satellite remnants that were sampled, which included large and small blocks of forest. These areas were used as sites for feeding, nesting or overnight rests, and also provided connectivity for birds' displacements. However, the frequency of macaw visits varied among the remnants, and this was related to habitat features such as patch size, human use of surrounding land, and the proximity to the protected park, to urban areas and to the birds' roosting areas. In general, landscape-scale parameters explained more of the variation in the frequency of visits by macaws than did patch-scale parameters. These results demonstrate the importance of landscape mosaics for the survival of blue-winged macaws.

Evaluation of seasonal dynamics and bioindication potential of macroalgal communities in a polluted tropical stream

Macroalgal communities and environmental variables were analyzed seasonally along a polluted tropical stream in São Paulo State, Brazil, We aimed to improve the knowledge of tropical macroalgal communities, to study the longitudinal and seasonal dynamics of these communities in influenced environments, to evaluate the relationship of algal frequency and abundance with selected environmental variables, and to look for potential macroalgal species indicators. The seasonal abundance pattern was similar to natural or low influenced systems and was mainly determined by rainfall regime. However, community composition was closely related to some chemical water pollution indicators, such as phosphorus and nitrogen compounds. Some species are suggested as potential indicators of organic pollution (e.g. Oscillatoria ornata, Stigeoclonium helveticum and Schizomeris leibleinii), but more detailed studies have to be developed to determine the tolerance limits of these species. on the basis of our results and literature data, the use of occurrence of Oscillatoriales in relation to other orders of Cyanoprokaryota is suggested to be a good indicator of organic pollution in tropical lotic ecosystems.

Bose-Einstein condensation dynamics in three dimensions by the pseudospectral and finite-difference methods

We suggest a pseudospectral method for solving the three-dimensional time-dependent Gross-Pitaevskii (GP) equation, and use it to study the resonance dynamics of a trapped Bose-Einstein condensate induced by a periodic variation in the atomic scattering length. When the frequency of oscillation of the scattering length is an even multiple of one of the trapping frequencies along the x, y or z direction, the corresponding size of the condensate executes resonant oscillation. Using the concept of the differentiation matrix, the partial-differential GP equation is reduced to a set of coupled ordinary differential equations, which is solved by a fourth-order adaptive step-size control Runge-Kutta method. The pseudospectral method is contrasted with the finite-difference method for the same problem, where the time evolution is performed by the Crank-Nicholson algorithm. The latter method is illustrated to be more suitable for a three-dimensional standing-wave optical-lattice trapping potential.

Bose-Einstein condensation dynamics from the numerical solution of the Gross-Pitaevskii equation

We study certain stationary and time-evolution problems of trapped Bose-Einstein condensates using the numerical solution of the Gross-Pitaevskii (GP) equation with both spherical and axial symmetries. We consider time-evolution problems initiated by suddenly changing the interatomic scattering length or harmonic trapping potential in a stationary condensate. These changes introduce oscillations in the condensate which are studied in detail. We use a time iterative split-step method for the solution of the time-dependent GP equation, where all nonlinear and linear non-derivative terms are treated separately from the time propagation with the kinetic energy terms. Even for an arbitrarily strong nonlinear term this leads to extremely accurate and stable results after millions of time iterations of the original equation.