Coordinate and time-dependent diffusion dynamics in protein folding

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding

We show that diffusion can play an important role in protein-folding kinetics. We explicitly calculate the diffusion coefficient of protein folding in a lattice model. We found that diffusion typically is configuration- or reaction coordinate-dependent. The diffusion coefficient is found to be decreasing with respect to the progression of folding toward the native state, which is caused by the collapse to a compact state constraining the configurational space for exploration. The configuration- or position-dependent diffusion coefficient has a significant contribution to the kinetics in addition to the thermodynamic free-energy barrier. It effectively changes (increases in this case) the kinetic barrier height as well as the position of the corresponding transition state and therefore modifies the folding kinetic rates as well as the kinetic routes. The resulting folding time, by considering both kinetic diffusion and the thermodynamic folding free-energy profile, thus is slower than the estimation from the thermodynamic free-energy barrier with constant diffusion but is consistent with the results from kinetic simulations. The configuration- or coordinate-dependent diffusion is especially important with respect to fast folding, when there is a small or no free-energy barrier and kinetics is controlled by diffusion. Including the configurational dependence will challenge the transition state theory of protein folding. The classical transition state theory will have to be modified to be consistent. The more detailed folding mechanistic studies involving phi value analysis based on the classical transition state theory also will have to be modified quantitatively.

Energy localization in the Phi(4) oscillator chain

We study energy localization in a finite one-dimensional Phi(4) oscillator chain with initial energy in a single oscillator of the chain. We numerically calculate the effective number of degrees of freedom sharing the energy on the lattice as a function of time. We find that for energies smaller than a critical value, energy equipartition among the oscillators is reached in a relatively short time. on the other hand, above the critical energy, a decreasing number of particles sharing the energy is observed. We give an estimate of the effective number of degrees of freedom as a function of the energy. Our results suggest that localization is due to the appearance, above threshold, of a breather-like structure. Analytic arguments are given, based on the averaging theory and the analysis of a discrete nonlinear Schrodinger equation approximating the dynamics, to support and explain the numerical results.

Singular Value Decomposition and Ligand Binding Analysis

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

An analysis of embeddedness in the value creation in interorganisational networks: an illustrative example in Brazil

The purpose of this article is to propose a methodological approach to analyse how the positioning of actors in an interorganisational network can influence the elements of value creation. This study fills a gap in the existing literature by exploring the relationship between the positioning of actors and the value creation in a context of interorganisational networks. The case study method was employed and the data was obtained from four companies of an interorganisational network, located in Brazil, which produces earthmoving equipments. The central actor in this network is benefited through access to resources, power and information of the other network actors. The centrality position seems to help this company in the absorption and diffusion of knowledge among the other network actors. The research indicates, that a dense core (through strong ties) and redundancy (for triangulation and knowledge absorption), benefited the following value creation elements: tangible; intangible; services and economic.

Analysis of the four wave mixing effect (FWM) in a dispersion decreasing fiber (DDF) for a WDM system

We did a numerical investigation of the propagation of short light pulses in the region of 1.55 mu m and the conversion efficiency (CE) for the four wave mixing generation (FWM) of ordinary and dispersion decreasing fibers for use in wavelength division multiplexing (WDM) systems, Our simulations studies three different profiles, linear, hyperbolic. and constant, One conclude that for all the profiles there is decrease of the conversion efficiency with the increase in the channel separation. The hyperbolic profile present a higher efficiency of around 1000 above in magnitude compared with the others profiles at 0.2 nm of channel separation. We calculate the conversion efficiency versus the fiber length for the three profiles. The conversion efficiency for the hyperbolic profile is higher when compared to the constant and linear profiles. The other interesting point of the hyperbolic profile is that the increase of the CE in the beginning of the fiber does not show my oscillation in the CE value (log eta), which was observed for the constant and linear profiles. For all the profiles there is an increase of the conversion efficiency with the increase of the pump power. The compression factor C-i for the generated FWM signal at omega(3) was measured along the DDF's and the constant profile fibers. One can conclude that with the use of decreasing dispersion profile (DDF) fibers one can have a control of the (CE) conversion efficiency and the compression factor of the four wave mixing (FWM) generation in WDM systems. (c) 2005 Elsevier B.V. All rights reserved.

ECONOMIC ANALYSIS of AMAZON RIVER PRAWN FARMING TO THE MARKETS FOR LIVE BAIT and JUVENILES IN PANTANAL, BRAZIL

The implementation of a hypothetical aquaculture facility with hatchery, nursery and grow-out earthen ponds for raising the Amazon River Prawn Macrobrachium amazonicum in the Pantanal was considered. Eight larviculture cycles per year were projected: four to produce post-larvae for stocking in grow-out bait ponds, and four to stock nursery tanks to sell juveniles as seed to grow-out farms, which produce prawns for human consumption. Annual production would be 146,880 dozen bait prawns and 2,938 thousand juveniles. The assumed sale prices were US$ 1.38 per dozen baits and US$ 15.39 per thousand juveniles. The net present value was US$ 555,890.79, internal rate of return was 48% per year, payback period was 2.4 years and benefit-cost ratio was 3.90. The breakeven price to cover total costs per dozen baits was US$ 0.70 and per thousand juveniles was US$ 17.00, indicating that the selling price assumed for juveniles in base scenario is not realistic. Net return was US$ 84,773.80. The results indicate that this activity would be a lucrative and attractive investment in the Pantanal.

Genetic diversity of natural populations of Anemopaegma arvense (Bignoniaceae) in the Cerrado of São Paulo State, Brazil

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

Analysis of the Priestley-Taylor alpha parameter for a bean crop

This work deals with the Priestley-Taylor model for evapotranspiration in different grown stages of a bean crop. Priestley and Taylor derived a practical Formulation for energy partitioning between the sensible and latent heat fluxes through the a parameter. Bowen ratio energy balance (BREB) was carried out for daily sensible and latent heat flux estimations in three different crop stages. Mean daily values of Priestley-Taylor a parameter were determined for eleven days during the crop cycle. Diurnal variation patterns of a are presented for the growing, flowering and graining periods. The mean values of 1.13 +/- 0.33, 1.26 +/- 0.74, 1.22 +/- 0.55 were obtained for a day in the growing, in the flowering and for graining periods, respectively. Eleven days values of a are shown and gave a mean value of 1.23 +/- 0.10 which agree on the reported literature.

Compositional analysis for an unbiased measure of soil aggregation

Soil aggregation is an index of soil structure measured by mean weight diameter (MWD) or scaling factors often interpreted as fragmentation fractal dimensions (D-f). However, the MWD provides a biased estimate of soil aggregation due to spurious correlations among aggregate-size fractions and scale-dependency. The scale-invariant D-f is based on weak assumptions to allow particle counts and sensitive to the selection of the fractal domain, and may frequently exceed a value of 3, implying that D-f is a biased estimate of aggregation. Aggregation indices based on mass may be computed without bias using compositional analysis techniques. Our objective was to elaborate compositional indices of soil aggregation and to compare them to MWD and D-f using a published dataset describing the effect of 7 cropping systems on aggregation. Six aggregate-size fractions were arranged into a sequence of D-1 balances of building blocks that portray the process of soil aggregation. Isometric log-ratios (ilrs) are scale-invariant and orthogonal log contrasts or balances that possess the Euclidean geometry necessary to compute a distance between any two aggregation states, known as the Aitchison distance (A(x,y)). Close correlations (r>0.98) were observed between MWD, D-f, and the ilr when contrasting large and small aggregate sizes. Several unbiased embedded ilrs can characterize the heterogeneous nature of soil aggregates and be related to soil properties or functions. Soil bulk density and penetrater resistance were closely related to A(x,y) with reference to bare fallow. The A(x,y) is easy to implement as unbiased index of soil aggregation using standard sieving methods and may allow comparisons between studies. (C) 2012 Elsevier B.V. All rights reserved.

Breeding value accuracy estimates for growth traits using random regression and multi-trait models in Nelore cattle

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

Physiochemical analysis and centesimal composition of Pleurotus ostreatus mushroom grown in residues from the Amazon

O presente estudo teve como objetivo avaliar a composição nutricional dos cogumelos produzidos em substratos alternativos à base de resíduos agrícolas e agroindustriais da Amazônia. Determinou-se C, N, pH, umidade, sólidos solúveis, proteína, lipídios, fibra total, cinzas, carboidratos e energia. Os substratos foram formulados a partir de serragem de Simarouba amara Aubl. (marupá), Ochroma piramidale Cav. ex. Lam. (pau de balsa) e do estipe de Bactris gasipaes Kunth (pupunheira) e de Saccharum officinarum (cana-de-açúcar). Os resultados demonstraram que: a composição nutricional do P. ostreatus variou com o substrato de cultivo e; O P. ostreatus pode ser considerado um importante alimento devido suas características nutricionais: altos teores de proteínas, carboidratos metabolizáveis e fibras; baixos teores de lipídios e de calorias.

Analysis of relative humidity sensors at the WMO Radiosonde intercomparison experiment in Brazil

The quality of the vertical distribution measurements of humidity in the atmosphere is very important in meteorology due to the crucial role that water vapor plays in the earth's energy budget. The radiosonde is the humidity measurement device that provides the best vertical resolution. Also, radiosondes are the operational devices that are used to measure the vertical profile of atmospheric water vapor. The World Meteorological Organization (WMO) has carried out several intercomparison experiments at different climatic zones in order to identify the differences between the available commercial sensors. This article presents the results of an experiment that was carried out in Brazil in 2001 in which major commercial radiosonde manufacturers [e.g., Graw Radiosondes GmbH & Co., KG (Germany); MODEM (France); InterMet Systems (United States); Sippican, Inc. (United States); and Vaisala (Finland)] were involved. One of the main goals of this experiment was to evaluate the performance of the different humidity sensors in a tropical region. This evaluation was performed for different atmospheric layers and distinct periods of the day. It also considers the computation of the integrated water vapor (IWV). The results showed that the humidity measurements achieved by the different sensors were quite similar in the low troposphere (the bias median value regarding the RS80 was around 1.8%) and were quite dispersed in the superior layers (the median rms regarding the RS80 was around 14.9%).

Thermodynamic analysis of direct steam reforming of ethanol in molten carbonate fuel cell

Fuel cell as molten carbonate fuel cell (MCFC) operates at high temperatures. Thus, cogeneration processes may be performed, generating heat for its own process or for other purposes of steam generation in the industry. The use of ethanol is one of the best options because this is a renewable and less environmentally offensive fuel, and is cheaper than oil-derived hydrocarbons, as in the case of Brazil. In that country, because of technical, environmental, and economic advantages, the use of ethanol by steam reforming process has been the most investigated process. The objective of this study is to show a thermodynamic analysis of steam reforming of ethanol, to determine the best thermodynamic conditions where the highest volumes of products are produced, making possible a higher production of energy, that is, a more efficient use of resources. To attain this objective, mass and energy balances were performed. Equilibrium constants and advance degrees were calculated to get the best thermodynamic conditions to attain higher reforming efficiency and, hence, higher electric efficiency, using the Nernst equation. The advance degree (according to Castellan 1986, Fundamentos da Fisica/Quimica, Editora LTC, Rio de Janeiro, p. 529, in Portuguese) is a coefficient that indicates the evolution of a reaction, achieving a maximum value when all the reactants' content is used of reforming increases when the operation temperature also increases and when the operation pressure decreases. However, at atmospheric pressure (1 atm), the advance degree tends to stabilize in temperatures above 700 degrees C; that is, the volume of supplemental production of reforming products is very small with respect to high use of energy resources necessary. The use of unused ethanol is also suggested for heating of reactants before reforming. The results show the behavior of MCFC. The current density, at the same tension, is higher at 700 degrees C than other studied temperatures such as 600 and 650 degrees C. This fact occurs due to smaller use of hydrogen at lower temperatures that varies between 46.8% and 58.9% in temperatures between 600 and 700 degrees C. The higher calculated current density is 280 mA/cm(2). The power density increases when the volume of ethanol to be used also increases due to higher production of hydrogen. The highest produced powers at 190 mA/cm(2) are 99.8, 109.8, and 113.7 mW/cm(2) for 873, 923, and 973 K, respectively. The thermodynamic efficiency has the objective to show the connection among operational conditions and energetic factors, which are some parameters that describe a process of internal steam reforming of ethanol.

Identification of lubricant contamination by biodiesel using vibration analysis and neural network

Purpose - The purpose of this paper is to provide information on lubricant contamination by biodiesel using vibration and neural network.Design/methodology/approach - The possible contamination of lubricants is verified by analyzing the vibration and neural network of a bench test under determinated conditions.Findings - Results have shown that classical signal analysis methods could not reveal any correlation between the signal and the presence of contamination, or contamination grade. on other hand, the use of probabilistic neural network (PNN) was very successful in the identification and classification of contamination and its grade.Research limitations/implications - This study was done for some specific kinds of biodiesel. Other types of biodiesel could be analyzed.Practical implications Contamination information is presented in the vibration signal, even if it is not evident by classical vibration analysis. In addition, the use of PNN gives a relatively simple and easy-to-use detection tool with good confidence. The training process is fast, and allows implementation of an adaptive training algorithm.Originality/value - This research could be extended to an internal combustion engine in order to verify a possible contamination by biodiesel.