Modelagem de proteínas por homologia

Modeling methods to derive 3D-structure of proteins have been recently developed. Protein homology-modeling, also known as comparative protein modeling, is nowadays the most accurate protein modeling method. This technique can produce useful models for about an order of magnitude more protein sequences than there have been structures determined by experiment in the same amount of time. All current protein homology-modeling methods consist of four sequential steps: fold assignment and template selection, template-target alignment, model building, and model evaluation. In this paper we discuss in some detail the protein-homology paradigm, its predictive power and its limitations.

Phase diagram and complex patterns in the modeling of the bromate-oxalic acid-Ce-acetone oscillating reaction

Simulations have been carried out on the bromate - oxalic acid - Ce(IV) - acetone oscillating reaction, under flow conditions, using Field and Boyd's model (J. Phys. Chem. 1985, 89, 3707). Many different complex dynamic behaviors were found, including simple periodic oscillations, complex periodic oscillations, quasiperiodicity and chaos. Some of these complex oscillations can be understood as belonging to a Farey sequence. The many different behaviors were systematized in a phase diagram which shows that some regions of complex patterns were nested with one inside the other. The existence of almost all known dynamic behavior for this system allows the suggestion that it can be used as a model for some very complex phenomena that occur in biological systems.

Supercritical CO2 recovery of caffeine from green coffee oil: new experimental solubility data and modeling

The caffeine solubility in supercritical CO2 was studied by assessing the effects of pressure and temperature on the extraction of green coffee oil (GCO). The Peng-Robinson¹ equation of state was used to correlate the solubility of caffeine with a thermodynamic model and two mixing rules were evaluated: the classical mixing rule of van der Waals with two adjustable parameters (PR-VDW) and a density dependent one, proposed by Mohamed and Holder² with two (PR-MH, two parameters adjusted to the attractive term) and three (PR-MH3 two parameters adjusted to the attractive and one to the repulsive term) adjustable parameters. The best results were obtained with the mixing rule of Mohamed and Holder² with three parameters.

Temperature measurements by oh lif and chemiluminescence kinetic modeling for ethanol flames

OH LIF-thermometry was applied to premixed ethanol flames at atmospheric pressure in a burner for three flame conditions. Flame temperatures were simulated from energy equation with PREMIX code of CHEMKIN software package for comparison. A kinetic modeling based on a model validated through chemiluminescence measurements and on a set of reactions for nitrogen chemistry was evaluated. Marinov's mechanism was also tested. Sensitivity analysis was performed for fuel-rich flame condition with Φ = 1.34. Simulated temperatures from both reaction mechanisms evaluated were higher than experimental values. However, the proposed kinetic modeling resulted in temperature profiles qualitatively very close to the experimental.

QSAR modeling: um novo pacote computacional open source para gerar e validar modelos QSAR

QSAR modeling is a novel computer program developed to generate and validate QSAR or QSPR (quantitative structure- activity or property relationships) models. With QSAR modeling, users can build partial least squares (PLS) regression models, perform variable selection with the ordered predictors selection (OPS) algorithm, and validate models by using y-randomization and leave-N-out cross validation. An additional new feature is outlier detection carried out by simultaneous comparison of sample leverage with the respective Studentized residuals. The program was developed using Java version 6, and runs on any operating system that supports Java Runtime Environment version 6. The use of the program is illustrated. This program is available for download at lqta.iqm.unicamp.br.

Kinetic modeling of the biosorption of Cd2+ ions from aqueous solutions onto Eichhornia crassipes roots using potentiometry: low-cost alternative to conventional methods

This work presents the use of potentiometric measurements for kinetic studies of biosorption of Cd2+ ions from aqueous solutions on Eichhornia crassipes roots. The open circuit potential of the Cd/Cd2+ electrode of the first kind was measured during the bioadsorption process. The amount of Cd2+ ions accumulated was determined in real time. The data were fit to different models, with the pseudo-second-order model proving to be the best in describing the data. The advantages and limitations of the methodology proposed relative to the traditional method are discussed.

Use data from permanent sampling points in growth and yield modeling

This study was carried to evaluate the efficiency of the Bitterlich method in growth and yield modeling of the even-aged Eucalyptus stands. 25 plots were setup in Eucalyptus grandis cropped under a high bole system in the Central Western Region of Minas Gerais, Brazil. The sampling points were setup in the center of each plot. The data of four annual mesurements were colleted and used to adjust the three model types using the age, the site index and the basal area as independent variables. The growths models were fitted for volume and mass of trees. The efficiency of the Bitterlich method was confirmed for generating the data for growth and yield modeling.

Hipsometric relationship modeling using data sampled in tree scaling and inventory plots

This work evaluated eight hypsometric models to represent tree height-diameter relationship, using data obtained from the scaling of 118 trees and 25 inventory plots. Residue graphic analysis and percent deviation mean criteria, qui-square test precision, residual standard error between real and estimated heights and the graybill f test were adopted. The identity of the hypsometric models was also verified by applying the F(Ho) test on the plot data grouped to the scaling data. It was concluded that better accuracy can be obtained by using the model prodan, with h and d1,3 data measured in 10 trees by plots grouped into these scaling data measurements of even-aged forest stands.

MODELING A COMPUTER APPLICATION FOR MANAGEMENT OF MAINTENANCE ACTIVITIES OF UNPAVED ROADS

ABSTRACTThis study presents a contribution to the modeling of a computer application employing a method of serviceability performance for unpaved roads, aiming the management of maintenance/restoration activities of the primary surface layer. The proposed methodology consisted of field inspections during dry (April to September) and rainy (October to March) periods, during which objective evaluations were performed to survey of defects and their densities and degrees of severity. To aid the functional classification of analyzed road sections and the determination of the defect with major influence on the serviceability of these roads, the method of serviceability performance proposed by Silva (2009)was implemented in the Visual Basic for Applications (VBA) language in Microsoft Excel software. With the use of the computer application proposed it was possible to identify among the defects analyzed in field, through the index of serviceability of the sampling unit per defect type (ISUdef), which one had the greatest influence on determining the relative serviceability index per road section (IST). The results allow us to conclude that the computer application Road achieved satisfactory results, since the objective evaluation criteria applied to road sections denotes consistency regarding their serviceability.

MODELING AND SIMULATION OF RELIEF INFLUENCE ON EUCALYPTUS FORESTS: INTERACTION BETWEEN SOLAR IRRADIANCE AND PRODUCTIVITY

ABSTRACT This study aimed to verify the differences in radiation intensity as a function of distinct relief exposure surfaces and to quantify these effects on the leaf area index (LAI) and other variables expressing eucalyptus forest productivity for simulations in a process-based growth model. The study was carried out at two contrasting edaphoclimatic locations in the Rio Doce basin in Minas Gerais, Brazil. Two stands with 32-year-old plantations were used, allocating fixed plots in locations with northern and southern exposure surfaces. The meteorological data were obtained from two automated weather stations located near the study sites. Solar radiation was corrected for terrain inclination and exposure surfaces, as it is measured based on the plane, perpendicularly to the vertical location. The LAI values collected in the field were used. For the comparative simulations in productivity variation, the mechanistic 3PG model was used, considering the relief exposure surfaces. It was verified that during most of the year, the southern surfaces showed lower availability of incident solar radiation, resulting in up to 66% losses, compared to the same surface considered plane, probably related to its geographical location and higher declivity. Higher values were obtained for the plantings located on the northern surface for the variables LAI, volume and mean annual wood increase, with this tendency being repeated in the 3PG model simulations.

Computational modeling for irrigated agriculture planning. Part I: general description and linear programming

Linear programming models are effective tools to support initial or periodic planning of agricultural enterprises, requiring, however, technical coefficients that can be determined using computer simulation models. This paper, presented in two parts, deals with the development, application and tests of a methodology and of a computational modeling tool to support planning of irrigated agriculture activities. Part I aimed at the development and application, including sensitivity analysis, of a multiyear linear programming model to optimize the financial return and water use, at farm level for Jaíba irrigation scheme, Minas Gerais State, Brazil, using data on crop irrigation requirement and yield, obtained from previous simulation with MCID model. The linear programming model outputted a crop pattern to which a maximum total net present value of R$ 372,723.00 for the four years period, was obtained. Constraints on monthly water availability, labor, land and production were critical in the optimal solution. In relation to the water use optimization, it was verified that an expressive reductions on the irrigation requirements may be achieved by small reductions on the maximum total net present value.

Computational modeling for irrigated agriculture planning. Part II: risk analysis

Techniques of evaluation of risks coming from inherent uncertainties to the agricultural activity should accompany planning studies. The risk analysis should be carried out by risk simulation using techniques as the Monte Carlo method. This study was carried out to develop a computer program so-called P-RISCO for the application of risky simulations on linear programming models, to apply to a case study, as well to test the results comparatively to the @RISK program. In the risk analysis it was observed that the average of the output variable total net present value, U, was considerably lower than the maximum U value obtained from the linear programming model. It was also verified that the enterprise will be front to expressive risk of shortage of water in the month of April, what doesn't happen for the cropping pattern obtained by the minimization of the irrigation requirement in the months of April in the four years. The scenario analysis indicated that the sale price of the passion fruit crop exercises expressive influence on the financial performance of the enterprise. In the comparative analysis it was verified the equivalence of P-RISCO and @RISK programs in the execution of the risk simulation for the considered scenario.

Modeling and simulation of forced-air cooling of strawberries using variable convective coefficient

In the forced-air cooling process of fruits occurs, besides the convective heat transfer, the mass transfer by evaporation. The energy need in the evaporation is taken from fruit that has its temperature lowered. In this study it has been proposed the use of empirical correlations for calculating the convective heat transfer coefficient as a function of surface temperature of the strawberry during the cooling process. The aim of this variation of the convective coefficient is to compensate the effect of evaporation in the heat transfer process. Linear and exponential correlations are tested, both with two adjustable parameters. The simulations are performed using experimental conditions reported in the literature for the cooling of strawberries. The results confirm the suitability of the proposed methodology.

Characterization of soil parameters of two soils of Rio Grande do Sul in modeling the prediction of tractive effort

The interaction between the soil and tillage tool can be examined using different parameters for the soil and the tool. Among the soil parameters are the shear stress, cohesion, internal friction angle of the soil and the pre-compression stress. The tool parameters are mainly the tool geometry and depth of operation. Regarding to the soils of Rio Grande do Sul there are hardly any studies and evaluations of the parameters that have importance in the use of mathematical models to predict tensile loads. The objective was to obtain parameters related to the soils of Rio Grande do Sul, which are used in soil-tool analysis, more specifically on mathematical models that allow the calculation of tractive effort for symmetric and narrow tools. Two of the main soils of Rio Grande do Sul, an Albaqualf and a Paleudult were studied. Equations that relate the cohesion, internal friction angle of the soil, adhesion, soil-tool friction angle and pre-compression stress as a function of water content in the soil were obtained, leading to important information for use of mathematical models for tractive effort calculation.

Mathematical modeling applied to the growth of tilapia in net cages in the sub middle of the São Francisco river

This study aimed to apply mathematical models to the growth of Nile tilapia (Oreochromis niloticus) reared in net cages in the lower São Francisco basin and choose the model(s) that best represents the conditions of rearing for the region. Nonlinear models of Brody, Bertalanffy, Logistic, Gompertz, and Richards were tested. The models were adjusted to the series of weight for age according to the methods of Gauss, Newton, Gradiente and Marquardt. It was used the procedure "NLIN" of the System SAS® (2003) to obtain estimates of the parameters from the available data. The best adjustment of the data were performed by the Bertalanffy, Gompertz and Logistic models which are equivalent to explain the growth of the animals up to 270 days of rearing. From the commercial point of view, it is recommended that commercialization of tilapia from at least 600 g, which is estimated in the Bertalanffy, Gompertz and Logistic models for creating over 183, 181 and 184 days, and up to 1 Kg of mass , it is suggested the suspension of the rearing up to 244, 244 and 243 days, respectively.