Structural modeling of high-affinity thyroid receptor-ligand complexes

Understanding the molecular basis of the binding modes of natural and synthetic ligands to nuclear receptors is fundamental to our comprehension of the activation mechanism of this important class of hormone regulated transcription factors and to the development of new ligands. Thyroid hormone receptors (TR) are particularly important targets for pharmaceuticals development because TRs are associated with the regulation of metabolic rates, body weight, and circulating levels of cholesterol and triglycerides in humans. While several high-affinity ligands are known, structural information is only partially available. In this work we obtain structural models of several TR-ligand complexes with unknown structure by docking high affinity ligands to the receptors` ligand binding domain with subsequent relaxation by molecular dynamics simulations. The binding modes of these ligands are discussed providing novel insights into the development of TR ligands. The experimental binding free energies are reasonably well-reproduced from the proposed models using a simple linear interaction energy free-energy calculation scheme.

Modeling and simulation of the anode in direct ethanol fuels cells

Mathematical modeling has been extensively applied to the study and development of fuel cells. In this work, the objective is to characterize a mechanistic model for the anode of a direct ethanol fuel cell and perform appropriate simulations. The software Comsol Multiphysics (R) (and the Chemical Engineering Module) was used in this work. The software Comsol Multiphysics (R) is an interactive environment for modeling scientific and engineering applications using partial differential equations (PDEs). Based on the finite element method, it provides speed and accuracy for several applications. The mechanistic model developed here can supply details of the physical system, such as the concentration profiles of the components within the anode and the coverage of the adsorbed species on the electrode surface. Also, the anode overpotential-current relationship can be obtained. To validate the anode model presented in this paper, experimental data obtained with a single fuel cell operating with an ethanol solution at the anode were used. (C) 2008 Elsevier B.V. All rights reserved.

Open Circuit Interaction of Formic Acid with Oxidized Pt Surfaces: Experiments, Modeling, and Simulations

We report in this work the study of the interaction between formic acid and an oxidized platinum surface under open circuit conditions. The investigation was carried out with the aid of in situ infrared spectroscopy, and results analyzed in terms of a mathematical model and numerical simulations. It has been found that during the first seconds of the interaction a small amount of CO(2) is produced and absolutely no adsorbed CO was observed. A sudden drop in potential then follows, which is accompanied by a steep increase first of CO(2) production and then by adsorbed CO. The steep transient was rationalized in terms of an autocatalytic production of free platinum sites which enhances the overall rate of reaction. Modeling and simulation showed nearly quantitative agreement with the experimental observations and provided further insight into some experimentally inaccessible variables such as surface free sites. Finally, based on the understanding provided from the combined experimental and theoretical approach, we discuss the general aspects influencing the open circuit transient.

Modeling of weeds interference periods in bean

Objetivou-se com este trabalho determinar o período de convivência anterior à interferência das plantas daninhas (PAI) e o período anterior ao dano no rendimento econômico (PADRE) na cultura do feijão, em diferentes espaçamentos (0,45 e 0,60 m) e densidade de plantas (10 e 15 plantas m-1). Os tratamentos foram constituídos de períodos de convivência entre a cultura e as plantas daninhas (0 a 10, 0 a 20, 0 a 30, 0 a 40, 0 a 50, 0 a 60, 0 a 70 e 0 a 80 dias), mais uma testemunha sem convívio com as plantas daninhas. Adotou-se o delineamento experimental de blocos casualizados, com quatro repetições. Os períodos anteriores à interferência (PAI) da cultura foram de 23, 27, 13 e 19 dias após emergência, e os períodos anteriores ao dano no rendimento econômico (PADRE), de 10, 9, 8 e 8 dias, para os tratamentos com espaçamento de 0,45 m e densidades de semeadura de 10 e 15 plantas m-1 e para aqueles com espaçamento de 0,60 m e densidades de semeadura de 10 e 15 plantas m-1, respectivamente, o que reduziu a produtividade de grãos em 63, 50, 42 e 57%, respectivamente, com a presença das plantas daninhas durante todo o ciclo do feijoeiro.

Fuzzy modeling to predict chicken egg hatchability in commercial hatchery

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

Modeling upper eyelid kinematics during spontaneous and reflex blinks

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Determinação experimental e modelagem termodinâmica do ponto de turbidez de sistemas aquosos com tensoativos nonilfenolpolietoxilados

The nonionic surfactants are composed of substances whose molecules in solution, does not ionize. The solubility of these surfactants in water due to the presence of functional groups that have strong affinity for water. When these surfactants are heated is the formation of two liquid phases, evidenced by the phenomenon of turbidity. This study was aimed to determine the experimental temperature and turbidity nonilfenolpoliethoxyled subsequently perform a thermodynamic modeling, considering the models of Flory-Huggins and the empirical solid-liquid equilibrium (SLE). The method used for determining the turbidity point was the visual method (Inoue et al., 2008). The experimental methodology consisted of preparing synthetic solutions of 0,25%, 0,5%, 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 12,5%, 15%, 17% and 20% by weight of surfactant. The nonionic surfactants used according to their degree of ethoxylation (9.5, 10, 11, 12 and 13). During the experiments the solutions were homogenized and the bath temperature was gradually increased while the turbidity of the solution temperature was checked visually Inoue et al. (2003). These temperature data of turbidity were used to feed the models evaluated and obtain thermodynamic parameters for systems of surfactants nonilfenolpoliethoxyled. Then the models can be used in phase separation processes, facilitating the extraction of organic solvents, therefore serve as quantitative and qualitative parameters. It was observed that the solidliquid equilibrium model (ESL) was best represented the experimental data.

Estudo da secagem do feijão verde (Vigna unguiculata L. Walp) - análise experimental do processo combinado leito fixo/leito de jorro

Green bean is considered as one of most traditional Brazilian Northeast dishes. Green beans drying preliminary experiments show that combine processes, fixed-bed/spouted bed, resulted in dehydrated beans with uniform humidity and the recovery of the beans properties after their rehydration. From this assays was defined an initial humidity suited for the spouted bed process. A fixed-bed pre-drying process until a level of 40% humidity gave the best results. The spouted bed characteristic hydrodynamic curves were presented for different beans loads, where changes in the respective beans physical properties were evidenced during the fluidynamic assay, due simultaneous drying process. One 22 factorial experimental design was carried out with three repetition in the central point, considering as entry variables: drying air velocity and temperature. The response variables were the beans brakeage, water fraction evaporated during 20 and 50 minutes of drying and the humidity ratio. They are presented still the modeling of the drying of the green beans in fine layer in the drier of tray and the modeling of the shrinking of the beans of the drying processes fixed-bed and spouted bed

Comparação entre planejamento estatístico experimental e análise dimensional em operações de mistura e separação para sistema óleo-água

This work aims to determine a better methodology to help predicting some operational parameters to a new design of mixer-settler on treating wastewater produced by petroleum industry, called MDIF (Misturador-Decantador à Inversão de Fases/ Mixer-Settler based on Phase Inversion MSPI). The data from this research were obtained from the wastewater treatment unit, called MSPI-TU, installed on a wastewater treatment plant (WTP) of PETROBRAS/UO-RNCE. The importance in determining the better methodology to predict the results of separation and extraction efficiency of the equipment, contributes significantly to determine the optimum operating variables for the control of the unit. The study was based on a comparison among the experimental efficiency (E) obtained by operating MSPI-TU, the efficiency obtained by experimental design equation (Eplan) from the software Statistica Experimental Design® (version 7.0), and the other obtained from a modeling equation based on a dimensional analysis (Ecalc). The results shows that the experimental design equation gives a good prediction of the unit efficiencies with better data reliability, regarding to the condition before a run operation. The average deviation between the proposed by statistic planning model equation and experimental data was 0.13%. On the other hand, the efficiency calculated by the equation which represents the dimensional analysis, may result on important relative deviations (up 70%). Thus, the experimental design is confirmed as a reliable tool, with regard the experimental data processing of the MSPI-TU

Two-dimensional modeling of material failure in reinforced concrete by means of a continuum strong discontinuity approach

The paper presents a new methodology to model material failure, in two-dimensional reinforced concrete members, using the Continuum Strong Discontinuity Approach (CSDA). The mixture theory is used as the methodological approach to model reinforced concrete as a composite material, constituted by a plain concrete matrix reinforced with two embedded orthogonal long fiber bundles (rebars). Matrix failure is modeled on the basis of a continuum damage model, equipped with strain softening, whereas the rebars effects are modeled by means of phenomenological constitutive models devised to reproduce the axial non-linear behavior, as well as the bondslip and dowel effects. The proposed methodology extends the fundamental ingredients of the standard Strong Discontinuity Approach, and the embedded discontinuity finite element formulations, in homogeneous materials, to matrix/fiber composite materials, as reinforced concrete. The specific aspects of the material failure modeling for those composites are also addressed. A number of available experimental tests are reproduced in order to illustrate the feasibility of the proposed methodology. (c) 2007 Elsevier B.V. All rights reserved.

A mixture theory based method for three-dimensional modeling of reinforce concrete members with embedded crack finite elements

The paper presents a methodology to model three-dimensional reinforced concrete members by means of embedded discontinuity elements based on the Continuum Strong Discontinuous Approach (CSDA). Mixture theory concepts are used to model reinforced concrete as a 31) composite material constituted of concrete with long fibers (rebars) bundles oriented in different directions embedded in it. The effects of the rebars are modeled by phenomenological constitutive models devised to reproduce the axial non-linear behavior, as well as the bond-slip and dowel action. The paper presents the constitutive models assumed for the components and the compatibility conditions chosen to constitute the composite. Numerical analyses of existing experimental reinforced concrete members are presented, illustrating the applicability of the proposed methodology.

Mathematical modeling of the ester oil-refrigerant R134A mixture two-phase flow with foam formation through a small diameter tube

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Modeling the dielectric response of lanthanum modified lead zirconate titanate ferroelectric ceramics-an approach to the phase transitions in relaxor ferroelectrics

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

Spatial pattern detection modeling of thrips (Thrips tabaci) on onion fields

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

The use of classification methods for modeling the antioxidant activity of flavonoid compounds

A study using two classification methods (SDA and SIMCA) was carried out in this work with the aim of investigating the relationship between the structure of flavonoid compounds and their free-radical-scavenging ability. In this work, we report the use of chemometric methods (SDA and SIMCA) able to select the most relevant variables (steric, electronic, and topological) responsible for this ability. The results obtained with the SDA and SIMCA methods agree perfectly with our previous model, in which we used other chemometric methods (PCA, HCA and KNN) and are also corroborated with experimental results from the literature. This is a strong indication of how reliable the selection of variables is.