Electrochemical genosensors for the detection of Bonamia parasite. Selection of single strand-DNA (ssDNA) probes by simulation of the secondary structure folding

A post-PCR nucleic acid work by comparing experimental data, from electrochemical genosensors, and bioinformatics data, derived from the simulation of the secondary structure folding and prediction of hybridisation reaction, was carried out in order to rationalize the selection of ssDNA probes for the detection of two Bonamia species, B. exitiosa and B. ostreae, parasites of Ostrea edulis.Six ssDNA probes (from 11 to 25 bases in length, 2 thiolated and 4 biotinylated) were selected within different regions of B. ostreae and B. exitiosa PCR amplicons (300 and 304 bases, respectively) with the aim to discriminate between these parasite species. ssDNA amplicons and probes were analyzed separately using the "Mfold Web Server" simulating the secondary structure folding behaviour. The hybridisation of amplicon-probe was predicted by means of "Dinamelt Web Server". The results were evaluated considering the number of hydrogen bonds broken and formed in the simulated folding and hybridisation process, variance in gaps for each sequence and number of available bases. In the experimental part, thermally denatured PCR products were captured at the sensor interface via sandwich hybridisation with surface-tethered probes (thiolated probes) and biotinylated signalling probes. A convergence between analytical signals and simulated results was observed, indicating the possibility to use bioinformatic data for ssDNA probes selection to be incorporated in genosensors. (C) 2011 Elsevier B.V. All rights reserved.

Simulation of the energy performance of maize production integrated to pig farming

Foi avaliado o desempenho energético da suinocultura integrada à produção de milho em grão em sistema de plantio direto mecanizado. Nesta concepção de integração proposta, os dejetos suínos são utilizados como fertilizantes na produção de milho. O sistema foi delimitado envolvendo as atividades associadas ao manejo dos suínos e de produção do milho (manejo do solo, cultivo e colheita). O período de análise considerado foi de um ano, o que possibilita a produção de três lotes de suínos e duas safras de milho. Para avaliar o desempenho energético, foram criados três indicadores: eficiência energética, eficiência de uso de fontes não renováveis e o custo de energia não renovável para a produção de proteína. As entradas energéticas são compostas pelos insumos e pela infraestrutura, utilizados na criação dos suínos e na produção de milho, e pela radiação solar incidente no agrossistema. Já as saídas são representadas pelos seus produtos (suínos terminados e o milho). Os resultados obtidos nas simulações apontam que a integração melhora o desempenho energético das granjas suinícolas, aumentando a eficiência energética (186%) e a eficiência não renovável (352%), além de reduzir o custo de energia não renovável para a produção de proteína (‑58%).

An improved tabu-based vector optimal algorithm for design optimizations of electromagnetic devices

This paper introduces an improved tabu-based vector optimal algorithm for multiobjective optimal designs of electromagnetic devices. The improvements include a division of the entire search process, a new method for fitness assignment, a novel scheme for the generation and selection of neighborhood solutions, and so forth. Numerical results on a mathematical function and an engineering multiobjective design problem demonstrate that the proposed method can produce virtually the exact Pareto front, in both parameter and objective spaces, even though the iteration number used by it is only about 70% of that required by its ancestor.

Effects of powder preparation and sintering procedure on microstructure and dielectric properties of PLZT ceramics

PLZT ceramics belong to one of the very important groups of functional materials that make a basis for the production of a large range of electronic devices. The microstructure and properties of ceramics depend on the powder preparation and thermal processing conditions. Various techniques have been used to obtain chemically homogeneous and fine starting powders. PLZT powders have been prepared by two different production routes: by a modified Pechini method, using a polymeric precursor method (PMM) and by a partial oxalate method. A two-step sintering process, including a hot pressing, was carried out at 1100 and 1200degreesC Distinct phases obtained during the sintering process have been investigated by SEM and EDS techniques and dielectric properties such as permittivity and dielectric loss were measured in a frequency range from 1 to 20 kHz.. A significant difference in microstructure and dielectric properties, depending on powder origin and sintering procedure, has been noticed.

Numerical simulation of magnetic-field-enhanced plasma immersion ion implantation in cylindrical geometry

Recent studies have demonstrated that the sheath dynamics in plasma immersion ion implantation (PIII) is significantly affected by an external magnetic field. In this paper, a two-dimensional computer simulation of a magnetic-field-enhanced PHI system is described. Negative bias voltage is applied to a cylindrical target located on the axis of a grounded vacuum chamber filled with uniform molecular nitrogen plasma. A static magnetic field is created by a small coil installed inside the target holder. The vacuum chamber is filled with background nitrogen gas to form a plasma in which collisions of electrons and neutrals are simulated by the Monte Carlo algorithm. It is found that a high-density plasma is formed around the target due to the intense background gas ionization by the magnetized electrons drifting in the crossed E x B fields. The effect of the magnetic field intensity, the target bias, and the gas pressure on the sheath dynamics and implantation current of the PHI system is investigated.

Simulation of within field variability of corn yield with Ceres-Maize model

The CERES-Maize model was used to estimate the spatial variability in corn (Zea mays L.) yield for 1995 and 1996 using data measured on soil profiles located on a 30.5 m grid within a 3.9 ha field in Michigan. The model was calibrated for one grid profile for the 1995 and then used to simulate corn yield for all grid points for the 2 yrs. For the calibration for 1995, the model predicted corn yield within 2%. For 1995, the model predicted yield variability very well (r(2) = 0.85), producing similar yield maps with differences generally within +/- 300 kg ha(-1). For 1996, the model predicted low grain yields (1167 kg ha(-1)) compared with measured (8928 kg ha(-1)) because the model does not account for horizontal water movement within the landscape or water contributions from a water table. Under nonlimiting water conditions, the model performed well (average of 8717 vs. 8948 kg ha(-1)) but under-estimated the measured yield variability.

Increase on incineration capacity and NOx control for air enrichment in the experimental simulation of aqueous residue incineration

An experimental investigation of air enrichment in a combustion chamber designed to incinerate aqueous residues is presented. Diesel fuel and liquefied petroleum gas (LPG) were used independently as fuels. An increase of 85% in the incineration capacity was obtained with nearly 50% O-2 in the oxidant gas, in comparison to incineration with air only. The incineration capacity continues increasing for enrichment levels above 50% O-2 , although at a lower pace. For complete oxy-flame combustion (100% O-2 ), the increase of the incineration capacity was about 110% relative to the starting conditions and about 13.5% relative to the condition with 50% O-2 . The CO concentration measured near the flame front decreases drastically with the increase of O-2 content in the oxidant gas. At the chamber exit, the CO concentration was always near zero, indicating that the chamber residence time was sufficient to complete fuel oxidation in any test setting. For diesel fuel, the NOx was entirely formed in the first region of the combustion chamber. For diesel fuel, there was some increase in the NOx concentration up to 35% of O-2 ; this increase became very sharp after that. From 60 ppm, at operation with air only, the NOx concentration raises to 200 ppm at 35% O-2 , and then to 2900 ppm at 74% O-2 . The latter corresponds to six times more NOx in terms of the ratio of mass of NO to mass of residue, compared to the situation of combustion with air only. For LPG, the NOx concentrations reached 4200 ppm at 80% O-2 , corresponding to nine times more, also in terms of the ratio of mass of NO to mass of residue, in comparison with combustion with air only. Results of different techniques used to control the NOx emission during air enrichment are discussed: (a) variation of the recirculated zone intensity, (b) increase of the spray Sauter mean diameter, (c) fuel staging, (d) oxidizer staging, and (e) ammonia injection. The present paper shows that NOx emission may be controlled without damage of the increase of incineration capacity by the enrichment and with low emission of partial oxidation pollutants such as CO.

Modeling and simulation of cephalosporin C production in a fed-batch tower-type bioreactor

Immobilized cell utilization in tower-type bioreactor is one of the main alternatives being studied to improve the industrial bioprocess. Other alternatives for the production of beta -lactam antibiotics, such as a cephalosporin C fed-batch p recess in an aerated stirred-tank bioreactor with free cells of Cepha-losporium acremonium or a tower-type bioreactor with immobilized cells of this fungus, have proven to be more efficient than the batch profess. In the fed-batch process, it is possible to minimize the catabolite repression exerted by the rapidly utilization of carbon sources (such as glucose) in the synthesis of antibiotics by utilizing a suitable flow rate of supplementary medium. In this study, several runs for cephalosporin C production, each lasting 200 h, were conducted in a fed-batch tower-type bioreactor using different hydrolyzed sucrose concentrations, For this study's model, modifications were introduced to take into account the influence of supplementary medium flow rate. The balance equations considered the effect of oxygen limitation inside the bioparticles. In the Monod-type rate equations, eel concentrations, substrate concentrations, and dissolved oxygen were included as reactants affecting the bioreaction rate. The set of differential equations was solved by the numerical method, and the values of the parameters were estimated by the classic nonlinear regression method following Marquardt's procedure with a 95% confidence interval. The simulation results showed that the proposed model fit well with the experimental data,and based on the experimental data and the mathematical model an optimal mass flow rate to maximize the bioprocess productivity could be proposed.

Simulation of free surface flows in a distributed memory environment

A parallel technique, for a distributed memory machine, based on domain decomposition for solving the Navier-Stokes equations in cartesian and cylindrical coordinates in two dimensions with free surfaces is described. It is based on the code by Tome and McKee (J. Comp. Phys. 110 (1994) 171-186) and Tome (Ph.D. Thesis, University of Strathclyde, Glasgow, 1993) which in turn is based on the SMAC method by Amsden and Harlow (Report LA-4370, Los Alamos Scientific Laboratory, 1971), which solves the Navier-Stokes equations in three steps: the momentum and Poisson equations and particle movement, These equations are discretized by explicit and 5-point finite differences. The parallelization is performed by splitting the computation domain into vertical panels and assigning each of these panels to a processor. All the computation can then be performed using nearest neighbour communication. Test runs comparing the performance of the parallel with the serial code, and a discussion of the load balancing question are presented. PVM is used for communication between processes. (C) 1999 Elsevier B.V. B.V. All rights reserved.

Simulation of electron density maps for two-dimensional crystal structures using Mathematica

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

Dynamic modeling and simulation of a flexible robotic manipulator

This work focuses on the dynamic modeling of a flexible robotic manipulator with two flexible links and two revolute joints, which rotates in the horizontal plane. The dynamic equations are derived using the Newton-Euler formulation and the finite element method, based on elementary beam theory. Computer simulation results are presented to illustrate this study. The dynamic model becomes necessary for use in future design and control applications.