Molecular modeling databases: A new way in the search of protein targets for drug development

DBMODELING is a relational database of annotated comparative protein structure models and their metabolic, pathway characterization. It is focused on enzymes identified in the genomes of Mycobacterium tuberculosis and Xylella fastidiosa. The main goal of the present database is to provide structural models to be used in docking simulations and drug design. However, since the accuracy of structural models is highly dependent on sequence identity between template and target, it is necessary to make clear to the user that only models which show high structural quality should be used in such efforts. Molecular modeling of these genomes generated a database, in which all structural models were built using alignments presenting more than 30% of sequence identity, generating models with medium and high accuracy. All models in the database are publicly accessible at http://www.biocristalografia.df.ibilce.unesp.br/tools. DBMODELING user interface provides users friendly menus, so that all information can be printed in one stop from any web browser. Furthermore, DBMODELING also provides a docking interface, which allows the user to carry out geometric docking simulation, against the molecular models available in the database. There are three other important homology model databases: MODBASE, SWISSMODEL, and GTOP. The main applications of these databases are described in the present article. © 2007 Bentham Science Publishers Ltd.

The use of planarians as in vivo animal model to study laser biomodulation effects

A variety of effects is attributed to the photo stimulation of tissues, such as improved healing of ulcers, analgesic and anti-inflammatory effects, stimulation of the proliferation of cells of different origins and stimulation of bone repair. Some investigations that make qualitative evaluations, like wound healing and evaluation of pain and edema, can be conducted in human subjects. However, deeper investigations on the mechanisms of action of the light stimulus and other quantitative works that requires biopsies or destructive analysis has to be carried out in animal models or in cell cultures. In this work, we propose the use of planarians as a model to study laser-tissue interaction. Contrasting with cell cultures and unicellular organisms, planarians are among the simplest organism having tissue layers, central nerve system, digestive and excretory system that might have been platforms for the evolution of the complex and highly organized tissues and organs found in higher organisms. For the present study, 685 nm laser radiation was employed. Planarians were cut transversally, in a plane posterior to the auricles. The body fragments were left to regenerate and the proliferation dynamics of stem cells was studied by using histological analysis. Maximum cell count was obtained for the laser treated group at the 4th experimental day. At that experimental time, we also had the largest difference between the irradiated and the non-irradiated control group. We concluded that the studied flatworm could be an interesting animal model for in vivo studies of laser-tissue interactions.

Generating VHDL-AMS models of digital-to-analogue converters from MATLAB®/SIMULINK®

Today, the trend within the electronics industry is for the use of rapid and advanced simulation methodologies in association with synthesis toolsets. This paper presents an approach developed to support mixed-signal circuit design and analysis. The methodology proposed shows a novel approach to the problem of developing behvioural model descriptions of mixed-signal circuit topologies, by construction of a set of subsystems, that supports the automated mapping of MATLAB®/SIMULINK® models to structural VHDL-AMS descriptions. The tool developed, named MS 2SV, reads a SIMULINK® model file and translates it to a structural VHDL-AMS code. It also creates the file structure required to simulate the translated model in the System Vision™. To validate the methodology and the developed program, the DAC08, AD7524 and AD5450 data converters were studied and initially modelled in MATLAB®/ SIMULINK®. The VHDL-AMS code generated automatically by MS 2SV, (MATLAB®/SIMULINK® to System Vision™), was then simulated in the System Vision™. The simulation results show that the proposed approach, which is based on VHDL-AMS descriptions of the original model library elements, allows for the behavioural level simulation of complex mixed-signal circuits.

Efficient parametric adjustment of fuzzy inference system using unconstrained optimization

This paper presents a new methodology for the adjustment of fuzzy inference systems, which uses technique based on error back-propagation method. The free parameters of the fuzzy inference system, such as its intrinsic parameters of the membership function and the weights of the inference rules, are automatically adjusted. This methodology is interesting, not only for the results presented and obtained through computer simulations, but also for its generality concerning to the kind of fuzzy inference system used. Therefore, this methodology is expandable either to the Mandani architecture or also to that suggested by Takagi-Sugeno. The validation of the presented methodology is accomplished through estimation of time series and by a mathematical modeling problem. More specifically, the Mackey-Glass chaotic time series is used for the validation of the proposed methodology. © Springer-Verlag Berlin Heidelberg 2007.

An alternative process for butanol production: Continuous flash fermentation

The objective of this work is to introduce and demonstrate the technical feasibility of the continuous flash fermentation for the production of butanol. The evaluation was carried out through mathematical modeling and computer simulation which is a good approach in such a process development stage. The process consists of three interconnected units, as follows: the fermentor, the cell retention system (tangential microfiltration) and the vacuum flash vessel (responsible for the continuous recovery of butanol from the broth). The efficiency of this process was experimentally validated for the ethanol fermentation, whose main results are also shown. With the proposed design the concentration of butanol in the fermentor was lowered from 11.3 to 7.8 g/l, which represented a significant reduction in the inhibitory effect. As a result, the final concentration of butanol was 28.2 g/l for a broth with 140 g/l of glucose. Solvents productivity and yield were, respectively, 11.7 g/l.h and 33.5 % for a sugar conversion of 95.6 %. Positive aspects about the flash fermentation process are the solvents productivity, the use of concentrated sugar solution and the final butanol concentration. The last two features can be responsible for a meaningful reduction in the distillation costs and result in environmental benefits due to lower quantities of wastewater generated by the process. © 2008 Berkeley Electronic Press. All rights reserved.

On non-linear and non-ideal interactions in two vibrating problems

In practical situations, the dynamics of the forcing function on a vibrating system cannot be considered as given a priori, and it must be taken as a consequence of the dynamics of the whole system. In other words, the forcing source has limited power, as that provided by a DC motor for an example, and thus its own dynamics is influenced by that of the vibrating system being forced. This increases the number of degrees of freedom of the problem, and it is called a non-ideal problem. In this work, we considerer two non-ideal problems analyzed by using numerical simulations. The existence of the Sommerfeld effect was verified, that is, the effect of getting stuck at resonance (energy imparted to the DC motor being used to excite large amplitude motions of the supporting structure). We considered two kinds of non-ideal problem: one related to the transverse vibrations of a shaft carrying two disks and another to a piezoceramic bar transducer powered by a vacuum tube generated by a non-ideal source Copyright © 2007 by ASME.

Viabilidade econômica e seleção de sistemas de irrigação utilizando simulação e dominância estocástica

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

An investigations on local and global behavior of a (SMA) oscillator of 3 - DOF driven by a limited power supply

SMART material systems offer great possibilities in terms of providing novel and economical solutions to engineering problems. The technological advantages of these materials over traditional ones are due to their unique microstructure and molecular properties. Smart materials such as shape memory alloys (SMA), has been used in such diverse areas of engineering science, nowadays. In this paper, we present a numerical investigation of the dynamics interaction of a nonideal structure (NIS). We analyze the phenomenon of the passage through resonance region in the steady state processes. We remarked that this kind of problem can lead to the so-called Sommerfeld effect: steady state frequencies of the DC motor will usually increase as more power (voltage) is given to it in a step-by-step fashion. When a resonance condition with the structure it is reached, the better part of this energy it is consumed to generate large amplitude vibrations of the foundation without sensible change of the motor frequency as before. The results obtained by using numerical simulations are discussed in details. Copyright © 2009 by ASME.

Influence of high insertion torque on implant placement - an anisotropic bone stress analysis

The aim of this study was to evaluate the influence of the high values of insertion torques on the stress and strain distribution in cortical and cancellous bones. Based on tomography imaging, a representative mathematical model of a partial maxilla was built using Mimics 11.11 and Solid Works 2010 softwares. Six models were built and each of them received an implant with one of the following insertion torques: 30, 40, 50, 60, 70 or 80 Ncm on the external hexagon. The cortical and cancellous bones were considered anisotropic. The bone/implant interface was considered perfectly bonded. The numerical analysis was carried out using Ansys Workbench 10.0. The convergence of analysis (6%) drove the mesh refinement. Maximum principal stress (σ max) and maximum principal strain (ε max) were obtained for cortical and cancellous bones around to implant. Pearson's correlation test was used to determine the correlation between insertion torque and stress concentration in the periimplant bone tissue, considering the significance level at 5%. The increase in the insertion torque generated an increase in the σ max and ε max values for cortical and cancellous bone. The σmax was smaller for the cancellous bone, with greater stress variation among the insertion torques. The ε max was higher in the cancellous bone in comparison to the cortical bone. According to the methodology used and the limits of this study, it can be concluded that higher insertion torques increased tensile and compressive stress concentrations in the periimplant bone tissue.

Dynamics of a continuous flash fermentation for butanol production

The ABE (acetone, butanol, ethanol) fermentation is characterized by its low productivity. In this paper, this issue is overcome with an innovative industrial process that employs the flash fermentation technology. The process consists of three interconnected units, as follows: fermentor, cell retention system (tangential microfiltration) and vacuum flash vessel (responsible for the continuous recovery of butanol from the broth). The dynamic behaviour of the process is described by a nonlinear mathematical model with kinetic parameters determined experimentally. From simulations of the mathematical model the dynamic characteristics of the process were investigated. Analyzes of the open-loop dynamic behavior of the process, after step perturbations in the manipulated variables, determined the best control structures for the process. Copyright © 2010, AIDIC Servizi S.r.l.

Modeling for performance analysis of electromagnetic zero-sequence suppressor

The purpose of this work is to present a frequency domain model to demonstrate the operation of an electromagnetic arrangement for controlling the injection of zero-sequence currents in the electrical system. Considering the diversity of sequential distribution of harmonic components of a current, the device proposed can be used in the process of mitigation of zero-sequence components. This device, here called electromagnetic suppressor, consists of a blocker and filter both electromagnetic, whose joint operation can provide paths of high and low impedances that can be conveniently adjusted in order to search for a desired performance. This study presents physical considerations, mathematical modeling and computer simulations that clearly demonstrate the viability of this application as a more viable alternative in the conception of filtering systems. The performance analysis is based on the frequency response of harmonic transmittances. The efficacy of this technique in direct actions to maximize the harmonic mitigation process is demonstrated. ©2010 IEEE.

Photoelastic comparison of single tooth implant-abutment-bone of platform switching vs conventional implant designs

Objectives: The maintenance and stability of peri-implantar soft tissue seem to be related to the crestal bone around the implant platform and different implant designs connections might affect this phenomenon. The aim of this study was to evaluate by photoelastic analysis the stress distribution in the cervical and apical site of implant-abutment interface of conventional implant joints (external hex, internal hex and cone morse) and compare to the novel platform switching design. Materials and methods: It was fabricated photoelastic models using five different implant-abutment connection, one set of external hex (Alvim Ti, Neodent, Curitiba, Brazil), one set of internal hex (Full Osseotite, Biomet 3i, Florida, USA), one cone morse set (Alvim CM, Neodent, Curitiba, Brazil), and two sets of internal hex plus platform switching concept (Alvim II Plus, Neodent, Curitiba, Brazil) (Certain Prevail, Biomet 3i, Florida, USA). These models were submitted to two compressive loads, axial from 20 kgf (load I) and another (load II), inclined 45° from 10 kgf. During the qualitative analysis, digital pictures were taken from a polariscope, for each load situation. For the quantitative analyses in both situations of load, the medium, minimum and maximum in MPa values of shear strain were determined in the cervical and apical site. The Kruskal-Wallis test was used to compare the results between the different systems and between cervical and apical site were compared using Mann-Whitney U test. Results: The results from qualitative analysis showed less concentration of strain in the cervical area to the internal hex plus platform switching (Certain Prevail), in both situation of load. The same results were get in the quantitative analysis, showing less stress concentrations around the implant Certain Prevail with internal hex plus the novel design (17.9 MPa to load I and 29.5 MPa to load II), however, without statistical significant difference between the systems. Conclusion: The minor stress concentration strongly suggest the use of platform switching design as a manner to prevent bone loss around the implant-abutment platform. Clinical Significance: From the result of this study its possible to make clinical decision for implant system which provides implant components with platform switching characteristics.

Optimal phasor measurement units placement for fault location on overhead electric power distribution feeders

This paper proposes a new approach for optimal phasor measurement units placement for fault location on electric power distribution systems using Greedy Randomized Adaptive Search Procedure metaheuristic and Monte Carlo simulation. The optimized placement model herein proposed is a general methodology that can be used to place devices aiming to record the voltage sag magnitudes for any fault location algorithm that uses voltage information measured at a limited set of nodes along the feeder. An overhead, three-phase, three-wire, 13.8 kV, 134-node, real-life feeder model is used to evaluate the algorithm. Tests show that the results of the fault location methodology were improved thanks to the new optimized allocation of the meters pinpointed using this methodology. © 2011 IEEE.

Reactive power support pricing of distributed generators with primary energy source uncertainty

In this paper, a novel methodology to price the reactive power support ancillary service of Distributed Generators (DGs) with primary energy source uncertainty is shown. The proposed methodology provides the service pricing based on the Loss of Opportunity Costs (LOC) calculation. An algorithm is proposed to reduce the uncertainty present in these generators using Multiobjective Power Flows (MOPFs) implemented in multiple probabilistic scenarios through Monte Carlo Simulations (MCS), and modeling the time series associated with the generation of active power from DGs through Markov Chains (MC). © 2011 IEEE.

Mathematical decomposition technique applied to the probabilistic power flow problem

In this paper a framework based on the decomposition of the first-order optimality conditions is described and applied to solve the Probabilistic Power Flow (PPF) problem in a coordinated but decentralized way in the context of multi-area power systems. The purpose of the decomposition framework is to solve the problem through a process of solving smaller subproblems, associated with each area of the power system, iteratively. This strategy allows the probabilistic analysis of the variables of interest, in a particular area, without explicit knowledge of network data of the other interconnected areas, being only necessary to exchange border information related to the tie-lines between areas. An efficient method for probabilistic analysis, considering uncertainty in n system loads, is applied. The proposal is to use a particular case of the point estimate method, known as Two-Point Estimate Method (TPM), rather than the traditional approach based on Monte Carlo simulation. The main feature of the TPM is that it only requires resolve 2n power flows for to obtain the behavior of any random variable. An iterative coordination algorithm between areas is also presented. This algorithm solves the Multi-Area PPF problem in a decentralized way, ensures the independent operation of each area and integrates the decomposition framework and the TPM appropriately. The IEEE RTS-96 system is used in order to show the operation and effectiveness of the proposed approach and the Monte Carlo simulations are used to validation of the results. © 2011 IEEE.