Search results for: fractional order systems

Authors: Marcel Chevalier, Léo Dupont, Sylvain Marié, Frédérique Roffet, Elena Stolyarova, William Templier, Costin Vasile

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Industrial end users are currently facing an increasing need to reduce the risk of unexpected failures and optimize their maintenance. This calls for both short-term analysis and long-term ageing anticipation. At Schneider Electric, we tackle those two issues using both Machine Learning and First Principles models. Machine learning models are incrementally trained from normal data to predict expected values and detect statistically significant short-term deviations. Ageing models are constructed from breaking down physical systems into sub-assemblies, then determining relevant degradation modes and associating each one to the right kinetic law. Validating such anomaly detection and maintenance models is challenging, both because actual incident and ageing data are rare and distorted by human interventions, and incremental learning depends on human feedback. To overcome these difficulties, we propose to simulate physics, systems and humans – including asset maintenance operations – in order to validate the overall approaches in accelerated time and possibly choose between algorithmic alternatives.

Keywords: Degradation models, ageing, anomaly detection, soft sensor, incremental learning.

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Authors: Marco Kennemann, Steffen C. Eickemeyer, Peter Nyhuis

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An increasingly dynamic and complex environment poses huge challenges to production enterprises, especially with regards to logistics. The Logistic Operating Curve Theory, developed at the Institute of Production Systems and Logistics (IFA) of the Leibniz University of Hanover, is a recognized approach to describing logistic interactions, nevertheless, it reaches its limits when it comes to the dynamic aspects. In order to facilitate a timely and optimal Logistic Positioning a method is developed for quickly and reliably identifying dynamic processing states.

Keywords: Dynamics, Logistic Operating Curves, Production Logistics, Production Planning and Control

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Authors: P. Nazemzadeh, A. Dideban, M. Zareiee

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In this paper the effect of faults in the elements and parts of discrete event systems is investigated. In the occurrence of faults, some states of the system must be changed and some of them must be forbidden. For this goal, different states of these elements are examined and a model for fail-safe behavior of each state is introduced. Replacing new models of the target elements in the preliminary model by a systematic method, leads to a fail-safe discrete event system.

Keywords: Discrete event systems, Fail-safe, Petri nets, Supervisory control.

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Authors: Vikram Jeganathan, A. V. Sai Balasubramanian, N. Ravi Shankar, S. Subbaraman, R. Rengaraj

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Heating systems are a necessity for regions which brace extreme cold weather throughout the year. To maintain a comfortable temperature inside a given place, heating systems making use of- Hydronic boilers- are used. The principle of a single pipe system serves as a base for their working. It is mandatory for these heating systems to control the room temperature, thus maintaining a warm environment. In this paper, the concept of regulation of the room temperature over a wide range is established by using an Adaptive Fuzzy Controller (AFC). This fuzzy controller automatically detects the changes in the outside temperatures and correspondingly maintains the inside temperature to a palatial value. Two separate AFC's are put to use to carry out this function: one to determine the quantity of heat needed to reach the prospective temperature required and to set the desired temperature; the other to control the position of the valve, which is directly proportional to the error between the present room temperature and the user desired temperature. The fuzzy logic controls the position of the valve as per the requirement of the heat. The amount by which the valve opens or closes is controlled by 5 knob positions, which vary from minimum to maximum, thereby regulating the amount of heat flowing through the valve. For the given test system data, different de-fuzzifier methods have been implemented and the results are compared. In order to validate the effectiveness of the proposed approach, a fuzzy controller has been designed by obtaining a test data from a real time system. The simulations are performed in MATLAB and are verified with standard system data. The proposed approach can be implemented for real time applications.

Keywords: Adaptive fuzzy controller, Hydronic heating system

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Authors: Kevser Simsek, Rahime Gunay

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In this paper, we focused primarily on Istanbul data that is gathered by using intelligent transportation systems (ITS), and considered the developments in traffic information delivery and future applications that are being planned for implementation. Since traffic congestion is increasing and travel times are becoming less consistent and less predictable, traffic information delivery has become a critical issue. Considering the fuel consumption and wasted time in traffic, advanced traffic information systems are becoming increasingly valuable which enables travelers to plan their trips more accurately and easily.

Keywords: Data Fusion, Istanbul, ITS, Real Time Information, Traffic Information, Travel Time, Urban Mobility

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Authors: Tamás Hartványi, Ferenc Tóth

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European telecommunication distribution center performance is measured by service lead time and quality. Operation model is CTO (customized to order) namely, a high mix customization of telecommunication network equipment and parts. CTO operation contains material receiving, warehousing, network and server assembly to order and configure based on customer specifications. Variety of the product and orders does not support mass production structure. One of the success factors to satisfy customer is to have a proper aggregated planning method for the operation in order to have optimized human resources and highly efficient asset utilization. Research will investigate several methods and find proper way to have an order book simulation where practical optimization problem may contain thousands of variables and the simulation running times of developed algorithms were taken into account with high importance. There are two operation research models that were developed, customer demand is given in orders, no change over time, customer demands are given for product types, and changeover time is constant.

Keywords: CTO, aggregated planning, demand simulation, changeover time.

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Authors: A. Bayoumi, M. Abdallah, F. Hage Chehade

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Structures on the ground surface bear impact from the tunneling-induced settlement, especially when twin tunnels are constructed. The tunneling influence on the structure is considered as a critical issue based on the construction procedure and relative position of tunnels. Lebanon is suffering from a traffic phenomenon caused by the lack of transportation systems. After several traffic counts and geotechnical investigations in Beirut city, efforts aim for the construction of tunneling systems. In this paper, we present a non-linear numerical modeling of the effect of the twin tunnels constructions on the structures located at soil surface for a particular site in Beirut. A parametric study, which concerns the geometric configuration of tunnels, the distance between their centers, the construction order, and the position of the structure, is performed. The tunnel-soil-structure interaction is analyzed by using the non-linear finite element modeling software PLAXIS 2D. The results of the surface settlement and the bending moment of the structure reveal significant influence when the structure is moved away, especially in vertical aligned tunnels.

Keywords: Bending moment, construction procedure, elastic modulus, relative position, soil, structure location, surface settlement, twin tunnels.

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Authors: N. Kaewpraek, W. Assawinchaichote

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This paper considers an H_∞ TS fuzzy state-derivative feedback controller for a class of nonlinear dynamical systems. A Takagi-Sugeno (TS) fuzzy model is used to approximate a class of nonlinear dynamical systems. Then, based on a linear matrix inequality (LMI) approach, we design an H_∞ TS fuzzy state-derivative feedback control law which guarantees L₂-gain of the mapping from the exogenous input noise to the regulated output to be less or equal to a prescribed value. We derive a sufficient condition such that the system with the fuzzy controller is asymptotically stable and H_∞ performance is satisfied. Finally, we provide and simulate a numerical example is provided to illustrate the stability and the effectiveness of the proposed controller.

Keywords: H∞ fuzzy control, LMI, Takagi-Sugano (TS) fuzzy model, nonlinear dynamic systems, state-derivative feedback.

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Authors: Da-Xue Chen, Guang-Hui Liu

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In this paper, we study the oscillation of a class of second-order nonlinear neutral damped variable delay dynamic equations on time scales. By using a generalized Riccati transformation technique, we obtain some sufficient conditions for the oscillation of the equations. The results of this paper improve and extend some known results. We also illustrate our main results with some examples.

Keywords: Oscillation theorem, second-order nonlinear neutral dynamic equation, variable delay, damping, Riccati transformation.

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Authors: R.Muthuvelayudham, T.Viruthagiri

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Response Surface Methodology (RSM) is a powerful and efficient mathematical approach widely applied in the optimization of cultivation process. Cellulase enzyme production by Trichoderma reesei RutC30 using agricultural waste rice straw and banana fiber as carbon source were investigated. In this work, sequential optimization strategy based statistical design was employed to enhance the production of cellulase enzyme through submerged cultivation. A fractional factorial design (26-2) was applied to elucidate the process parameters that significantly affect cellulase production. Temperature, Substrate concentration, Inducer concentration, pH, inoculum age and agitation speed were identified as important process parameters effecting cellulase enzyme synthesis. The concentration of lignocelluloses and lactose (inducer) in the cultivation medium were found to be most significant factors. The steepest ascent method was used to locate the optimal domain and a Central Composite Design (CCD) was used to estimate the quadratic response surface from which the factor levels for maximum production of cellulase were determined.

Keywords: Banana fiber, Cellulase, Optimization, Rice straw

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Authors: Gheida J. Shahrour, Martin J. Russell

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The 3D body movement signals captured during human-human conversation include clues not only to the content of people’s communication but also to their culture and personality. This paper is concerned with automatic extraction of this information from body movement signals. For the purpose of this research, we collected a novel corpus from 27 subjects, arranged them into groups according to their culture. We arranged each group into pairs and each pair communicated with each other about different topics. A state-of-art recognition system is applied to the problems of person, culture, and topic recognition. We borrowed modeling, classification, and normalization techniques from speech recognition. We used Gaussian Mixture Modeling (GMM) as the main technique for building our three systems, obtaining 77.78%, 55.47%, and 39.06% from the person, culture, and topic recognition systems respectively. In addition, we combined the above GMM systems with Support Vector Machines (SVM) to obtain 85.42%, 62.50%, and 40.63% accuracy for person, culture, and topic recognition respectively. Although direct comparison among these three recognition systems is difficult, it seems that our person recognition system performs best for both GMM and GMM-SVM, suggesting that intersubject differences (i.e. subject’s personality traits) are a major source of variation. When removing these traits from culture and topic recognition systems using the Nuisance Attribute Projection (NAP) and the Intersession Variability Compensation (ISVC) techniques, we obtained 73.44% and 46.09% accuracy from culture and topic recognition systems respectively.

Keywords: Person Recognition, Topic Recognition, Culture Recognition, 3D Body Movement Signals, Variability Compensation.

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Authors: Chien-Cheng Kuo

Abstract:

We design and discuss metal-dielectric antireflection coating on metallic substrates for Solar Selective Absorbers of Concentrating Solar Power Systems. The average reflectance is 8.5% at 400-3000nm and 84.4% at 3000nm-10000nm of the metal-dielectric structure.

Keywords: Concentrating solar power systems, solar thermal, solar selective absorber, absorptance, emittance.

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Authors: Abhishek Swaroop, Awadhesh Kumar Singh

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The group mutual exclusion (GME) problem is an interesting generalization of the mutual exclusion problem. Several solutions of the GME problem have been proposed for message passing distributed systems. However, none of these solutions is suitable for real time distributed systems. In this paper, we propose a token-based distributed algorithms for the GME problem in soft real time distributed systems. The algorithm uses the concepts of priority queue, dynamic request set and the process state. The algorithm uses first come first serve approach in selecting the next session type between the same priority levels and satisfies the concurrent occupancy property. The algorithm allows all n processors to be inside their CS provided they request for the same session. The performance analysis and correctness proof of the algorithm has also been included in the paper.

Keywords: Concurrency, Group mutual exclusion, Priority, Request set, Token.

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Authors: Joseph C. Chen, Venkata Mohan Kudapa

Abstract:

Development of two real-time surface roughness (Ra) prediction systems for milling operations was attempted. The systems used not only cutting parameters, such as feed rate and spindle speed, but also the cutting current generated and corrected by a clamp type energy sensor. Two different approaches were developed. First, a fuzzy inference system (FIS), in which the fuzzy logic rules are generated by experts in the milling processes, was used to conduct prediction modeling using current cutting data. Second, a neuro-fuzzy system (ANFIS) was explored. Neuro-fuzzy systems are adaptive techniques in which data are collected on the network, processed, and rules are generated by the system. The inference system then uses these rules to predict Ra as the output. Experimental results showed that the parameters of spindle speed, feed rate, depth of cut, and input current variation could predict Ra. These two systems enable the prediction of Ra during the milling operation with an average of 91.83% and 94.48% accuracy by FIS and ANFIS systems, respectively. Statistically, the ANFIS system provided better prediction accuracy than that of the FIS system.

Keywords: Surface roughness, input current, fuzzy logic, neuro-fuzzy, milling operations.

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Authors: Ganesh. Vulasala, Sivanagaraju. Sirigiri, Ramana. Thiruveedula

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This paper presents an efficient approach to feeder reconfiguration for power loss reduction and voltage profile imprvement in unbalanced radial distribution systems (URDS). In this paper Genetic Algorithm (GA) is used to obtain solution for reconfiguration of radial distribution systems to minimize the losses. A forward and backward algorithm is used to calculate load flows in unbalanced distribution systems. By simulating the survival of the fittest among the strings, the optimum string is searched by randomized information exchange between strings by performing crossover and mutation. Results have shown that proposed algorithm has advantages over previous algorithms The proposed method is effectively tested on 19 node and 25 node unbalanced radial distribution systems.

Keywords: Distribution system, Load flows, Reconfiguration, Genetic Algorithm.

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Authors: Faheem Ahmed, Fareed Ahmed, Yongheng Guo, Yong Yang

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This paper deals with a high-order accurate Runge Kutta Discontinuous Galerkin (RKDG) method for the numerical solution of the wave equation, which is one of the simple case of a linear hyperbolic partial differential equation. Nodal DG method is used for a finite element space discretization in 'x' by discontinuous approximations. This method combines mainly two key ideas which are based on the finite volume and finite element methods. The physics of wave propagation being accounted for by means of Riemann problems and accuracy is obtained by means of high-order polynomial approximations within the elements. High order accurate Low Storage Explicit Runge Kutta (LSERK) method is used for temporal discretization in 't' that allows the method to be nonlinearly stable regardless of its accuracy. The resulting RKDG methods are stable and high-order accurate. The L1 ,L2 and L∞ error norm analysis shows that the scheme is highly accurate and effective. Hence, the method is well suited to achieve high order accurate solution for the scalar wave equation and other hyperbolic equations.

Keywords: Nodal Discontinuous Galerkin Method, RKDG, Scalar Wave Equation, LSERK

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Authors: Younis R. Elhaddad, Aiman S.Gannous

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The particular interests of this paper is to explore if the simple Genetic Algorithms (GA) starts with population of only two individuals and applying different crossover technique over these parents to produced 104 children, each one has different attributes inherited from their parents; is better than starting with population of 100 individuals; and using only one type crossover (order crossover OX). For this reason we implement GA with 52 different crossover techniques; each one produce two children; which means 104 different children will be produced and this may discover more search space, also we implement classic GA with order crossover and many experiments were done over 3 Travel Salesman Problem (TSP) to find out which method is better, and according to the results we can say that GA with Multi-crossovers is much better.

Keywords: Artificial intelligence, genetic algorithm, order crossover, travel salesman problem.

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Authors: J. Mizuno, S. Takahashi

Abstract:

In this paper, design and fabrication of an actuated parallel-plate mirror based on a 3D-printer is described. The mirror and electrode layers are fabricated separately and assembled thereafter. The alignment is performed by dowel pin-hole pairs fabricated on the respective layers. The electrodes are formed on the surface of the electrode layer by Au ion sputtering using a suitable mask, which is also fabricated by a 3D-printer.For grounding the mirror layer, except the contact area with the electrode paths, all the surface is Au ion sputtered. 3D-printers are widely used for creating 3D models or mock-ups. The authors have recently proposed that these models can perform electromechanical functions such as actuators by suitably masking them followed by metallization process. Since the smallest possible fabrication size is in the order of sub-millimeters, these electromechanical devices are named by the authors as SMEMS (Sub-Milli Electro-Mechanical Systems) devices. The proposed mirror described in this paper which consists of parallel-plate electrostatic actuators is also one type of SMEMS devices. In addition, SMEMS is totally environment-clean compared to MEMS (Micro Electro-Mechanical Systems) fabrication processes because any hazardous chemicals or gases are utilized.

Keywords: MEMS, parallel-plate mirror, SMEMS, 3D-printer.

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Authors: Petru V. Notingher, Stefan Busoi, Laurentiu M. Dumitran, Cristina Stancu, Gabriel Tanasescu, Emanuel Balescu

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Degradation of polymeric insulation systems of electrical equipments increases the space charge density and the concentration of electrical dipoles. By consequence, the maximum values and the slopes of absorption/resorption (A/R) currents can change with insulation systems ageing. In this paper, an analysis of the nature of the A/R currents and the importance of their components, especially the polarization current and the current given by the space charge, is presented. The experimental study concerns the A/R currents measurements of plane samples (made from CALMICAGLAS tapes), virgin and thermally accelerated aged. The obtained results show that the ageing process produces an increase of the values and a decrease of shapes of the A/R currents. Finally, the possibility of estimating insulations ageing state and lifetime from A/R currents measurements is discussed.

Keywords: Insulation Systems, Absorption/Resorption Currents, Ageing, Lifetime.

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Authors: F. Khaber, K. Zehar, A. Hamzaoui

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In this paper, we introduce a robust state feedback controller design using Linear Matrix Inequalities (LMIs) and guaranteed cost approach for Takagi-Sugeno fuzzy systems. The purpose on this work is to establish a systematic method to design controllers for a class of uncertain linear and non linear systems. Our approach utilizes a certain type of fuzzy systems that are based on Takagi-Sugeno (T-S) fuzzy models to approximate nonlinear systems. We use a robust control methodology to design controllers. This method not only guarantees stability, but also minimizes an upper bound on a linear quadratic performance measure. A simulation example is presented to show the effectiveness of this method.

Keywords: Takagi-Sugeno fuzzy model, state feedback, linear matrix inequalities, robust stability.

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Authors: Mahmoud Beshr, Ivan Andonovic, Moustafa H. Aly

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Visible Light Communication (VLC) offers advantages of low energy consumption, licence free and RF interference free operation. One application area for VLC is in the provision of health centred services circumventing issues of interference with any biomedical device within the environment. VLC performamce is affected by natural light restricting systems avilability and relibility. The paper presents an analysis of the performance of VLC systems under different meteorological conditions. The evaluation considered the impact of natural light as a function of different reflection surfaces in different room sizes.

Keywords: Visible light communication, impulse reponse , performance analysis , natural light.

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Authors: Lu Zou, Dianfu MA, Ying Wang, Xianqi Zhao

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Avionic software architecture has transit from a federated avionics architecture to an integrated modular avionics (IMA) .ARINC 653 (Avionics Application Standard Software Interface) is a software specification for space and time partitioning in Safety-critical avionics Real-time operating systems. Methods to transform the abstract avionics application logic function to the executable model have been brought up, however with less consideration about the code generating input and output model specific for ARINC 653 platform and inner-task synchronous dynamic interaction order sequence. In this paper, we proposed an AADL-based model-driven design methodology to fulfill the purpose to automatically generating Cµ executable model on ARINC 653 platform from the ARINC653 architecture which defined as AADL653 in order to facilitate the development of the avionics software constructed on ARINC653 OS. This paper presents the mapping rules between the AADL653 elements and the elements in Cµ language, and define the code generating rules , designs an automatic C µ code generator .Then, we use a case to illustrate our approach. Finally, we give the related work and future research directions.

Keywords: IMA, ARINC653, AADL653, code generation.

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Authors: Ružarovský, Roman, Danišová, Nina, Velíšek, Karol

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In this contribution is presented a complex design of individual objects identification in the workplace of intelligent assembly cell. Intelligent assembly cell is situated at Institute of Manufacturing Systems and Applied Mechanics and is used for pneumatic actuator assembly. Pneumatic actuator components are pneumatic roller, cover, piston and spring. Two identification objects alternatives for assembly are designed in the workplace of industrial robot. In the contribution is evaluated and selected suitable alternative for identification – 2D codes reader. The complex design of individual object identification is going out of intelligent manufacturing systems knowledge. Intelligent assembly and manufacturing systems as systems of new generation are gradually loaded in to the mechanical production, when they are removeing human operation out of production process and they also short production times.

Keywords: system, cell, intelligent, mechanics, device

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Authors: Omar B. Yaakob, Yasser M. Ahmed, Ahmad F. Said

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There is an essential need for obtaining the mathematical representation of fish body undulations, which can be used for designing and building new innovative types of marine propulsion systems with less environmental impact. This research work presents a case study to derive the mathematical model for fish body movement. Observation and capturing image methods were used in this study in order to obtain a mathematical representation of Clariasbatrachus fish (catfish). An experiment was conducted by using an aquarium with dimension 0.609 m x 0.304 m x 0.304 m, and a 0.5 m ruler was attached at the base of the aquarium. Progressive Scan Monochrome Camera was positioned at 1.8 m above the base of the aquarium to provide swimming sequences. Seven points were marked on the fish body using white marker to indicate the fish movement and measuring the amplitude of undulation. Images from video recordings (20 frames/s) were analyzed frame by frame using local coordinate system, with time interval 0.05 s. The amplitudes of undulations were obtained for image analysis from each point that has been marked on fish body. A graph of amplitude of undulations versus time was plotted by using computer to derive a mathematical fit. The function for the graph is polynomial with nine orders.

Keywords: Fish locomotion, body undulation, steady and unsteady swimming modes.

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Authors: Muhammad Haitham Albahnassi, Adnan Malki, Shokri Almekdad

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In this paper, a method for reconfiguring bandwidth in a circular dual-mode resonator is presented. The method concerns the optimized geometry of a structure that may be used to host the tuning elements, which are typically RF (Radio Frequency) switches. The tuning elements themselves, and their performance during tuning, are not the focus of this paper. The designed resonator is able to reconfigure its fractional bandwidth by adjusting the inter-coupling level between the degenerate modes, while at the same time improving its response by adjusting the external-coupling level and keeping the center frequency fixed. The inter-coupling level has been adjusted by changing the dimensions of the perturbation element, while the external-coupling level has been adjusted by changing one of the feeder dimensions. The design was arrived at via optimization. Agreeing simulation and measurement results of the designed and implemented filters showed good improvements in return loss values and the stability of the center frequency.

Keywords: Dual-mode resonators, perturbation element, perturbation theory, reconfigurable filters, software defined radio (SDR), cognitine radio.

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Authors: Tianxiu Lu, Peiyong Zhu

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This paper is mainly concerned with a kind of coupled map lattices (CMLs). New definitions of dense δ-chaos and dense chaos (which is a special case of dense δ-chaos with δ = 0) in discrete spatiotemporal systems are given and sufficient conditions for these systems to be densely chaotic or densely δ-chaotic are derived.

Keywords: Discrete spatiotemporal systems, coupled map lattices, dense δ-chaos, Li-Yorke pairs.

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Authors: Ileladewa Adeoye Abiodun, Cheng Wai Khuen

Abstract:

Multi-Agent Systems (MAS) emerged in the pursuit to improve our standard of living, and hence can manifest complex human behaviors such as communication, decision making, negotiation and self-organization. The Social Network Services (SNSs) have attracted millions of users, many of whom have integrated these sites into their daily practices. The domains of MAS and SNS have lots of similarities such as architecture, features and functions. Exploring social network users- behavior through multiagent model is therefore our research focus, in order to generate more accurate and meaningful information to SNS users. An application of MAS is the e-Auction and e-Rental services of the Universiti Cyber AgenT(UniCAT), a Social Network for students in Universiti Tunku Abdul Rahman (UTAR), Kampar, Malaysia, built around the Belief- Desire-Intention (BDI) model. However, in spite of the various advantages of the BDI model, it has also been discovered to have some shortcomings. This paper therefore proposes a multi-agent framework utilizing a modified BDI model- Belief-Desire-Intention in Dynamic and Uncertain Situations (BDIDUS), using UniCAT system as a case study.

Keywords: Distributed Data Mining, Multi-Agent Systems, Preference-Based, SNS.

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Authors: H. Mohammadiun, A. Kianifar, A. Kargar

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Nowadays, there is little information, concerning the heat shield systems, and this information is not completely reliable to use in so many cases. for example, the precise calculation cannot be done for various materials. In addition, the real scale test has two disadvantages: high cost and low flexibility, and for each case we must perform a new test. Hence, using numerical modeling program that calculates the surface recession rate and interior temperature distribution is necessary. Also, numerical solution of governing equation for non-charring material ablation is presented in order to anticipate the recession rate and the heat response of non-charring heat shields. the governing equation is nonlinear and the Newton- Rafson method along with TDMA algorithm is used to solve this nonlinear equation system. Using Newton- Rafson method for solving the governing equation is one of the advantages of the solving method because this method is simple and it can be easily generalized to more difficult problems. The obtained results compared with reliable sources in order to examine the accuracy of compiling code.

Keywords: Ablation rate, surface recession, interior temperaturedistribution, non charring material ablation, Newton Rafson method.

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Authors: Mohamed A. El-Kady, Badr M. Alshammari

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In a recent major industry-supported research and development study, a novel framework was developed and applied for assessment of reliability and quality performance levels in reallife power systems with practical large-scale sizes. The new assessment methodology is based on three metaphors (dimensions) representing the relationship between available generation capacities and required demand levels. The paper shares the results of the successfully completed stud and describes the implementation of the new methodology on practical zones in the Saudi electricity system.

Keywords: Power systems; large-scale analysis, reliability; performance assessment, linear programming.

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Authors: Paola Lecca, Lorenzo Dematte, Corrado Priami

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The present models and simulation algorithms of intracellular stochastic kinetics are usually based on the premise that diffusion is so fast that the concentrations of all the involved species are homogeneous in space. However, recents experimental measurements of intracellular diffusion constants indicate that the assumption of a homogeneous well-stirred cytosol is not necessarily valid even for small prokaryotic cells. In this work a mathematical treatment of diffusion that can be incorporated in a stochastic algorithm simulating the dynamics of a reaction-diffusion system is presented. The movement of a molecule A from a region i to a region j of the space is represented as a first order reaction Ai k- ! Aj , where the rate constant k depends on the diffusion coefficient. The diffusion coefficients are modeled as function of the local concentration of the solutes, their intrinsic viscosities, their frictional coefficients and the temperature of the system. The stochastic time evolution of the system is given by the occurrence of diffusion events and chemical reaction events. At each time step an event (reaction or diffusion) is selected from a probability distribution of waiting times determined by the intrinsic reaction kinetics and diffusion dynamics. To demonstrate the method the simulation results of the reaction-diffusion system of chaperoneassisted protein folding in cytoplasm are shown.

Keywords: Reaction-diffusion systems, diffusion coefficient, stochastic simulation algorithm.

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