Search results for: Fused deposition modeling (FDM)

Authors: S. Rajabi, M. ArdebiliPoor, M. Shahabadi

Abstract:

In this paper we propose a method for modeling the correlation between the received signals by two or more antennas operating in a multipath environment. Considering the maximum excess delay in the channel being modeled, an elliptical region surrounding both transmitter and receiver antennas is produced. A number of scatterers are randomly distributed in this region and scatter the incoming waves. The amplitude and phase of incoming waves are computed and used to obtain statistical properties of the received signals. This model has the distinguishable advantage of being applicable for any configuration of antennas. Furthermore the common PDF (Probability Distribution Function) of received wave amplitudes for any pair of antennas can be calculated and used to produce statistical parameters of received signals.

Keywords: MIMO (Multiple Input Multiple Output), SIMO (Single Input Multiple Output), GBSBEM (Geometrically Based Single Bounce Elliptical Model).

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Authors: Y. Galerkin, K. Soldatova, A. Drozdov

Abstract:

The 6th version of Universal modeling method for centrifugal compressor stage calculation is described. Identification of the new mathematical model was made. As a result of identification the uniform set of empirical coefficients is received. The efficiency definition error is 0,86 % at a design point. The efficiency definition error at five flow rate points (except a point of the maximum flow rate) is 1,22 %. Several variants of the stage with 3D impellers designed by 6th version program and quasi threedimensional calculation programs were compared by their gas dynamic performances CFD (NUMECA FINE TURBO). Performance comparison demonstrated general principles of design validity and leads to some design recommendations.

Keywords: Compressor design, loss model, performance prediction, test data, model stages, flow rate coefficient, work coefficient.

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Authors: Mbala Mukenga, Edison Muzenda, Kalala Jalama, Reinout Meijboom

Abstract:

TiO2 supported nano-ZnO catalyst was prepared by deposition-precipitation and tested for the trans-esterification reaction of soybean oil to biodiesel. The TiO2 support stabilized the nano-ZnO in a dispersed form with limited crystallite size compared to the unsupported ZnO. The final ZnO dispersion and crystallite size and the material transfer resistance in the catalyst significantly influenced the supported nano-ZnO catalyst performance.

Keywords: nano-ZnO, soybean oil, TiO2, trans-esterification

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Authors: Josefina Barnachea Janier, Radzuan B. Razali, Afza Shafie, Brahim Belhaouari Samir

Abstract:

In the Enhanced Oil Recovery (EOR) method, use of Carbon dioxide flooding whereby CO₂ is injected into an oil reservoir to increase output when extracting oil resulted significant recovery worldwide. The carbon dioxide function as a pressurizing agent when mixed into the underground crude oil will reduce its viscosity and will enable a rapid oil flow. Despite the CO₂’s advantage in the oil recovery, it may result to asphaltene precipitation a problem that will cause the reduction of oil produced from oil wells. In severe cases, asphaltene precipitation can cause costly blockages in oil pipes and machinery. This paper presents reviews of several studies done on mathematical modeling of asphaltene precipitation. The synthesized result from several researches done on this topic can be used as guide in order to better understand asphaltene precipitation. Likewise, this can be used as initial reference for students, and new researchers doing study on asphaltene precipitation.

Keywords: Asphaltene precipitation, crude oil, carbon dioxide flooding, enhanced oil recovery.

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Authors: Shervin Khazaeli, Shahab Haj-zamani

Abstract:

Recently, advanced geotechnical engineering problems related to soil movement, particle loss, and modeling of local failure (i.e. discontinua) as well as modeling the in-contact structures (i.e. continua) are of the great interest among researchers. The aim of this research is to meet the requirements with respect to the modeling of the above-mentioned two different domains simultaneously. To this end, a coupled numerical method is introduced based on Discrete Element Method (DEM) and eXtended-Finite Element Method (X-FEM). In the coupled procedure, DEM is employed to capture the interactions and relative movements of soil particles as discontinua, while X-FEM is utilized to model in-contact structures as continua, which may consist of different types of discontinuities. For verification purposes, the new coupled approach is utilized to examine benchmark problems including different contacts between/within continua and discontinua. Results are validated by comparison with those of existing analytical and numerical solutions. This study proves that extended-finite-discrete element method can be used to robustly analyze not only contact problems, but also other types of discontinuities in continua such as (i) crack formations and propagations, (ii) voids and bimaterial interfaces, and (iii) combination of previous cases. In essence, the proposed method can be used vastly in advanced soil-structure interaction problems to investigate the micro and macro behaviour of the surrounding soil and the response of the embedded structure that contains discontinuities.

Keywords: Contact problems, discrete element method, extended-finite element method, soil-structure interaction.

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Authors: Mikhail P. Strongin, Ragupathi Soundararajan

Abstract:

The purpose of this work is fast design optimization of the seal chamber. The study includes the mass transfer between lower and upper chamber on seal chamber for hot water application pumps. The use of Fluent 12.1 commercial code made it possible to capture complex flow with heat-mass transfer, radiation, Tailor instability, and buoyancy effect. Realizable k-epsilon model was used for turbulence modeling. Radiation heat losses were taken into account. The temperature distribution at seal region is predicted with respect to heat addition. Results show the possibilities of the model simplifications by excluding the water domain in low chamber from calculations. CFD simulations permit to improve seal chamber design to meet target water temperature around the seal. This study can be used for the analysis of different seal chamber configurations.

Keywords: CFD, heat transfer, seal chamber, high temperature water

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Authors: Kyoungjin Kim

Abstract:

Nanoscale thermites such as the composite mixture of nano-sized aluminum and molybdenum trioxide powders possess several technical advantages such as much higher reaction rate and shorter ignition delay, when compared to the conventional energetic formulations made of micron-sized metal and oxidizer particles. In this study, the self-propagation of combustion wave in compacted pellets of nanoscale thermite composites is modeled and computationally investigated by utilizing the activation energy reduction of aluminum particles due to nanoscale particle sizes. The present computational model predicts the speed of combustion wave propagation which is good agreement with the corresponding experiments of thermite reaction. Also, several characteristics of thermite reaction in nanoscale composites are discussed including the ignition delay and combustion wave structures.

Keywords: Nanoparticles, Thermite reaction, Combustion wave, Numerical modeling.

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Authors: Dariush Jafari, Seyed Ali Jafari

Abstract:

The recommended limit for cadmium concentration in potable water is less than 0.005 mg/L. A continuous biosorption process using indigenous red seaweed, Gracilaria corticata, was performed to remove cadmium from the potable water. The process was conducted under fixed conditions and the breakthrough curves were achieved for three consecutive sorption-desorption cycles. A modeling based on Artificial Neural Network (ANN) was employed to fit the experimental breakthrough data. In addition, a simplified semi empirical model, Thomas, was employed for this purpose. It was found that ANN well described the experimental data (R2>0.99) while the Thomas prediction were a bit less successful with R2>0.97. The adjusted design parameters using the nonlinear form of Thomas model was in a good agreement with the experimentally obtained ones. The results approve the capability of ANN to predict the cadmium concentration in potable water.

Keywords: ANN, biosorption, cadmium, packed-bed, potable water.

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Authors: A. Naamane, M. Hasnaoui

Abstract:

Numerical modeling of fluid flows, whether compressible or incompressible, laminar or turbulent presents a considerable contribution in the scientific and industrial fields. However, the development of an approximate model of a supersonic flow requires the introduction of specific and more precise techniques and methods. For this purpose, the object of this paper is modeling a supersonic flow of inviscid fluid around a dihedral airfoil. Based on the thin airfoils theory and the non-dimensional stationary Steichen equation of a two-dimensional supersonic flow in isentropic evolution, we obtained a solution for the downstream velocity potential of the oblique shock at the second order of relative thickness that characterizes a perturbation parameter. This result has been dealt with by the asymptotic analysis and characteristics method. In order to validate our model, the results are discussed in comparison with theoretical and experimental results. Indeed, firstly, the comparison of the results of our model has shown that they are quantitatively acceptable compared to the existing theoretical results. Finally, an experimental study was conducted using the AF300 supersonic wind tunnel. In this experiment, we have considered the incident upstream Mach number over a symmetrical dihedral airfoil wing. The comparison of the different Mach number downstream results of our model with those of the existing theoretical data (relative margin between 0.07% and 4%) and with experimental results (concordance for a deflection angle between 1° and 11°) support the validation of our model with accuracy.

Keywords: Asymptotic modelling, dihedral airfoil, supersonic flow, supersonic wind tunnel.

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Authors: Y. Galerkin, A. Rekstin, K. Soldatova

Abstract:

Universal modeling method well proven for industrial compressors was applied for design of the high flow rate supersonic stage. Results were checked by ANSYS CFX and NUMECA Fine Turbo calculations. The impeller appeared to be very effective at transonic flow velocities. Stator elements efficiency is acceptable at design Mach numbers too. Their loss coefficient versus inlet flow angle performances correlates well with Universal modeling prediction. The impeller demonstrates ability of satisfactory operation at design flow rate. Supersonic flow behavior in the impeller inducer at the shroud blade to blade surface Φ des deserves additional study.

Keywords: Centrifugal compressor stage, supersonic impeller, inlet flow angle, loss coefficient, return channel, shock wave, vane diffuser.

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Authors: S. Farzi

Abstract:

Recently, a lot of attention has been devoted to advanced techniques of system modeling. PNN(polynomial neural network) is a GMDH-type algorithm (Group Method of Data Handling) which is one of the useful method for modeling nonlinear systems but PNN performance depends strongly on the number of input variables and the order of polynomial which are determined by trial and error. In this paper, we introduce GPNN (genetic polynomial neural network) to improve the performance of PNN. GPNN determines the number of input variables and the order of all neurons with GA (genetic algorithm). We use GA to search between all possible values for the number of input variables and the order of polynomial. GPNN performance is obtained by two nonlinear systems. the quadratic equation and the time series Dow Jones stock index are two case studies for obtaining the GPNN performance.

Keywords: GMDH, GPNN, GA, PNN.

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Authors: Pranav Ravikumar, Arunabha Bera, Vijay K. Mehra, Anand Kumar

Abstract:

This paper solves the Non Linear Schrodinger Equation using the Split Step Fourier method for modeling an optical fiber. The model generates a complex wave of optical pulses and using the results obtained two graphs namely Loss versus Wavelength and Dispersion versus Wavelength are generated. Taking Chromatic Dispersion and Polarization Mode Dispersion losses into account, the graphs generated are compared with the graphs formulated by JDS Uniphase Corporation which uses standard values of dispersion for optical fibers. The graphs generated when compared with the JDS Uniphase Corporation plots were found to be more or less similar thus verifying that the model proposed is right. MATLAB software was used for doing the modeling.

Keywords: Modulation, Non Linear Schrodinger Equation, Optical fiber, Split Step Fourier Method.

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Authors: Oguz Ustun, Erdal Bekiroglu

Abstract:

In the present study, position estimation of switched reluctance motor (SRM) has been achieved on the basis of the artificial neural networks (ANNs). The ANNs can estimate the rotor position without using an extra rotor position sensor by measuring the phase flux linkages and phase currents. Flux linkage-phase current-rotor position data set and supervised backpropagation learning algorithm are used in training of the ANN based position estimator. A 4-phase SRM have been used to verify the accuracy and feasibility of the proposed position estimator. Simulation results show that the proposed position estimator gives precise and accurate position estimations for both under the low and high level reference speeds of the SRM

Keywords: Artificial neural networks, modeling andsimulation, position observer, switched reluctance motor.

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Authors: Michael Gerges, Ograbe Ahiakwo, Martin Jaeger, Ahmad Asaad

Abstract:

Recent advances of Building Information Modeling (BIM) especially in the Middle East have increased remarkably. Dubai has been taking a lead on this by making it mandatory for BIM to be adopted for all projects that involve complex architecture designs. This is because BIM is a dynamic process that assists all stakeholders in monitoring the project status throughout different project phases with great transparency. It focuses on utilizing information technology to improve collaboration among project participants during the entire life cycle of the project from the initial design, to the supply chain, resource allocation, construction and all productivity requirements. In view of this trend, the paper examines the extent of applying BIM in the State of Kuwait, by exploring practitioners’ perspectives on BIM, especially their perspectives on main barriers and main advantages. To this end structured interviews were carried out based on questionnaires and with a range of different construction professionals. The results revealed that practitioners perceive improved communication and mitigated project risks by encouraged collaboration between project participants. However, it was also observed that the full implementation of BIM in the State of Kuwait requires concerted efforts to make clients demanding BIM, counteract resistance to change among construction professionals and offer more training for design team members. This paper forms part of an on-going research effort on BIM and its application in the State of Kuwait and it is on this basis that further research on the topic is proposed.

Keywords: Building Information Modeling, BIM, construction industry, Kuwait.

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Authors: Asif Mansoor, Nasiruddin Khan, Noreen Jamil

Abstract:

In this communication a quantitative modeling approach is applied to construct model for the exchange of gases from open sewer channel to the atmosphere. The data for the exchange of gases of the open sewer channel for the year January 1979 to December 2006 is utilized for the construction of the model. The study reveals that stream flow of the open sewer channel exchanges the toxic gases continuously with time varying scale. We find that the quantitative modeling approach is more parsimonious model for these exchanges. The usual diagnostic tests are applied for the model adequacy. This model is beneficial for planner and managerial bodies for the improvement of implemented policies to overcome future environmental problems.

Keywords: Open sewer channel, Industrial waste, Municipalwaste, Gases exchange, Atmosphere, Stochastic models, Diagnosticschecks.

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Authors: Mohammed Nasir Kajama, Ngozi Claribelle Nwogu, Edward Gobina

Abstract:

Pt/γ-Al2O3 membrane catalysts were prepared via an evaporative-crystallization deposition method. The obtained Pt/γ- Al2O3 catalyst activity was tested after characterization (SEM-EDAX observation, BET measurement, permeability assessment) in the catalytic oxidation of selected volatile organic compound (VOC) i.e. propane, fed in mixture of oxygen. The VOC conversion (nearly 90%) obtained by varying the operating temperature showed that flow-through membrane reactor might do better in the abatement of VOCs.

Keywords: VOC combustion, flow-through membrane reactor, platinum supported alumina catalysts.

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Authors: Amit Sachan

Abstract:

The network designing and data modeling developments which are the two significant research tasks in direction to tolerate power control of Microgrid concluded using IEC 61850 data models and facilities. The current casing areas of IEC 61580 include infrastructures in substation automation systems, among substations and to DERs. So, for LV microgrid power control, previously using the IEC 61850 amenities to control the smart electrical devices, we have to model those devices as IEC 61850 data models and design a network topology to maintenance all-in-one communiqué amid those devices. In adding, though IEC 61850 assists modeling a portion by open-handed several object models for common functions similar measurement, metering, monitoring…etc., there are motionless certain missing smithereens for building a multiplicity of functions for household appliances like tuning the temperature of an electric heater or refrigerator.

Keywords: IEC 61850, RCMC, HCMC, DER Unit Controller.

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Authors: H. Shahabi

Abstract:

since in natural accidents, facilities that relate to this vita element are underground so, it is difficult to find quickly some right, exact and definite information about water utilities. There fore, this article has done operationally in Boukan city in Western Azarbaijan of Iran and it tries to represent operation and capabilities of Geographical Information system (GIS) in urban water management at the time of natural accidents. Structure of this article is that firstly it has established a comprehensive data base related to water utilities by collecting, entering, saving and data management, then by modeling water utilities we have practically considered its operational aspects related to water utility problems in urban regions.

Keywords: Natural Disaster, Geographical Information system (GIS), Modeling and network analysis, Boukan city in Western Azerbaijan, Iran

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Authors: S. Yaman, S. Rostami

Abstract:

In this study, a black box modeling of the coupled-tank system is obtained by using fuzzy sets. The derived model is tested via adaptive neuro fuzzy inference system (ANFIS). In order to achieve a better control performance, the parameters of three different controller types, classical proportional integral controller (PID), fuzzy PID and function tuner method, are tuned by one of the evolutionary computation method, genetic algorithm. All tuned controllers are applied to the fuzzy model of the coupled-tank experimental setup and analyzed under the different reference input values. According to the results, it is seen that function tuner method demonstrates better robust control performance and guarantees the closed loop stability.

Keywords: Function tuner method, fuzzy modeling, fuzzy PID controller, genetic algorithm.

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Authors: Sh. Minapoor, S. Ajeli, M. Javadi Toghchi

Abstract:

Non-crimp 3D orthogonal fabric composite is one of the textile-based composite materials that are rapidly developing light-weight engineering materials. The present paper focuses on geometric and micromechanical modeling of non-crimp 3D orthogonal carbon fabric and composites reinforced with it for aerospace applications. In this research meso-finite element (FE) modeling employs for stress analysis in different load conditions. Since mechanical testing of expensive textile carbon composites with specific application isn't affordable, simulation composite in a virtual environment is a helpful way to investigate its mechanical properties in different conditions.

Keywords: 3D orthogonal woven composite, Aerospace applications, Finite element method, Mechanical properties.

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Authors: A. Buruzs, M. F. Hatwágner, A. Torma, L. T. Kóczy

Abstract:

The development, operation and maintenance of Integrated Waste Management Systems (IWMS) affects essentially the sustainable concern of every region. The features of such systems have great influence on all of the components of sustainability. In order to reach the optimal way of processes, a comprehensive mapping of the variables affecting the future efficiency of the system is needed such as analysis of the interconnections among the components and modeling of their interactions. The planning of a IWMS is based fundamentally on technical and economical opportunities and the legal framework. Modeling the sustainability and operation effectiveness of a certain IWMS is not in the scope of the present research. The complexity of the systems and the large number of the variables require the utilization of a complex approach to model the outcomes and future risks. This complex method should be able to evaluate the logical framework of the factors composing the system and the interconnections between them. The authors of this paper studied the usability of the Fuzzy Cognitive Map (FCM) approach modeling the future operation of IWMS’s. The approach requires two input data set. One is the connection matrix containing all the factors affecting the system in focus with all the interconnections. The other input data set is the time series, a retrospective reconstruction of the weights and roles of the factors. This paper introduces a novel method to develop time series by content analysis.

Keywords: Content analysis, factors, integrated waste management system, time series.

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Authors: Ryszard Matysiak, Grzegorz Kamieniarz

Abstract:

The deterministic quantum transfer-matrix (QTM) technique and its mathematical background are presented. This important tool in computational physics can be applied to a class of the real physical low-dimensional magnetic systems described by the Heisenberg hamiltonian which includes the macroscopic molecularbased spin chains, small size magnetic clusters embedded in some supramolecules and other interesting compounds. Using QTM, the spin degrees of freedom are accurately taken into account, yielding the thermodynamical functions at finite temperatures. In order to test the application for the susceptibility calculations to run in the parallel environment, the speed-up and efficiency of parallelization are analyzed on our platform SGI Origin 3800 with p = 128 processor units. Using Message Parallel Interface (MPI) system libraries we find the efficiency of the code of 94% for p = 128 that makes our application highly scalable.

Keywords: Deterministic simulations, low-dimensional magnets, modeling of complex systems, parallelization.

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Authors: Muhammad Marsudi, Dzuraidah Abdul Wahab, Che Hassan Che Haron

Abstract:

Modeling of a manufacturing system enables one to identify the effects of key design parameters on the system performance and as a result to make correct decision. This paper proposes a manufacturing system modeling approach using a spreadsheet model based on queuing network theory, in which a static capacity planning model and stochastic queuing model are integrated. The model was used to improve the existing system utilization in relation to product design. The model incorporates few parameters such as utilization, cycle time, throughput, and batch size. The study also showed that the validity of developed model is good enough to apply and the maximum value of relative error is 10%, far below the limit value 32%. Therefore, the model developed in this study is a valuable alternative model in evaluating a manufacturing system

Keywords: Manufacturing system, product design, spreadsheet model, utilization.

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Authors: A. Nielen, S. Mütze-Niewöhner, C. M. Schlick

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In view of growing competition in the service sector, services are as much in need of modeling, analysis and improvement as business or working processes. Graphical process models are important means to capture process-related know-how for an effective management of the service process. In this contribution, a human performance analysis of process model development paying special attention to model development time and the working method was conducted. It was found that modelers with higher application experience need significantly less time for mental activities than modelers with lower application experience, spend more time on labeling graphical elements, and achieved higher process model quality in terms of activity label quality.

Keywords: Model quality, predetermined motion time system, process modeling, working method.

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Authors: Reza Kazemi , Iman Mousavinejad

Abstract:

Steer-By-Wire ( SBW ) has several advantages of packaging flexibility , advanced vehicle control system ,and superior performance . SBW has no mechanical linkage between the steering gear and the steering column. It is possible to control the steering wheel and the front-wheel steering independently. SBW system is composed of two motors controlled by ECU. One motor in the steering wheel is to improve the driver's steering feel and the other motor in the steering linkage is to improve the vehicle maneuverability and stability. This paper shows a new approach at modeling of SBW system by Bond Graph theory. The mechanical parts , the steering wheel motor and the front wheel motor will be modeled by this theory. The work in the paper will help to guide further researches on control algorithm of the SBW system .

Keywords: Steer-By-Wire ( SBW ), Bond Graph theory, Electronic-Control-Unit ( ECU ) , Modeling

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Authors: Ali Ben Abbes, ImedRiadh Farah, Vincent Barra

Abstract:

Remotely sensed data are a significant source for monitoring and updating databases for land use/cover. Nowadays, changes detection of urban area has been a subject of intensive researches. Timely and accurate data on spatio-temporal changes of urban areas are therefore required. The data extracted from multi-temporal satellite images are usually non-stationary. In fact, the changes evolve in time and space. This paper is an attempt to propose a methodology for changes detection in urban area by combining a non-stationary decomposition method and stochastic modeling. We consider as input of our methodology a sequence of satellite images I₁, I₂, … I_n at different periods (t = 1, 2, ..., n). Firstly, a preprocessing of multi-temporal satellite images is applied. (e.g. radiometric, atmospheric and geometric). The systematic study of global urban expansion in our methodology can be approached in two ways: The first considers the urban area as one same object as opposed to non-urban areas (e.g. vegetation, bare soil and water). The objective is to extract the urban mask. The second one aims to obtain a more knowledge of urban area, distinguishing different types of tissue within the urban area. In order to validate our approach, we used a database of Tres Cantos-Madrid in Spain, which is derived from Landsat for a period (from January 2004 to July 2013) by collecting two frames per year at a spatial resolution of 25 meters. The obtained results show the effectiveness of our method.

Keywords: Multi-temporal satellite image, urban growth, Non-stationarity, stochastic modeling.

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Authors: Martin Kendra, Tomas Skrucany, Jozef Gnap, Jan Ponicky

Abstract:

Paper deals with the modeling and simulation of energy consumption and GHG production of two different modes of regional passenger transport – road and railway. These two transport modes use the same type of fuel – diesel. Modeling and simulation of the energy consumption in transport is often used due to calculation satisfactory accuracy and cost efficiency. Paper deals with the calculation based on EN standards and information collected from technical information from vehicle producers and characteristics of tracks. Calculation included maximal theoretical capacity of bus and train and real passenger’s measurement from operation. Final energy consumption and GHG production is calculated by using software simulation. In evaluation of the simulation is used system “well to wheel”.

Keywords: Bus, energy consumption, GHG, production, simulation, train.

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Authors: Irfan Rafique, Philip Lew, Maissom Qanber Abbasi, Zhang Li

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The world wide web coupled with the ever-increasing sophistication of online technologies and software applications puts greater emphasis on the need of even more sophisticated and consistent quality requirements modeling than traditional software applications. Web sites and Web applications (WebApps) are becoming more information driven and content-oriented raising the concern about their information quality (InQ). The consistent and consolidated modeling of InQ requirements for WebApps at different stages of the life cycle still poses a challenge. This paper proposes an approach to specify InQ requirements for WebApps by reusing and extending the ISO 25012:2008(E) data quality model. We also discuss learnability aspect of information quality for the WebApps. The proposed ISO 25012 based InQ framework is a step towards a standardized approach to evaluate WebApps InQ.

Keywords: Data Quality Model, Information learnability, Information Quality, Web applications.

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Authors: M. Y. Ismail, M. Inam, A. F. M. Zain, N. Misran

Abstract:

Progressive phase distribution is an important consideration in reflectarray antenna design which is required to form a planar wave in front of the reflectarray aperture. This paper presents a detailed mathematical model in order to determine the required reflection phase values from individual element of a reflectarray designed in Ku-band frequency range. The proposed technique of obtaining reflection phase can be applied for any geometrical design of elements and is independent of number of array elements. Moreover the model also deals with the solution of reflectarray antenna design with both centre and off-set feed configurations. The theoretical modeling has also been implemented for reflectarrays constructed on 0.508mm thickness of different dielectric substrates. The results show an increase in the slope of the phase curve from 4.61°/mm to 22.35°/mm by varying the material properties.

Keywords: Mathematical modeling, Progressive phase distribution, Reflectarray antenna, Reflection phase.

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Authors: Werner Sandmann, Verena Wolf

Abstract:

Stochastic models of biological networks are well established in systems biology, where the computational treatment of such models is often focused on the solution of the so-called chemical master equation via stochastic simulation algorithms. In contrast to this, the development of storage-efficient model representations that are directly suitable for computer implementation has received significantly less attention. Instead, a model is usually described in terms of a stochastic process or a "higher-level paradigm" with graphical representation such as e.g. a stochastic Petri net. A serious problem then arises due to the exponential growth of the model-s state space which is in fact a main reason for the popularity of stochastic simulation since simulation suffers less from the state space explosion than non-simulative numerical solution techniques. In this paper we present transition class models for the representation of biological network models, a compact mathematical formalism that circumvents state space explosion. Transition class models can also serve as an interface between different higher level modeling paradigms, stochastic processes and the implementation coded in a programming language. Besides, the compact model representation provides the opportunity to apply non-simulative solution techniques thereby preserving the possible use of stochastic simulation. Illustrative examples of transition class representations are given for an enzyme-catalyzed substrate conversion and a part of the bacteriophage λ lysis/lysogeny pathway.

Keywords: Computational Modeling, Biological Networks, Stochastic Models, Markov Chains, Transition Class Models.

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