Search results for: dynamics. modeling

Authors: J.Yojina, W. Ngamsaad, N. Nuttavut, D.Triampo, Y. Lenbury, W. Triampo, P. Kanthang, S.Sriyab

Abstract:

The dynamics of Min proteins plays a center role in accurate cell division. Although the nucleoids may presumably play an important role in prokaryotic cell division, there is a lack of models to account for its participation. In this work, we apply the lattice Boltzmann method to investigate protein oscillation based on a mesoscopic model that takes into account the nucleoid-s role. We found that our numerical results are in reasonably good agreement with the previous experimental results On comparing with the other computational models without the presence of nucleoids, the highlight of our finding is that the local densities of MinD and MinE on the cytoplasmic membrane increases, especially along the cell width, when the size of the obstacle increases, leading to a more distinct cap-like structure at the poles. This feature indicated the realistic pattern and reflected the combination of Min protein dynamics and nucleoid-s role.

Keywords: lattice Boltzmann method, cell division, Minproteins oscillation, nucleoid

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Authors: Sérgio S. de Jesus, Edgar Leonardo Martínez, Aulus R.R. Binelli, Aline Santana, Rubens Maciel Filho

Abstract:

The speed profiles, gas holdup (e_G) and global oxygen transfer coefficient (k_La) from a stirred airlift bioreactor using water as the fluid model, was investigated by computational fluid dynamics modeling. The parameters predicted by the computer model were validated with the experimental dates. The CFD results were very close to those obtained experimentally. During the simulation it was verified a prevalent impeller effect at low speeds, propelling a large volume of fluid against the walls of the vessel, which without recirculation, results in low values of e_G and k_La; however, by increasing air velocity, the impeller effect is smaller with the air flow being greater, in the region of the riser, causing fluid recirculation, which explains the increase in e_G and k_La.

Keywords: CFD, Hydrodynamics, Mass transfer, Stirred airlift bioreactor.

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Authors: López-Gutiérrez R.M., Rodríguez-Orozco E., Cruz-Hernández C., Inzunza-González E., Posadas-Castillo C., García-Guerrero E.E., Cardoza-Avendaño L.

Abstract:

In this paper, we use Generalized Hamiltonian systems approach to synchronize a modified sixth-order Chua's circuit, which generates hyperchaotic dynamics. Synchronization is obtained between the master and slave dynamics with the slave being given by an observer. We apply this approach to transmit private information (analog and binary), while the encoding remains potentially secure.

Keywords: Hyperchaos synchronization, sixth-order Chua's circuit, observers, simulation, secure communication.

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Authors: Yi Liu

Abstract:

In this paper, computational fluid dynamics (CFD) is utilized to characterize a prototype biolistic delivery system, the biomedical device based on the contoured-shock-tube design (CST), with the aim at investigating shocks induced flow instabilities within the contoured shock tube. The shock/interface interactions, the growth of perturbation at an interface between two fluids of different density are interrogated. The key features of the gas dynamics and gas-particle interaction are discussed

Keywords: Simulation, Shock wave, Particle, Interface, Supersonic, Richtmyer-Meshkov Instability

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Authors: Mohammad R. Kavian Nezhad, Carlos F. Lange, Brian A. Fleck

Abstract:

This research presents the validation study of a computational fluid dynamics (CFD) model developed to simulate the scalar dispersion emitted from rooftop sources around the buildings at the University of Alberta North Campus. The ANSYS CFX code was used to perform the numerical simulation of the wind regime and pollutant dispersion by solving the 3D steady Reynolds-averaged Navier-Stokes (RANS) equations on a building-scale high-resolution grid. The validation study was performed in two steps. First, the CFD model performance in 24 cases (eight wind directions and three wind speeds) was evaluated by comparing the predicted flow fields with the available data from the previous measurement campaign designed at the North Campus, using the standard deviation method (SDM), while the estimated results of the numerical model showed maximum average percent errors of approximately 53% and 37% for wind incidents from the North and Northwest, respectively. Good agreement with the measurements was observed for the other six directions, with an average error of less than 30%. In the second step, the reliability of the implemented turbulence model, numerical algorithm, modeling techniques, and the grid generation scheme was further evaluated using the Mock Urban Setting Test (MUST) dispersion dataset. Different statistical measures, including the fractional bias (FB), the mean geometric bias (MG), and the normalized mean square error (NMSE), were used to assess the accuracy of the predicted dispersion field. Our CFD results are in very good agreement with the field measurements.

Keywords: CFD, plume dispersion, complex urban geometry, validation study, wind flow.

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Authors: Ni Ni Soe , Masahiro Nakagawa

Abstract:

Functional near infrared spectroscopy (fNIRS) is a practical non-invasive optical technique to detect characteristic of hemoglobin density dynamics response during functional activation of the cerebral cortex. In this paper, fNIRS measurements were made in the area of motor cortex from C4 position according to international 10-20 system. Three subjects, aged 23 - 30 years, were participated in the experiment. The aim of this paper was to evaluate the effects of different motor activation tasks of the hemoglobin density dynamics of fNIRS signal. The chaotic concept based on deterministic dynamics is an important feature in biological signal analysis. This paper employs the chaotic properties which is a novel method of nonlinear analysis, to analyze and to quantify the chaotic property in the time series of the hemoglobin dynamics of the various motor imagery tasks of fNIRS signal. Usually, hemoglobin density in the human brain cortex is found to change slowly in time. An inevitable noise caused by various factors is to be included in a signal. So, principle component analysis method (PCA) is utilized to remove high frequency component. The phase pace is reconstructed and evaluated the Lyapunov spectrum, and Lyapunov dimensions. From the experimental results, it can be conclude that the signals measured by fNIRS are chaotic.

Keywords: Chaos, hemoglobin, Lyapunov spectrum, motorimagery, near infrared spectroscopy (NIRS), principal componentanalysis (PCA).

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Authors: M. H. Ayazi, M. Qamari, N.Hedayat, A. Rohani

Abstract:

Simulation of the flow and sedimentation process in the reservoir dams can be made by two methods of physical and mathematical modeling. The study area was within a region which ranged from the Jelogir hydrometric station to the Karkheh reservoir dam aimed at investigating the effects of stream tubes on the GSTARS-3 model behavior. The methodologies was to run the model based on 5 stream tubes in order to observe the influence of each scenario on longitudinal profiles, cross-section, flow velocity and bed load sediment size. Results further suggest that the use of two stream tubes or more which result in the semi-two-dimensional model will yield relatively closer results to the observational data than a singular stream tube modeling. Moreover, the results of modeling with three stream tubes shown to yield a relatively close results with the observational data. The overall conclusion of the paper is with applying various stream tubes; it would be possible to yield a significant influence on the modeling behavior Vis-a Vis the bed load sediment size.

Keywords: Karkheh, stream tubes, GSTARS-3 Model, Jelogir hydrometric station.

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Authors: Seyed Abolhasan Naeini, M. Mortezaee

Abstract:

Various factors such as the method of installation, the pile type, the pile material and the pile shape, can affect the final bearing capacity of a pile executed in the soil; among them, the method of installation is of special importance. The physical modeling is among the best options in the laboratory study of the piles behavior. Therefore, the current paper first presents and reviews the frustum confining vessel (FCV) as a suitable tool for physical modeling of deep foundations. Then, by describing the loading tests of two open-ended and closed-end steel piles, each of which has been performed in two methods, “with displacement" and "without displacement", the effect of end conditions and installation method on the final bearing capacity of the pile is investigated. The soil used in the current paper is silty sand of Firuzkuh, Iran. The results of the experiments show that in general the without displacement installation method has a larger bearing capacity in both piles, and in a specific method of installation the closed ended pile shows a slightly higher bearing capacity.

Keywords: physical modeling, frustum confining vessel, pile, bearing capacity, installation method

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Authors: Amir Azizi, Amir Yazid B. Ali, Loh Wei Ping

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Throughput is an important measure of performance of production system. Analyzing and modeling of production throughput is complex in today-s dynamic production systems due to uncertainties of production system. The main reasons are that uncertainties are materialized when the production line faces changes in setup time, machinery break down, lead time of manufacturing, and scraps. Besides, demand changes are fluctuating from time to time for each product type. These uncertainties affect the production performance. This paper proposes Bayesian inference for throughput modeling under five production uncertainties. Bayesian model utilized prior distributions related to previous information about the uncertainties where likelihood distributions are associated to the observed data. Gibbs sampling algorithm as the robust procedure of Monte Carlo Markov chain was employed for sampling unknown parameters and estimating the posterior mean of uncertainties. The Bayesian model was validated with respect to convergence and efficiency of its outputs. The results presented that the proposed Bayesian models were capable to predict the production throughput with accuracy of 98.3%.

Keywords: Bayesian inference, Uncertainty modeling, Monte Carlo Markov chain, Gibbs sampling, Production throughput

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Authors: Y. N. Phang, E. F. Loh

Abstract:

Many researchers have suggested the use of zero inflated Poisson (ZIP) and zero inflated negative binomial (ZINB) models in modeling overdispersed medical count data with extra variations caused by extra zeros and unobserved heterogeneity. The studies indicate that ZIP and ZINB always provide better fit than using the normal Poisson and negative binomial models in modeling overdispersed medical count data. In this study, we proposed the use of Zero Inflated Inverse Trinomial (ZIIT), Zero Inflated Poisson Inverse Gaussian (ZIPIG) and zero inflated strict arcsine models in modeling overdispered medical count data. These proposed models are not widely used by many researchers especially in the medical field. The results show that these three suggested models can serve as alternative models in modeling overdispersed medical count data. This is supported by the application of these suggested models to a real life medical data set. Inverse trinomial, Poisson inverse Gaussian and strict arcsine are discrete distributions with cubic variance function of mean. Therefore, ZIIT, ZIPIG and ZISA are able to accommodate data with excess zeros and very heavy tailed. They are recommended to be used in modeling overdispersed medical count data when ZIP and ZINB are inadequate.

Keywords: Zero inflated, inverse trinomial distribution, Poisson inverse Gaussian distribution, strict arcsine distribution, Pearson’s goodness of fit.

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Authors: Dong-Hyun Kim, Yoo-Han Kim

Abstract:

In this study, aeroelastic response and performance analyses have been conducted for a 5MW-Class composite wind turbine blade model. Advanced coupled numerical method based on computational fluid dynamics (CFD) and computational flexible multi-body dynamics (CFMBD) has been developed in order to investigate aeroelastic responses and performance characteristics of the rotating composite blade. Reynolds-Averaged Navier-Stokes (RANS) equations with k-ω SST turbulence model were solved for unsteady flow problems on the rotating turbine blade model. Also, structural analyses considering rotating effect have been conducted using the general nonlinear finite element method. A fully implicit time marching scheme based on the Newmark direct integration method is applied to solve the coupled aeroelastic governing equations of the 3D turbine blade for fluid-structure interaction (FSI) problems. Detailed dynamic responses and instantaneous velocity contour on the blade surfaces which considering flow-separation effects were presented to show the multi-physical phenomenon of the huge rotating wind- turbine blade model.

Keywords: Computational Fluid Dynamics (CFD), Computational Multi-Body Dynamics (CMBD), Reynolds-averageNavier-Stokes (RANS), Fluid Structure Interaction (FSI), FiniteElement Method (FEM)

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Authors: Vikas Rastogi, Vipan Kumar, Loveleen Kumar Bhagi

Abstract:

The present work deals with the structural analysis of turbine blades and modeling of turbine blades. A common failure mode for turbine machines is high cycle of fatigue of compressor and turbine blades due to high dynamic stresses caused by blade vibration and resonance within the operation range of the machinery. In this work, proper damping system will be analyzed to reduce the vibrating blade. The main focus of the work is the modeling of under platform damper to evaluate the dynamic analysis of turbine-blade vibrations. The system is analyzed using Bond graph technique. Bond graph is one of the most convenient ways to represent a system from the physical aspect in foreground. It has advantage of putting together multi-energy domains of a system in a single representation in a unified manner. The bond graph model of dry friction damper is simulated on SYMBOLS-shakti® software. In this work, the blades are modeled as Timoshenko beam. Blade Vibrations under different working conditions are being analyzed numerically.

Keywords: Turbine blade vibrations, Friction dampers, Timoshenko Beam, Bond graph modeling.

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Authors: M. Behbahani-Nejad, Y. Shekari

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A reduced order modeling approach for natural gas transient flow in pipelines is presented. The Euler equations are considered as the governing equations and solved numerically using the implicit Steger-Warming flux vector splitting method. Next, the linearized form of the equations is derived and the corresponding eigensystem is obtained. Then, a few dominant flow eigenmodes are used to construct an efficient reduced-order model. A well-known test case is presented to demonstrate the accuracy and the computational efficiency of the proposed method. The results obtained are in good agreement with those of the direct numerical method and field data. Moreover, it is shown that the present reduced-order model is more efficient than the conventional numerical techniques for transient flow analysis of natural gas in pipelines.

Keywords: Eigenmode, Natural Gas, Reduced Order Modeling, Transient Flow.

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Authors: Samppa Suoniemi, Harri Terho, Rami Olkkonen

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In recent methodological articles related to structural equation modeling (SEM), the question of how to measure endogenous formative variables has been raised as an urgent, unresolved issue. This research presents an empirical application from the CRM system development context to test a recently developed technique, which makes it possible to measure endogenous formative constructs in structural models. PLS path modeling is used to demonstrate the feasibility of measuring antecedent relationships at the formative indicator level, not the formative construct level. Empirical results show that this technique is a promising approach to measure antecedent relationships of formative constructs in SEM.

Keywords: CRM system development, formative measures, PLS path modeling, research methodology.

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Authors: Carlos Gonzalez

Abstract:

When communicating using private and secure keys, there is always the doubt as to the identity of the message creator. We introduce an algorithm that uses the personal typing rhythm (keystroke dynamics) of the message originator to increase the trust of the authenticity of the message originator by the message recipient. The methodology proposes the use of a Rhythm Certificate Authority (RCA) to validate rhythm information. An illustrative example of the communication between Bob and Alice and the RCA is included. An algorithm of how to communicate with the RCA is presented. This RCA can be an independent authority or an enhanced Certificate Authority like the one used in public key infrastructure (PKI).

Keywords: Personal rhythm, public-key encryption, authentication, digital signature, keystroke dynamics.

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Authors: Mansour A. Al Qubeissi

Abstract:

The current paper presents a numerical approach in solving the conjugate heat transfer problems. A heat conduction code is coupled internally with a computational fluid dynamics solver for developing a couple conjugate heat transfer solver. Methodology of treating non-matching meshes at interface has also been proposed. The validation results of 1D and 2D cases for the developed conjugate heat transfer code have shown close agreement with the solutions given by analysis.

Keywords: Computational Fluid Dynamics, Conjugate Heat transfer, Heat Conduction, Heat Transfer

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Authors: Wajid A. Chishty, Stephen D. Lepera, Uri Vandsburger

Abstract:

Thermoacoustic instabilities in combustors have remained a topic of investigation for over a few decades due to the challenges it posses to the operation of low emission gas turbines. For combustors burning liquid fuel, understanding the cause-andeffect relationship between spray combustion dynamics and thermoacoustic oscillations is imperative for the successful development of any control methodology for its mitigation. The paper presents some very unique operating characteristics of a kerosene-fueled diffusion type combustor undergoing limit-cycle oscillations. Combustor stability limits were mapped using three different-sized injectors. The results show that combustor instability depends on the characteristics of the fuel spray. A simple analytic analysis is also reported in support of a plausible explanation for the unique combustor behavior. The study indicates that high amplitude acoustic pressure in the combustor may cause secondary breakdown of fuel droplets resulting in premixed pre-vaporized type burning of the diffusion type combustor.

Keywords: Secondary droplet breakup, Spray dynamics, Taylor Analogy Breakup Model, Thermoacoustic instabilities.

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Authors: Bindu Sankar, Jaideep Chakraborty, Rashmi Nawlakha, A. Venkatesan, S. Raghupathy, T. Jayanthi, S.A.V. Satya Murty

Abstract:

Component handling system is one of the important sub systems of Prototype Fast Breeder Reactor (PFBR) used for fuel handling. Core handling system is again a sub system of component handling system. Core handling system consists of in-vessel and ex-vessel subassembly handling. In-vessel core handling involves transfer arm, large rotatable plug and small rotatable plug operations. Modeling and simulation of in-vessel core handling is a part of development of Prototype Fast Breeder Reactor Operator Training Simulator. This paper deals with simulation and modeling of operations of transfer arm, large rotatable plug and small rotatable plug needed for in-vessel core handling. Process modeling was developed in house using platform independent Cµ code with OpenGL (Open Graphics Library). The control logic models and virtual panel were modeled using simulation tool.

Keywords: Animation, Core Handling System, Prototype Fast Breeder Reactor, Simulator

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Authors: Andra Blumberga, Armands Gravelsins, Haralds Vigants, Dagnija Blumberga

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The paper discovers biotechonomy development analysis by use of system dynamics modelling. The research is connected with investigations of biomass application for production of bioproducts with higher added value. The most popular bioresource is wood, and therefore, the main question today is about future development and eco-design of products. The paper emphasizes and evaluates energy sector which is open for use of wood logs, wood chips, wood pellets and so on. The main aim for this research study was to build a framework to analyse development perspectives for wood pellet production. To reach the goal, a system dynamics model of energy wood supplies, processing, and consumption is built. Production capacity, energy consumption, changes in energy and technology efficiency, required labour source, prices of wood, energy and labour are taken into account. Validation and verification tests with available data and information have been carried out and indicate that the model constitutes the dynamic hypothesis. It is found that the more is invested into pellets production, the higher the specific profit per production unit compared to wood logs and wood chips. As a result, wood chips production is decreasing dramatically and is replaced by wood pellets. The limiting factor for pellet industry growth is availability of wood sources. This is governed by felling limit set by the government based on sustainable forestry principles.

Keywords: Bioenergy, biotechonomy, system dynamics modelling, wood pellets.

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Authors: Erisasadat Sahebzamani, Núria Forcada, Francisco Lendinez

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Global climate change has become increasingly problematic over the past few decades. The construction industry has contributed to greenhouse gas emissions in recent decades. Considering these issues and the high demand for materials in the construction industry, Circular Economy (CE) is considered necessary to keep materials in the loop and extend their useful lives. By providing tangible benefits, Construction 4.0 facilitates the adoption of CE by reducing waste, updating standard work, sharing knowledge, and increasing transparency and stability. This study aims to present a framework for integrating CE and digital tools like Building Information Modeling (BIM) and Virtual Reality (VR) to examine the impact on the construction industry based on stakeholders' perspectives.

Keywords: Circular Economy, Building Information Modeling, Virtual Reality, stakeholder engagement.

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Authors: Abeer Samy, Oliver C. Saavedra Valeriano, Abdelazim Negm

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The Blue Nile Basin is the most important tributary of the Nile River. Egypt and Sudan are almost dependent on water originated from the Blue Nile. This multi-dependency creates conflicts among the three countries Egypt, Sudan, and Ethiopia making the management of these conflicts as an international issue. Good assessment of the water resources of the Blue Nile is an important to help in managing such conflicts. Hydrological models are good tool for such assessment. This paper presents a critical review of the nature and variability of the climate and hydrology of the Blue Nile Basin as a first step of using hydrological modeling to assess the water resources of the Blue Nile. Many several attempts are done to develop basin-scale hydrological modeling on the Blue Nile. Lumped and semi distributed models used averages of meteorological inputs and watershed characteristics in hydrological simulation, to analyze runoff for flood control and water resource management. Distributed models include the temporal and spatial variability of catchment conditions and meteorological inputs to allow better representation of the hydrological process. The main challenge of all used models was to assess the water resources of the basin is the shortage of the data needed for models calibration and validation. It is recommended to use distributed model for their higher accuracy to cope with the great variability and complexity of the Blue Nile basin and to collect sufficient data to have more sophisticated and accurate hydrological modeling.

Keywords: Blue Nile Basin, Climate Change, Hydrological Modeling, Watershed.

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Authors: Thiang, Handry Khoswanto, Rendy Pangaldus

Abstract:

Inverse kinematics analysis plays an important role in developing a robot manipulator. But it is not too easy to derive the inverse kinematic equation of a robot manipulator especially robot manipulator which has numerous degree of freedom. This paper describes an application of Artificial Neural Network for modeling the inverse kinematics equation of a robot manipulator. In this case, the robot has three degree of freedoms and the robot was implemented for drilling a printed circuit board. The artificial neural network architecture used for modeling is a multilayer perceptron networks with steepest descent backpropagation training algorithm. The designed artificial neural network has 2 inputs, 2 outputs and varies in number of hidden layer. Experiments were done in variation of number of hidden layer and learning rate. Experimental results show that the best architecture of artificial neural network used for modeling inverse kinematics of is multilayer perceptron with 1 hidden layer and 38 neurons per hidden layer. This network resulted a RMSE value of 0.01474.

Keywords: Artificial neural network, back propagation, inverse kinematics, manipulator, robot.

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Authors: H. Mahboubi, B. Moshiri, A. Khaki Seddigh

Abstract:

Recently, a great amount of interest has been shown in the field of modeling and controlling hybrid systems. One of the efficient and common methods in this area utilizes the mixed logicaldynamical (MLD) systems in the modeling. In this method, the system constraints are transformed into mixed-integer inequalities by defining some logic statements. In this paper, a system containing three tanks is modeled as a nonlinear switched system by using the MLD framework. Comparing the model size of the three-tank system with that of a two-tank system, it is deduced that the number of binary variables, the size of the system and its complexity tremendously increases with the number of tanks, which makes the control of the system more difficult. Therefore, methods should be found which result in fewer mixed-integer inequalities.

Keywords: Hybrid systems, mixed-integer inequalities, mixed logical dynamical systems, multi-tank system.

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Authors: M. Kalamani, S. Valarmathy, M. Krishnamoorthi

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In this paper, Fuzzy C-Means clustering with Expectation Maximization-Gaussian Mixture Model based hybrid modeling algorithm is proposed for Continuous Tamil Speech Recognition. The speech sentences from various speakers are used for training and testing phase and objective measures are between the proposed and existing Continuous Speech Recognition algorithms. From the simulated results, it is observed that the proposed algorithm improves the recognition accuracy and F-measure up to 3% as compared to that of the existing algorithms for the speech signal from various speakers. In addition, it reduces the Word Error Rate, Error Rate and Error up to 4% as compared to that of the existing algorithms. In all aspects, the proposed hybrid modeling for Tamil speech recognition provides the significant improvements for speechto- text conversion in various applications.

Keywords: Speech Segmentation, Feature Extraction, Clustering, HMM, EM-GMM, CSR.

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Authors: Aliakbar Akbari, Majid Hashemipour, Shiva Mirshahi

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Radio-frequency identification has entered as a beneficial means with conforming GS1 standards to provide the best solutions in the manufacturing area. It competes with other automated identification technologies e.g. barcodes and smart cards with regard to high speed scanning, reliability and accuracy as well. The purpose of this study is to improve production line-s performance by implementing RFID system in the manufacturing area on the basis of radio-frequency identification (RFID) system by 3D modeling in the program Cinema 4D R13 which provides obvious graphical scenes for users to portray their applications. Finally, with regard to improving system performance, it shows how RFID appears as a well-suited technology in a comparison of the barcode scanner to handle different kinds of raw materials in the production line base on logical process.

Keywords: Radio Frequency Identification, Manufacturing and Production Lines, 3D modeling

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Authors: Shagufta Tabassum

Abstract:

The study of dielectric properties in a binary mixture of liquids is very useful to understand the liquid structure, molecular interaction, dynamics, and kinematics of the mixture. Time-domain reflectometry (TDR) is a powerful tool for studying the cooperation and molecular dynamics of the H-bonded system. Here we discuss the basic calibration and normalization procedure for TDR measurements. Our aim is to explain different types of error occur during TDR measurements and how to minimize it.

Keywords: time domain reflectometry measurement technique, cable and connector loss, oscilloscope loss, normalization technique

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Authors: Akbar Zamaniyan, Alireza Behroozsarand, Hadi Ebrahimi

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Partial oxidation (POX) of light hydrocarbons (e.g. methane) is occurred in the first part of the autothermal reformer (ATR). The results of the detailed modeling of the reformer based on the thermodynamic model of the POX and 1D heterogeneous catalytic model for the fixed bed section are considered here. According to the results, the overall performance of the ATR can be improved by changing the important feed parameters.

Keywords: Autothermal Reformer, Partial Oxidation, Mathematical Modeling, Process Simulation, Syngas.

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Authors: M. Ghareh, L. Sepahi

Abstract:

Temperature rise in a transformer depends on variety of parameters such as ambient temperature, output current and type of the core. Considering these parameters, temperature rise estimation is still complicated procedure. In this paper, we present a new model based on simple electrical equivalent circuit. This method avoids the complication associated to accurate estimation and is in very good agreement with practice.

Keywords: Thermal modeling, temperature rise, equivalent thermal circuit.

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Authors: Refaat M Mohamed, Ayman El-Baz, Aly A. Farag

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This paper introduces a novel approach to estimate the clique potentials of Gibbs Markov random field (GMRF) models using the Support Vector Machines (SVM) algorithm and the Mean Field (MF) theory. The proposed approach is based on modeling the potential function associated with each clique shape of the GMRF model as a Gaussian-shaped kernel. In turn, the energy function of the GMRF will be in the form of a weighted sum of Gaussian kernels. This formulation of the GMRF model urges the use of the SVM with the Mean Field theory applied for its learning for estimating the energy function. The approach has been tested on synthetic texture images and is shown to provide satisfactory results in retrieving the synthesizing parameters.

Keywords: Image Modeling, MRF, Parameters Estimation, SVM Learning.

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Authors: Sérgio F. Sousa, Nuno M. F. S. A. Cerqueira, Marta A. S. Perez, Irina S. Moreira, António J. M.Ribeiro, Ana R. A. P. Neves, Maria J. Ramos, Pedro A. Fernandes

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In this work we report the recent progresses that have been achieved by our group in the last half decade on the field of computational proteomics. Specifically, we discuss the application of Molecular Dynamics Simulations and Electronic Structure Calculations in drug design, in the clarification of the structural and dynamic properties of proteins and enzymes and in the understanding of the catalytic and inhibition mechanism of cancer-related enzymes. A set of examples illustrate the concepts and help to introduce the reader into this important and fast moving field.

Keywords: Enzyme, Molecular Dynamics, Protein, Quantum Mechanics.

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