Search results for: molecular modeling

Authors: Sarma Cakula, Maija Sedleniece

Abstract:

Simulation and modeling computer programs are concerned with construction of models for analyzing different perspectives and possibilities in changing conditions environment. The paper presents theoretical justification and evaluation of qualitative e-learning development model in perspective of advancing modern technologies. There have been analyzed principles of qualitative e-learning in higher education, productivity of studying process using modern technologies, different kind of methods and future perspectives of e-learning in formal education. Theoretically grounded and practically tested model of developing e-learning methods using different technologies for different type of classroom, which can be used in professor-s decision making process to choose the most effective e-learning methods has been worked out.

Keywords: E-learning, modeling, E-learning methods development, personal knowledge management

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Authors: M. Sedighizadeh, A. Rezazadeh

Abstract:

A method has been developed for preparing load models for power flow and stability. The load modeling (LOADMOD) computer software transforms data on load class mix, composition, and characteristics into the from required for commonly–used power flow and transient stability simulation programs. Typical default data have been developed for load composition and characteristics. This paper defines LOADMOD software and describes the dynamic and static load modeling techniques used in this software and results of initial testing for BAKHTAR power system.

Keywords: Load Modelling, Static, Power Flow.

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Authors: Tsuyoshi Okita

Abstract:

For a given specific problem an efficient algorithm has been the matter of study. However, an alternative approach orthogonal to this approach comes out, which is called a reduction. In general for a given specific problem this reduction approach studies how to convert an original problem into subproblems. This paper proposes a formal modeling language to support this reduction approach in order to make a solver quickly. We show three examples from the wide area of learning problems. The benefit is a fast prototyping of algorithms for a given new problem. It is noted that our formal modeling language is not intend for providing an efficient notation for data mining application, but for facilitating a designer who develops solvers in machine learning.

Keywords: Formal language, statistical inference problem, reduction.

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Authors: Jaewon Jang, Gregory R. Miller

Abstract:

This paper presents work characterizing finite element performance boundaries within which live, interactive finite element modeling is feasible on current and emerging systems. These results are based on wide-ranging tests performed using a prototype finite element program implemented specifically for this study, thereby enabling the unified investigation of numerous direct and iterative solver strategies and implementations in a variety of modeling contexts. The results are intended to be useful for researchers interested in interactive analysis by providing baseline performance estimates, to give guidance in matching solution strategies to problem domains, and to spur further work addressing the challenge of extending the present boundaries.

Keywords: Finite Elements, Interactive Modeling, NumericalAnalysis.

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Authors: Rana Abdul Jabbar Khan, Muhammad Akmal

Abstract:

Personal computers draw non-sinusoidal current with odd harmonics more significantly. Power Quality of distribution networks is severely affected due to the flow of these generated harmonics during the operation of electronic loads. In this paper, mathematical modeling of odd harmonics in current like 3rd, 5th, 7th and 9th influencing the power quality has been presented. Live signals have been captured with the help of power quality analyzer for analysis purpose. The interesting feature is that Total Harmonic Distortion (THD) in current decreases with the increase of nonlinear loads has been verified theoretically. The results obtained using mathematical expressions have been compared with the practical results and exciting results have been found.

Keywords: Harmonic Distortion, Mathematical Modeling, Power Quality.

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Authors: W. P. Hu, J. V. Kumar, Jeffrey J. P. Tsai

Abstract:

The inhibition of SH2 domain regulated protein-protein interactions is an attractive target for developing an effective chemotherapeutic approach in the treatment of disease. Molecular simulation is a useful tool for developing new drugs and for studying molecular recognition. In this study, we searched potential drug compounds for the inhibition of SH2 domain by performing structural similarity search in PubChem Compound Database. A total of 37 compounds were screened from the database, and then we used the LibDock docking program to evaluate the inhibition effect. The best three compounds (AP22408, CID 71463546 and CID 9917321) were chosen for MD simulations after the LibDock docking. Our results show that the compound CID 9917321 can produce a more stable protein-ligand complex compared to other two currently known inhibitors of Src SH2 domain. The compound CID 9917321 may be useful for the inhibition of SH2 domain based on these computational results. Subsequently experiments are needed to verify the effect of compound CID 9917321 on the SH2 domain in the future studies.

Keywords: Nonpeptide inhibitor, Src SH2 domain, LibDock, molecular dynamics simulation.

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Authors: Paola Lecca

Abstract:

Modeling and simulation of biochemical reactions is of great interest in the context of system biology. The central dogma of this re-emerging area states that it is system dynamics and organizing principles of complex biological phenomena that give rise to functioning and function of cells. Cell functions, such as growth, division, differentiation and apoptosis are temporal processes, that can be understood if they are treated as dynamic systems. System biology focuses on an understanding of functional activity from a system-wide perspective and, consequently, it is defined by two hey questions: (i) how do the components within a cell interact, so as to bring about its structure and functioning? (ii) How do cells interact, so as to develop and maintain higher levels of organization and functions? In recent years, wet-lab biologists embraced mathematical modeling and simulation as two essential means toward answering the above questions. The credo of dynamics system theory is that the behavior of a biological system is given by the temporal evolution of its state. Our understanding of the time behavior of a biological system can be measured by the extent to which a simulation mimics the real behavior of that system. Deviations of a simulation indicate either limitations or errors in our knowledge. The aim of this paper is to summarize and review the main conceptual frameworks in which models of biochemical networks can be developed. In particular, we review the stochastic molecular modelling approaches, by reporting the principal conceptualizations suggested by A. A. Markov, P. Langevin, A. Fokker, M. Planck, D. T. Gillespie, N. G. van Kampfen, and recently by D. Wilkinson, O. Wolkenhauer, P. S. Jöberg and by the author.

Keywords: Mathematical structure, algorithmic implementation, biochemical network models.

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Authors: Rozhgar A. Khailany, Mehri Igci, Emine Bayraktar, Sakip Erturhan, Metin Karakok, Ahmet Arslan

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Kidney cancer is the most lethal urological cancer accounting for 3% of adult malignancies. VHL, a tumor-suppressor gene, is best known to be associated with renal cell carcinoma (RCC). The VHL functions as negative regulator of hypoxia inducible factors. Recent sequencing efforts have identified several novel frequent mutations of histone modifying and chromatin remodeling genes in ccRCC (clear cell RCC) including PBRM1 and SETD2. The PBRM1 gene encodes the BAF180 protein, which involved in transcriptional activation and repression of selected genes. SETD2 encodes a histone methyltransferase, which may play a role in suppressing tumor development. In this study, RNAs of 30 paired tumor and normal samples that were grouped according to the types of kidney cancer and clinical characteristics of patients, including gender and average age were examined by RT-PCR, SSCP and sequencing techniques. VHL, PBRM1 and SETD2 expressions were relatively down-regulated. However, statistically no significance was found (Wilcoxon signed rank test, p>0.05). Interestingly, no mutation was observed on the contrary of previous studies. Understanding the molecular mechanisms involved in the pathogenesis of RCC has aided the development of molecular-targeted drugs for kidney cancer. Further analysis is required to identify the responsible genes rather than VHL, PBRM1 and SETD2 in kidney cancer.

Keywords: Kidney cancer, molecular biomarker, expression analysis, mutation screening.

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Authors: A. Elsayed Ahmed, A. Hafez, A. N. Ouda, H. Eldin Hussein Ahmed, H. Mohamed Abd-Elkader

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Unmanned aircraft systems (UAS) are playing increasingly prominent roles in defense programs and defense strategies around the world. Technology advancements have enabled the development of it to do many excellent jobs as reconnaissance, surveillance, battle fighters, and communications relays. Simulating a small unmanned aerial vehicle (SUAV) dynamics and analyzing its behavior at the preflight stage is too important and more efficient. The first step in the UAV design is the mathematical modeling of the nonlinear equations of motion. . In this paper, a survey with a standard method to obtain the full non-linear equations of motion is utilized, and then the linearization of the equations according to a steady state flight condition (trimming) is derived. This modeling technique is applied to an Ultrastick-25e fixed wing UAV to obtain the valued linear longitudinal and lateral models. At the end the model is checked by matching between the behavior of the states of the nonlinear UAV and the resulted linear model with doublet at the control surfaces.

Keywords: Equations of motion, linearization, modeling, nonlinear model, UAV.

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Authors: Anthony Spiteri Staines

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This paper examines the modeling and analysis of a cruise control system using a Petri net based approach, task graphs, invariant analysis and behavioral properties. It shows how the structures used can be verified and optimized.

Keywords: Software Engineering, Real Time Analysis andDesign, Petri Nets, Task Graphs, Parallelism.

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Authors: R. Manaffar, R. Maleki, S. Zare, N. Agh, S. Soltanian, B. Sehatnia, P. Sorgeloos, P. Bossier, G. Van Stappen

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Artemia is one of the most conspicuous invertebrates associated with aquaculture. It can be considered as a model organism, offering numerous advantages for comprehensive and multidisciplinary studies using morphologic or molecular methods. Since DNA extraction is an important step of any molecular experiment, a new and a rapid method of DNA extraction from adult Artemia was described in this study. Besides, the efficiency of this technique was compared with two widely used alternative techniques, namely Chelex® 100 resin and SDS-chloroform methods. Data analysis revealed that the new method is the easiest and the most cost effective method among the other methods which allows a quick and efficient extraction of DNA from the adult animal.

Keywords: APD, Artemia, DNA extraction, Molecularexperiments

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Authors: Farhad Kolahan, Mohammad Bironro

Abstract:

This paper addresses modeling and optimization of process parameters in powder mixed electrical discharge machining (PMEDM). The process output characteristics include metal removal rate (MRR) and electrode wear rate (EWR). Grain size of Aluminum powder (S), concentration of the powder (C), discharge current (I) pulse on time (T) are chosen as control variables to study the process performance. The experimental results are used to develop the regression models based on second order polynomial equations for the different process characteristics. Then, a genetic algorithm (GA) has been employed to determine optimal process parameters for any desired output values of machining characteristics.

Keywords: Regression modeling, PMEDM, GeneticAlgorithm, Optimization.

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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: Ahmed S. Al-Abdulwahab

Abstract:

Generation system reliability assessment is an important task which can be performed using deterministic or probabilistic techniques. The probabilistic approaches have significant advantages over the deterministic methods. However, more complicated modeling is required by the probabilistic approaches. Power generation model is a basic requirement for this assessment. One form of the generation models is the well known capacity outage probability table (COPT). Different analytical techniques have been used to construct the COPT. These approaches require considerable mathematical modeling of the generating units. The unit-s models are combined to build the COPT which will add more burdens on the process of creating the COPT. Decimal to Binary Conversion (DBC) technique is widely and commonly applied in electronic systems and computing This paper proposes a novel utilization of the DBC to create the COPT without engaging in analytical modeling or time consuming simulations. The simple binary representation , “0 " and “1 " is used to model the states o f generating units. The proposed technique is proven to be an effective approach to build the generation model.

Keywords: Decimal to Binary, generation, reliability.

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Authors: A. Aljohani, M. Orif

Abstract:

The concentration of polycyclic aromatic hydrocarbons (PAH) in clams (A. glabrata) was examined in samples collected from Alseef Beach, 30 km south of Jeddah city. Gas chromatography-mass spectrometry (GC-MS) was used to analyze the 14 PAHs. The concentration of total PAHs was found to range from 11.521 to 40.149 ng/gdw with a mean concentration of 21.857 ng/gdw, which is lower compared to similar studies. The lower molecular weight PAHs with three rings comprised 18.14% of the total PAH concentrations in the clams, while the high molecular weight PAHs with four rings, five rings, and six rings account for 81.86%. Diagnostic ratios for PAH source distinction suggested pyrogenic or anthropogenic sources.

Keywords: Bivalves, biomonitoring, hydrocarbons, PAHs.

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Authors: Phumelele P. Kubheka, Pius A. Owolawi, Gbolahan Aiyetoro

Abstract:

Twitter is one of the most popular social media platforms where users share their opinions on different subjects. Twitter can be considered a great source for mining text due to the high volumes of data generated through the platform daily. Many industries such as telecommunication companies can leverage the availability of Twitter data to better understand their markets and make an appropriate business decision. This study performs topic modeling on Twitter data using Latent Dirichlet Allocation (LDA). The obtained results are benchmarked with another topic modeling technique, Latent Semantic Indexing (LSI). The study aims to retrieve topics on a Twitter dataset containing user tweets on South African Telcos. Results from this study show that LSI is much faster than LDA. However, LDA yields better results with higher topic coherence by 8% for the best-performing model in this experiment. A higher topic coherence score indicates better performance of the model.

Keywords: Big data, latent Dirichlet allocation, latent semantic indexing, Telco, topic modeling, Twitter.

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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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Authors: Gionata Carmignani, Mario G. C. A. Cimino, Franco Failli

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Business Processes (BPs) are the key instrument to understand how companies operate at an organizational level, taking an as-is view of the workflow, and how to address their issues by identifying a to-be model. In last year’s, the BP Model and Notation (BPMN) has become a de-facto standard for modeling processes. However, this standard does not incorporate explicitly the Problem- Solving (PS) knowledge in the Process Modeling (PM) results. Thus, such knowledge cannot be shared or reused. To narrow this gap is today a challenging research area. In this paper we present a framework able to capture the PS knowledge and to improve a workflow. This framework extends the BPMN specification by incorporating new general-purpose elements. A pilot scenario is also presented and discussed.

Keywords: Business Process Management, BPMN, Problem Solving, Process mapping.

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Authors: Mohamed A. Khlifi, Badr M. Alshammari

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This paper discusses the general methods to saturation in the steady-state, two axis (d & q) frame models of synchronous machines. In particular, the important role of the magnetic coupling between the d-q axes (cross-magnetizing phenomenon), is demonstrated. For that purpose, distinct methods of saturation modeling of dumper synchronous machine with cross-saturation are identified, and detailed models synthesis in d-q axes. A number of models are given in the final developed form. The procedure and the novel models are verified by a critical application to prove the validity of the method and the equivalence between all developed models is reported. Advantages of some of the models over the existing ones and their applicability are discussed.

Keywords: Cross-magnetizing, models synthesis, synchronous machine, saturated modeling, state-space vectors.

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Authors: Yasuo Obikane

Abstract:

This work is to study a roll of the fluctuating density gradient in the compressible flows for the computational fluid dynamics (CFD). A new anisotropy tensor with the fluctuating density gradient is introduced, and is used for an invariant modeling technique to model the turbulent density gradient correlation equation derived from the continuity equation. The modeling equation is decomposed into three groups: group proportional to the mean velocity, and that proportional to the mean strain rate, and that proportional to the mean density. The characteristics of the correlation in a wake are extracted from the results by the two dimensional direct simulation, and shows the strong correlation with the vorticity in the wake near the body. Thus, it can be concluded that the correlation of the density gradient is a significant parameter to describe the quick generation of the turbulent property in the compressible flows.

Keywords: Turbulence Modeling , Density Gradient Correlation, Compressible

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Authors: Rafayel A. Azizyan, Aram E. Gevogyan, Valeri B. Arakelyan, Emil S. Gevorgyan

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The mathematical modeling of different biological processes is usually used to predict or assess behavior of systems in which these processes take place. This study deals with mathematical and computer modeling of bi-substrate enzymatic reactions with ping-pong mechanism, which play an important role in different biochemical pathways. Besides that, three models of competitive inhibition were designed using different software packages. The main objective of this study is to represent the results from in silico investigation of bi-substrate enzymatic reactions with ordered pingpong mechanism in the presence of competitive inhibitors, as well as to describe in details the inhibition effects. The simulation of the models with certain kinetic parameters allowed investigating the behavior of reactions as well as determined some interesting aspects concerning influence of different cases of competitive inhibition. Simultaneous presence of two inhibitors, competitive to the S1 and S2 substrates have been studied. Moreover, we have found the pattern of simultaneous influence of both inhibitors.

Keywords: Mathematical modeling, bi-substrate enzymatic reactions, ping-pong mechanism, competitive inhibition.

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Authors: Anwar Jarndal

Abstract:

In this paper, a genetic-neural-network (GNN) based large-signal model for GaN HEMTs is presented along with its parameters extraction procedure. The model is easy to construct and implement in CAD software and requires only DC and S-parameter measurements. An improved decomposition technique is used to model self-heating effect. Two GNN models are constructed to simulate isothermal drain current and power dissipation, respectively. The two model are then composed to simulate the drain current. The modeling procedure was applied to a packaged GaN-on-Si HEMT and the developed model is validated by comparing its large-signal simulation with measured data. A very good agreement between the simulation and measurement is obtained.

Keywords: GaN HEMT, computer-aided design & modeling, neural networks, genetic optimization.

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Authors: Tao Qu, Chandra Prakash, Vikas Tomar

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The interfaces between organic and inorganic phases in natural materials have been shown to be a key factor contributing to their high performance. This work analyzes crack propagation in a 2-ply laminate subjected to uniaxial tensile mode-I crack propagation loading that has laminate properties derived based on biological material constituents (marine exoskeleton- chitin and calcite). Interfaces in such laminates are explicitly modeled based on earlier molecular simulations performed by authors. Extended finite element method and cohesive zone modeling based simulations coupled with theoretical analysis are used to analyze crack propagation. Analyses explicitly quantify the effect that interface mechanical property variation has on the delamination as well as the transverse crack propagation in examined 2-ply laminates.

Keywords: Chitin, composites, interfaces, fracture.

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Authors: P. C. Tewari, Rajiv Kumar, Dinesh Khanduja

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This paper discusses the performance modeling and availability analysis of Yarn Dyeing System of a Textile Industry. The Textile Industry is a complex and repairable engineering system. Yarn Dyeing System of Textile Industry consists of five subsystems arranged in series configuration. For performance modeling and analysis of availability, a performance evaluating model has been developed with the help of mathematical formulation based on Markov-Birth-Death Process. The differential equations have been developed on the basis of Probabilistic Approach using a Transition Diagram. These equations have further been solved using normalizing condition in order to develop the steady state availability, a performance measure of the system concerned. The system performance has been further analyzed with the help of decision matrices. These matrices provide various availability levels for different combinations of failure and repair rates for various subsystems. The findings of this paper are therefore, considered to be useful for the analysis of availability and determination of the best possible maintenance strategies which can be implemented in future to enhance the system performance.

Keywords: Availability Analysis, Markov Process, Performance Modeling, Steady State Availability.

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Authors: Yun-Pang Flötteröd, Jakob Erdmann

Abstract:

The human behaviors during evacuations are quite complex. One of the critical behaviors which affect the efficiency of evacuation is route choice. Therefore, the respective simulation modeling work needs to function properly. In this paper, Simulation of Urban Mobility’s (SUMO) current dynamic route modeling during evacuation, i.e. the rerouting functions, is examined with a real case study. The result consistency of the simulation and the reality is checked as well. Four influence factors (1) time to get information, (2) probability to cancel a trip, (3) probability to use navigation equipment, and (4) rerouting and information updating period are considered to analyze possible traffic impacts during the evacuation and to examine the rerouting functions in SUMO. Furthermore, some behavioral characters of the case study are analyzed with use of the corresponding detector data and applied in the simulation. The experiment results show that the dynamic route modeling in SUMO can deal with the proposed scenarios properly. Some issues and function needs related to route choice are discussed and further improvements are suggested.

Keywords: Evacuation, microscopic traffic simulation, rerouting, SUMO.

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Authors: Lambros V. Skarlas, Grigorios N. Beligiannis, Efstratios F. Georgopoulos, Adam V. Adamopoulos

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The aim of this contribution is to present a new approach in modeling the electrical activity of the human heart. A recurrent artificial neural network is being used in order to exhibit a subset of the dynamics of the electrical behavior of the human heart. The proposed model can also be used, when integrated, as a diagnostic tool of the human heart system. What makes this approach unique is the fact that every model is being developed from physiological measurements of an individual. This kind of approach is very difficult to apply successfully in many modeling problems, because of the complexity and entropy of the free variables describing the complex system. Differences between the modeled variables and the variables of an individual, measured at specific moments, can be used for diagnostic purposes. The sensor fusion used in order to optimize the utilization of biomedical sensors is another point that this paper focuses on. Sensor fusion has been known for its advantages in applications such as control and diagnostics of mechanical and chemical processes.

Keywords: Artificial Neural Networks, Diagnostic System, Health Condition Modeling Tool, Heart Diagnostics Model, Heart Electricity Model.

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Authors: Sema Kurtuluş, Kemal Kurtuluş

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The objective of this paper is to review and assess the methodological issues and problems in marketing research, data and knowledge mining in Turkey. As a summary, academic marketing research publications in Turkey have significant problems. The most vital problem seems to be related with modeling. Most of the publications had major weaknesses in modeling. There were also, serious problems regarding measurement and scaling, sampling and analyses. Analyses myopia seems to be the most important problem for young academia in Turkey. Another very important finding is the lack of publications on data and knowledge mining in the academic world.

Keywords: Marketing research, data mining, knowledge mining, research modeling, analyses.

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Authors: F. Hosseinpour, H. Hajihosseini

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Simulation is a very helpful and valuable work tool in manufacturing. It can be used in industrial field allowing the system`s behavior to be learnt and tested. Simulation provides a low cost, secure and fast analysis tool. It also provides benefits, which can be reached with many different system configurations. Topics to be discussed include: Applications, Modeling, Validating, Software and benefits of simulation. This paper provides a comprehensive literature review on research efforts in simulation.

Keywords: Manufacturing, modeling, simulation, training.

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Authors: Jatinder Kumar, Ajay Bansal

Abstract:

The present study deals with the modeling and simulation of flow through an annular reactor at different hydrodynamic conditions using computational fluid dynamics (CFD) to investigate the flow behavior. CFD modeling was utilized to predict velocity distribution and average velocity in the annular geometry. The results of CFD simulations were compared with the mathematically derived equations and already developed correlations for validation purposes. CFD modeling was found suitable for predicting the flow characteristics in annular geometry under laminar flow conditions. It was observed that CFD also provides local values of the parameters of interest in addition to the average values for the simulated geometry.

Keywords: Annular reactor, computational fluid dynamics (CFD), hydrodynamics, Rhodamine B

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Authors: R. Kongnuy, E. Naowanich

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In this paper we develop and analyze the model for the spread of Leptospirosis by age group in Thailand, between 1997 and 2010 by using mathematical modeling and computer simulation. Leptospirosis is caused by pathogenic spirochetes of the genus Leptospira. It is a zoonotic disease of global importance and an emerging health problem in Thailand. In Thailand, leptospirosis is a reportable disease, the top three age groups are 23.31% in 35-44 years olds group, 22.76% in 25-34 year olds group, 17.60% in 45-54 year olds group from reported leptospirosis between 1997 and 2010, with a peak in 35-44 year olds group. Our paper, the Leptosipirosis transmission by age group in Thailand is studied on the mathematical model. Some analytical and simulation results are presented.

Keywords: Age Group, Equilibrium State, Leptospirosis, Mathematical Modeling.

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