Search results for: Steady state analysis
4480 Identification of Coauthors in Scientific Database
Authors: Thiago M. R Dias, Gray F. Moita
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The analysis of scientific collaboration networks has contributed significantly to improving the understanding of how does the process of collaboration between researchers and also to understand how the evolution of scientific production of researchers or research groups occurs. However, the identification of collaborations in large scientific databases is not a trivial task given the high computational cost of the methods commonly used. This paper proposes a method for identifying collaboration in large data base of curriculum researchers. The proposed method has low computational cost with satisfactory results, proving to be an interesting alternative for the modeling and characterization of large scientific collaboration networks.
Keywords: Extraction and data integration, Information Retrieval, Scientific Collaboration.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 17124479 Static and Dynamic Complexity Analysis of Software Metrics
Authors: Kamaljit Kaur, Kirti Minhas, Neha Mehan, Namita Kakkar
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Software complexity metrics are used to predict critical information about reliability and maintainability of software systems. Object oriented software development requires a different approach to software complexity metrics. Object Oriented Software Metrics can be broadly classified into static and dynamic metrics. Static Metrics give information at the code level whereas dynamic metrics provide information on the actual runtime. In this paper we will discuss the various complexity metrics, and the comparison between static and dynamic complexity.Keywords: Static Complexity, Dynamic Complexity, Halstead Metric, Mc Cabe's Metric.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 32144478 Artemisia Species from Iran as Valuable Resources for Medicinal Uses
Authors: Mohammad Reza Naghavi, Farzad Alaeimoghadam, Hossein Ghafoori
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Artemisia species, which are medically beneficial, are widespread in temperate regions of both Northern and Southern hemispheres among which Iran is located. About 35 species of Artemisia are indigenous in Iran among them some are widespread in all or most provinces, yet some are restricted to some specific regions. In this review paper, initially, GC-Mass results of some experiments done in different provinces of Iran are mentioned among them some compounds are common among species, some others are mostly restricted to other species; after that, medical advantages based on some researches on species of this genus are reviewed; different qualities such as anti-leishmania, anti-bacteria, antiviral as well as anti-proliferative could be mentioned.
Keywords: Artemisia, GC-Mass analysis, medical advantage.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 28344477 Wafer Fab Operational Cost Monitoring and Controlling with Cost per Equivalent Wafer Out
Authors: Ian Kree, Davina Chin Lee Yien
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This paper presents Cost per Equivalent Wafer Out, which we find useful in wafer fab operational cost monitoring and controlling. It removes the loading and product mix effect in the cost variance analysis. The operation heads, therefore, could immediately focus on identifying areas for cost improvement. Without this, they would have to measure the impact of the loading variance and product mix variance between actual and budgeted prior to make any decision on cost improvement. Cost per Equivalent Wafer Out, thereby, increases efficiency in wafer fab operational cost monitoring and controlling.
Keywords: Cost Control, Cost Variance, Operational Expenditure, Semiconductor.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 24124476 Enterprise Infrastructure Related to the Product Value Transferred from Intellectual Capital
Authors: Chih Chin Yang
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The paper proposed a new theory of intellectual capital (so called IC) and a value approach in associated with production and market. After an in-depth review and research analysis of leading firms in this field, a holistic intellectual capital model is discussed, which involves transport, delivery supporting, and interface and systems of on intellectual capital. Through a quantity study, it is found that there is a significant relationship between the product value and infrastructure in a company. The product values are transferred from intellectual capital elements which includes three elements of content and the enterprise includes three elements of infrastructure in its market and product values of enterprise.
Keywords: Enterprise, product value, intellectual capital.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 15284475 Ray Tracing Modified 3D Image Method Simulation of Picocellular Propagation Channel Environment
Authors: F. Alwafie
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In this paper, we present the simulation of the propagation characteristics of the picocellular propagation channel environment. The first aim has been to find a correct description of the environment for received wave.
The result of the first investigations is that the environment of the indoor wave significantly changes as we change the electric parameters of material constructions. A modified 3D ray tracing image method tool has been utilized for the coverage prediction. A detailed analysis of the dependence of the indoor wave on the wideband characteristics of the channel: root mean square (RMS) delay spread characteristics and Mean excess delay, is also investigated.
Keywords: Propagation, Ray Tracing.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 19534474 Matrix Completion with Heterogeneous Observation Cost Using Sparsity-Number of Column-Space
Authors: Ilqar Ramazanli
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The matrix completion problem has been studied broadly under many underlying conditions. In many real-life scenarios, we could expect elements from distinct columns or distinct positions to have a different cost. In this paper, we explore this generalization under adaptive conditions. We approach the problem under two different cost models. The first one is that entries from different columns have different observation costs, but, within the same column, each entry has a uniform cost. The second one is any two entry has different observation cost, despite being the same or different columns. We provide complexity analysis of our algorithms and provide tightness guarantees.
Keywords: Matrix completion, adaptive learning, heterogeneous cost, Matroid optimization.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 4954473 Investigation of Relationship between Organizational Climate and Organizational Citizenship Behavior: A Research on Health Sector
Authors: Serdar Öge, Pınar Erdogan
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The main objective of this research is to describe the relationship between organizational climate and organizational citizenship behavior. In order to examine this relationship, a research is intended to be carried out in relevant institutions and organizations operating in the health sector in Turkey. It will be researched that whether there is a statistically significant relationship between organizational climate and organizational citizenship behavior through elated scientific research methods and statistical analysis. In addition, relationships between the dimensions of organizational climate and organizational citizenship behavior subscales will be questioned statistically.Keywords: Organizational climate, organizational citizenship, organizational citizenship behavior, climate.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 23464472 An Improved Phenomenological Model for Polymer Desorption
Authors: Joanna Sooknanan, Donna Comissiong
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We propose a phenomenological model for the process of polymer desorption. In so doing, we omit the usual theoretical approach of incorporating a fictitious viscoelastic stress term into the flux equation. As a result, we obtain a model that captures the essence of the phenomenon of trapping skinning, while preserving the integrity of the experimentally verified Fickian law for diffusion. An appropriate asymptotic analysis is carried out, and a parameter is introduced to represent the speed of the desorption front. Numerical simulations are performed to illustrate the desorption dynamics of the model. Recommendations are made for future modifications of the model, and provisions are made for the inclusion of experimentally determined frontal speeds.Keywords: Phenomenological Model, Polymer, Desorption, Trapping Skinning
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 12934471 Liberation as a Method for Monument Valorisation: The Case of the Defence Heritage Restoration
Authors: Donatella R. Fiorino, Marzia Loddo
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The practice of freeing monuments from subsequent additions crosses the entire history of conservation and it is traditionally connected to the aim of valorisation, both for cultural and educational purpose and recently even for touristic exploitation. Defence heritage has been widely interested by these cultural and technical moods from philological restoration to critic innovations. A renovated critical analysis of Italian episodes and in particular the Sardinian case of the area of San Pancrazio in Cagliari, constitute an important lesson about the limits of this practice and the uncertainty in terms of results, towards the definition of a sustainable good practice in the restoration of military architectures.
Keywords: Defensive architecture, Liberation, Valorisation for tourism, Historical restoration.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 20954470 Study the Behavior of Different Composite Short Columns (DST) with Prismatic Sections under Bending Load
Authors: V. Sadeghi Balkanlou, M. Reza Bagerzadeh Karimi, A. Hasanbakloo, B. Bagheri Azar
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In this paper, the behavior of different types of DST columns has been studied under bending load. Briefly, composite columns consist of an internal carbon steel tube and an external stainless steel wall that the between the walls are filled with concrete. Composite columns are expected to combine the advantages of all three materials and have the advantage of high flexural stiffness of CFDST columns. In this research, ABAQUS software is used for finite element analysis then the results of ultimate strength of the composite sections are illustrated.
Keywords: DST, Stainless steel, carbon steel, ABAQUS, Straigh Columns, Tapered Columns.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 35214469 Representing Data without Lost Compression Properties in Time Series: A Review
Authors: Nabilah Filzah Mohd Radzuan, Zalinda Othman, Azuraliza Abu Bakar, Abdul Razak Hamdan
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Uncertain data is believed to be an important issue in building up a prediction model. The main objective in the time series uncertainty analysis is to formulate uncertain data in order to gain knowledge and fit low dimensional model prior to a prediction task. This paper discusses the performance of a number of techniques in dealing with uncertain data specifically those which solve uncertain data condition by minimizing the loss of compression properties.
Keywords: Compression properties, uncertainty, uncertain time series, mining technique, weather prediction.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 16204468 Automatic Intelligent Analysis of Malware Behaviour
Authors: H. Dornhackl, K. Kadletz, R. Luh, P. Tavolato
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In this paper, we describe the use of formal methods to model malware behaviour. The modelling of harmful behaviour rests upon syntactic structures that represent malicious procedures inside malware. The malicious activities are modelled by a formal grammar, where API calls’ components are the terminals and the set of API calls used in combination to achieve a goal are designated non-terminals. The combination of different non-terminals in various ways and tiers make up the attack vectors that are used by harmful software. Based on these syntactic structures a parser can be generated which takes execution traces as input for pattern recognition.
Keywords: Malware behaviour, modelling, parsing, search, pattern matching.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 15244467 Are XBRL-based Financial Reports Better than Non-XBRL Reports? A Quality Assessment
Authors: Zhenkun Wang, Simon S. Gao
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Using a scoring system, this paper provides a comparative assessment of the quality of data between XBRL formatted financial reports and non-XBRL financial reports. It shows a major improvement in the quality of data of XBRL formatted financial reports. Although XBRL formatted financial reports do not show much advantage in the quality at the beginning, XBRL financial reports lately display a large improvement in the quality of data in almost all aspects. With the improved XBRL web data managing, presentation and analysis applications, XBRL formatted financial reports have a much better accessibility, are more accurate and better in timeliness.Keywords: Data Quality; Financial Report; Information; XBRL
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 25664466 Effect of Band Contact on the Temperature Distribution for Dry Friction Clutch
Authors: Oday I. Abdullah, J. Schlattmann
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In this study, the two dimensional heat conduction problem for the dry friction clutch disc is modeled mathematically analysis and is solved numerically using finite element method, to determine the temperature field when band contacts occurs between the rubbing surfaces during the operation of an automotive clutch. Temperature calculation have been made for contact area of different band width and the results obtained compared with these attained when complete contact occurs. Furthermore, the effects of slipping time and sliding velocity function are investigated as well. Both single and repeated engagements made at regular interval are considered.Keywords: Band contact, dry friction clutch, frictional heating, temperature field, 2D FEM.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 36304465 Mobility Analysis of the Population of Rabat-Salé-Zemmour-Zaer
Authors: F. Ghaiti
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In this paper, we present the 2006 survey study origin destination and price that we carried out during 2006 fall in the area in the Moroccan region of Rabat-Salé-Zemmour-Zaer. The survey concerns the people-s characteristics, their displacements behavior and the price that they will be able to pay for a tramway ticket. The main objective is to study a set of relative features to the households and to their displacement's habits and to their choices among public and privet transport modes. A comparison between this survey results and that of the 1996's is made. A pricing scheme is also given according to the tram capacity. (The Rabat-Salé tramway is under construction right now and it will be operational beginning 2010).
Keywords: Matrix O/D, Theory of pricing, Urban transport survey.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 26424464 Low Power Approach for Decimation Filter Hardware Realization
Authors: Kar Foo Chong, Pradeep K. Gopalakrishnan, T. Hui Teo
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There are multiple ways to implement a decimator filter. This paper addresses usage of CIC (cascaded-integrator-comb) filter and HB (half band) filter as the decimator filter to reduce the frequency sample rate by factor of 64 and detail of the implementation step to realize this design in hardware. Low power design approach for CIC filter and half band filter will be discussed. The filter design is implemented through MATLAB system modeling, ASIC (application specific integrated circuit) design flow and verified using a FPGA (field programmable gate array) board and MATLAB analysis.Keywords: CIC filter, decimation filter, half-band filter, lowpower.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 23984463 Analysis on Fun Elements of the SNG in ANIPANG
Authors: Jangwon Lee, Joonsung Yoon
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This study analyzes on the Social Network Game (SNG), ANIPANG, in order to discover its unique fun elements, so that suggest new methodologies for development of SNGs. ANIPANG is the most popular SNG in the South Korea on 2012. Recently, the game industry is paying close attention to mobile-based SNGs due to the rapid prevalence of smart-phones and social network services. However, SNGs are not online games simply. Although the fun of most online games is the victory through competition with other players or the game system, the fun of SNG is the communication through the collaboration with other players. Thus, features of users and environments of game should be considered for the game industry and for the fun of SNG to users.Keywords: Social Network Game, Casual user, Fun, ANIPANG.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 16014462 Research Analysis in Eclectic Theory (Kaboudan and Sfandiar)
Authors: Farideh Alizadeh, Mohd Nasir Hashim
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Present research investigates eclecticism in Iranian theatre on the basis of eclectic theory. Eclectic theatre is a new theory in postmodernism. The theory appeared during 60th – 70th century in some theatres such as “Conference of the Birds”. Special theatrical forms have been developed in many geographical- cultural areas of the world and are indigenous to that area. These forms, as compared with original forms, are considered to be traditional while being comprehensive, the form is considered to be national. Kaboudan and Sfandiar theatre has been influenced by elements of traditional form of Iran.
Keywords: Eclectic theatre, theatrical forms, tradition, play.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 21174461 Social and Economic Effects of Mining Industry Restructuring in Romania -Case Studies
Authors: Andra Costache, Gica Pehoiu
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As in other countries from Central and Eastern Europe, the economic restructuring occurred in the last decade of the twentieth century affected the mining industry in Romania, an oversize and heavily subsidized sector before 1989. After more than a decade since the beginning of mining restructuring, an evaluation of current social implications of the process it is required, together with an efficiency analysis of the adaptation mechanisms developed at governmental level. This article aims to provide an insight into these issues through case studies conducted in the most important coal basin of Romania, Petroşani Depression.Keywords: case studies, government programs, miningrestructuring, social effects.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 26604460 Learning Difficulties of Children with Disabilities
Authors: Chalise Kiran
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The learning difficulties of children with disabilities are always a matter of concern when we talk about educational needs and quality education of children with disabilities. This paper is the outcome of the review of the literature focused on the educational needs and learning difficulties of children with disabilities. For the paper, different studies written on children with disabilities and their education were collected through search engines. The literature put together were analyzed from the angle of learning difficulties faced by children with disabilities and the same were used as a precursor to arrive at the findings on the learning of the children. The analysis showed that children with disabilities face learning difficulties. The reasons for these difficulties could be attributed to factors in terms of authority, structure, school environment and behaviors of teachers and parents and the society as a whole.
Keywords: Children with disabilities, learning difficulties, education of children with disabilities, disabled children.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 4234459 Ginzburg-Landau Model for Curved Two-Phase Shallow Mixing Layers
Authors: Irina Eglite, Andrei A. Kolyshkin
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Method of multiple scales is used in the paper in order to derive an amplitude evolution equation for the most unstable mode from two-dimensional shallow water equations under the rigid-lid assumption. It is assumed that shallow mixing layer is slightly curved in the longitudinal direction and contains small particles. Dynamic interaction between carrier fluid and particles is neglected. It is shown that the evolution equation is the complex Ginzburg-Landau equation. Explicit formulas for the computation of the coefficients of the equation are obtained.Keywords: Shallow water equations, mixing layer, weakly nonlinear analysis, Ginzburg-Landau equation
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 14194458 Thermoelastic Damping of Inextensional Hemispherical Shell
Authors: S. Y. Choi, Y. H. Na, J. H. Kim
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In this work, thermoelastic damping effect on the hemi- spherical shells is investigated. The material is selected silicon, and heat conduction equation for thermal flow is solved to obtain the temperature profile in which bending approximation with inextensional assumption of the model. Using the temperature profile, eigen-value analysis is performed to get the natural frequencies of hemispherical shells. Effects of mode numbers, radii and radial thicknesses of the model on the natural frequencies are analyzed in detail. Furthermore, the quality factor (Q-factor) is defined, and discussed for the ring and hemispherical shell.Keywords: Thermoelastic damping, hemispherical shell, quality factor
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 20214457 Gamification as a Tool for Influencing Customers' Behaviour
Authors: B. Zatwarnicka-Madura
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The objective of the article was to identify the impacts of gamification on customers' behaviour. The most important applications of games in marketing and mechanisms of gamification are presented in the article. A detailed analysis of the influence of gamification on customers using two brands, Foursquare and Nike, was also presented. Research studies using auditory survey methods were carried out among 176 young respondents, who are potential targets of gamification. The studies confirmed a huge participation of young people in customer loyalty programs with relatively low participation in other gamificationbased marketing activities. The research findings clearly indicate that gamification mechanisms are the most attractive.
Keywords: Customer loyalty, games, gamification, social aspects.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 24184456 Synthesis of the Robust Regulators on the Basis of the Criterion of the Maximum Stability Degree
Authors: S. A. Gayvoronsky, T. A. Ezangina
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The robust control system objects with interval- undermined parameters is considers in this paper. Initial information about the system is its characteristic polynomial with interval coefficients. On the basis of coefficient estimations of quality indices and criterion of the maximum stability degree, the methods of synthesis of a robust regulator parametric is developed. The example of the robust stabilization system synthesis of the rope tension is given in this article.
Keywords: An interval polynomial, controller synthesis, analysis of quality factors, maximum degree of stability, robust degree of stability, robust oscillation, system accuracy.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 15934455 Classification of Germinatable Mung Bean by Near Infrared Hyperspectral Imaging
Authors: Kaewkarn Phuangsombat, Arthit Phuangsombat, Anupun Terdwongworakul
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Hard seeds will not grow and can cause mold in sprouting process. Thus, the hard seeds need to be separated from the normal seeds. Near infrared hyperspectral imaging in a range of 900 to 1700 nm was implemented to develop a model by partial least squares discriminant analysis to discriminate the hard seeds from the normal seeds. The orientation of the seeds was also studied to compare the performance of the models. The model based on hilum-up orientation achieved the best result giving the coefficient of determination of 0.98, and root mean square error of prediction of 0.07 with classification accuracy was equal to 100%.
Keywords: Mung bean, near infrared, germinatability, hard seed.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 11624454 Measuring the Efficiency of Medical Equipment
Authors: Panagiotis H. Tsarouhas
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the reliability analysis of the medical equipments can help to increase the availability and the efficiency of the systems. In this manuscript we present a simple method of decomposition that could be easily applied on the complex medical systems. Using this method we can easily calculate the effect of the subsystems or components on the reliability of the overall system. Furthermore, to investigate the effect of subsystems or components on system performance, we perform a numerical study varying every time the worst reliability of subsystem or component with another which has higher reliability. It can also be useful to engineers and designers of medical equipment, who wishes to optimize the complex systems.Keywords: Reliability, Availability, Series-parallel System, medical equipment.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 23964453 Optimal Assessment of Faulted Area around an Industrial Customer for Critical Sag Magnitudes
Authors: Marios N. Moschakis
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This paper deals with the assessment of faulted area around an industrial customer connected to a particular electric grid that will cause a certain sag magnitude on this customer. The faulted (critical or exposed) area’s length is calculated by adding all line lengths in the neighborhood of the critical node (customer). The applied method is the so-called Method of Critical Distances. By using advanced short-circuit analysis, the Critical Area can be accurately calculated for radial and meshed power networks due to all symmetrical and asymmetrical faults. For the demonstration of the effectiveness of the proposed methodology, a study case is used.
Keywords: Critical area, fault-induced voltage sags, industrial customers, power quality.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 16464452 Performance Analysis of Polycrystalline and Monocrystalline Solar Module in Dhaka, Bangladesh
Authors: N. J. Imu, N. Rabbani, Md E. Hossain
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Achieving national climate goals requires transforming the energy system and increasing the use of renewable energy in Bangladesh as renewable energy offers an environmentally friendly energy supply. In view of this, Bangladesh has set a goal of 100% renewable power generation by 2050. Among all the renewable energy, solar is the most effective and popular source of renewable energy in Bangladesh. In order to build up on-grid and off-grid solar systems to increase energy transformation, monocrystalline type (highly efficient) solar module, and the polycrystalline type (low-efficient) solar module are commonly used. Due to their low price and availability, polycrystalline-type solar modules dominated the local market in the past years. However, in recent times the use of monocrystalline types modules has increased considerably owing to the significant decrease in price difference that existed between these two modules. Despite the deployment of both mono- and poly-crystalline modules in the market, the proliferation of low-quality solar panels are dominating the market resulting in reduced generation of solar electricity than expected. This situation is further aggravated by insufficient information regarding the effect of solar irradiation on solar module performance in relation to the quality of the materials used for the production of the module. This research aims to evaluate the efficiency of monocrystalline and polycrystalline solar modules that are available in Bangladesh by considering seasonal variations. Both types of solar modules have been tested for three different capacities 45W, 60W, and 100W in Dhaka regions to evaluate their power generation capability under Standard Test Conditions (STC). Module testing data were recorded twelve months in a full year from January to December. Data for solar irradiation were collected using HT304N while HT I-V400 multifunction instrument was used for testing voltage and current of photovoltaic (PV) systems and complete power quality analyzer. Results obtained in this study indicated differences between the efficiencies of polycrystalline and monocrystalline solar modules under the country’s solar irradiation. The average efficiencies of 45W, 60W, and 100W monocrystalline solar panels were recorded as 11.73%, 13.41%, and 15.37% respectively while for polycrystalline panels were 8.66%, 9.37%, and 12.34%. Monocrystalline solar panels, which offer greater working output than polycrystalline ones, are also represented by the Pearson Correlation value. The output of polycrystalline solar panels fluctuated highly with the changes in irradiation and temperature whereas monocrystalline panels were much stable.
Keywords: Solar energy, solar irradiation, efficiency, polycrystalline solar module, monocrystalline solar module, SPSS analysis.
Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1604451 Electron Density Discrepancy Analysis of Energy Metabolism Coenzymes
Authors: Alan Luo, Hunter N. B. Moseley
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Many macromolecular structure entries in the Protein Data Bank (PDB) have a range of regional (localized) quality issues, be it derived from X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, or other experimental approaches. However, most PDB entries are judged by global quality metrics like R-factor, R-free, and resolution for X-ray crystallography or backbone phi-psi distribution statistics and average restraint violations for NMR. Regional quality is often ignored when PDB entries are re-used for a variety of structurally based analyses. The binding of ligands, especially ligands involved in energy metabolism, is of particular interest in many structurally focused protein studies. Using a regional quality metric that provides chemically interpretable information from electron density maps, a significant number of outliers in regional structural quality was detected across X-ray crystallographic PDB entries for proteins bound to biochemically critical ligands. In this study, a series of analyses was performed to evaluate both specific and general potential factors that could promote these outliers. In particular, these potential factors were the minimum distance to a metal ion, the minimum distance to a crystal contact, and the isotropic atomic b-factor. To evaluate these potential factors, Fisher’s exact tests were performed, using regional quality criteria of outlier (top 1%, 2.5%, 5%, or 10%) versus non-outlier compared to a potential factor metric above versus below a certain outlier cutoff. The results revealed a consistent general effect from region-specific normalized b-factors but no specific effect from metal ion contact distances and only a very weak effect from crystal contact distance as compared to the b-factor results. These findings indicate that no single specific potential factor explains a majority of the outlier ligand-bound regions, implying that human error is likely as important as these other factors. Thus, all factors, including human error, should be considered when regions of low structural quality are detected. Also, the downstream re-use of protein structures for studying ligand-bound conformations should screen the regional quality of the binding sites. Doing so prevents misinterpretation due to the presence of structural uncertainty or flaws in regions of interest.
Keywords: Biomacromolecular structure, coenzyme, electron density discrepancy analysis, X-ray crystallography.
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