Search results for: structure analysis

Authors: Basheer M. Al-Maqaleh, Kamal K. Bharadwaj

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Automated discovery of hierarchical structures in large data sets has been an active research area in the recent past. This paper focuses on the issue of mining generalized rules with crisp hierarchical structure using Genetic Programming (GP) approach to knowledge discovery. The post-processing scheme presented in this work uses flat rules as initial individuals of GP and discovers hierarchical structure. Suitable genetic operators are proposed for the suggested encoding. Based on the Subsumption Matrix(SM), an appropriate fitness function is suggested. Finally, Hierarchical Production Rules (HPRs) are generated from the discovered hierarchy. Experimental results are presented to demonstrate the performance of the proposed algorithm.

Keywords: Genetic Programming, Hierarchy, Knowledge Discovery in Database, Subsumption Matrix.

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Authors: Rafal Michalski, Jakub Zygadlo

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We present the concept and scientific methods and algorithms of our computation system called ATOMIC MATTERS. This is the first presentation of the new computer package, that allows its user to describe physical properties of atomic localized electron systems subject to electromagnetic interactions. Our solution applies to situations where an unclosed electron 2p/3p/3d/4d/5d/4f/5f subshell interacts with an electrostatic potential of definable symmetry and external magnetic field. Our methods are based on Crystal Electric Field (CEF) approach, which takes into consideration the electrostatic ligands field as well as the magnetic Zeeman effect. The application allowed us to predict macroscopic properties of materials such as: Magnetic, spectral and calorimetric as a result of physical properties of their fine electronic structure. We emphasize the importance of symmetry of charge surroundings of atom/ion, spin-orbit interactions (spin-orbit coupling) and the use of complex number matrices in the definition of the Hamiltonian. Calculation methods, algorithms and convention recalculation tools collected in ATOMIC MATTERS were chosen to permit the prediction of magnetic and spectral properties of materials in isostructural series.

Keywords: Atomic matters, crystal electric field, spin-orbit coupling, localized states, electron subshell, fine electronic structure.

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Authors: Wen-Shyong Tzou, Chih-Ching Huang, Chin-Hwa Hu, Ying-Tsang Lo, Tun-Wen Pai, Chia-Yin Chiang, Chung-Hao Li, Hong-Jyuan Jian

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Plasmin plays an important role in the human circulatory system owing to its catalytic ability of fibrinolysis. The immediate injection of plasmin in patients of strokes has intrigued many scientists to design vectors that can transport plasmin to the desired location in human body. Here we predict the structure of human plasmin and investigate the interaction of plasmin with the gold-nanoparticle. Because the crystal structure of plasminogen has been solved, we deleted N-terminal domain (Pan-apple domain) of plasminogen and generate a mimic of the active form of this enzyme (plasmin). We conducted a simulated annealing process on plasmin and discovered a very large conformation occurs. Kringle domains 1, 4 and 5 had been observed to leave its original location relative to the main body of the enzyme and the original doughnut shape of this enzyme has been transformed to a V-shaped by opening its two arms. This observation of conformational change is consistent with the experimental results of neutron scattering and centrifugation. We subsequently docked the plasmin on the simulated gold surface to predict their interaction. The V-shaped plasmin could utilize its Kringle domain and catalytic domain to contact the gold surface. Our findings not only reveal the flexibility of plasmin structure but also provide a guide for the design of a plasmin-gold nanoparticle.

Keywords: Docking, gold nanoparticle, molecular simulation, plasmin.

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Authors: Beata Zima, Octavio A. Márquez Reyes, Masoud Mohammadgholiha, Jochen Moll, Luca De Marchi

Abstract:

This document presents the approach of using compressed sensing in signal encoding and information transferring within a guided wave sensor network, comprised of specially designed frequency steerable acoustic transducers (FSATs). Wave propagation in a damaged plate was simulated using commercial FEM-based software COMSOL. Guided waves were excited by means of FSATs, characterized by the special shape of its electrodes, and modeled using PIC255 piezoelectric material. The special shape of the FSAT, allows for focusing wave energy in a certain direction, accordingly to the frequency components of its actuation signal, which makes a larger monitored area available. The process begins when a FSAT detects and records reflection from damage in the structure, this signal is then encoded and prepared for transmission, using a combined approach, based on Compressed Sensing Matching Pursuit and Quadrature Amplitude Modulation (QAM). After codification of the signal is in binary, the information is transmitted between the nodes in the network. The message reaches the last node, where it is finally decoded and processed, to be used for damage detection and localization purposes. The main aim of the investigation is to determine the location of detected damage using reconstructed signals. The study demonstrates that the special steerable capabilities of FSATs, not only facilitate the detection of damage but also permit transmitting the damage information to a chosen area in a specific direction of the investigated structure.

Keywords: Data compression, ultrasonic communication, guided waves, FEM analysis.

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Authors: Dale Dzemydiene, Aurelija Burinskiene, Arunas Miliauskas, Kristina Ciziuniene

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Data flow and the purpose of reporting the data are different and dependent on business needs. Different parameters are reported and transferred regularly during freight delivery. This business practices form the dataset constructed for each time point and contain all required information for freight moving decisions. As a significant amount of these data is used for various purposes, an integrating methodological approach must be developed to respond to the indicated problem. The proposed methodology contains several steps: (1) collecting context data sets and data validation; (2) multi-objective analysis for optimizing freight transfer services. For data validation, the study involves Grubbs outliers analysis, particularly for data cleaning and the identification of statistical significance of data reporting event cases. The Grubbs test is often used as it measures one external value at a time exceeding the boundaries of standard normal distribution. In the study area, the test was not widely applied by authors, except when the Grubbs test for outlier detection was used to identify outsiders in fuel consumption data. In the study, the authors applied the method with a confidence level of 99%. For the multi-objective analysis, the authors would like to select the forms of construction of the genetic algorithms, which have more possibilities to extract the best solution. For freight delivery management, the schemas of genetic algorithms' structure are used as a more effective technique. Due to that, the adaptable genetic algorithm is applied for the description of choosing process of the effective transportation corridor. In this study, the multi-objective genetic algorithm methods are used to optimize the data evaluation and select the appropriate transport corridor. The authors suggest a methodology for the multi-objective analysis, which evaluates collected context data sets and uses this evaluation to determine a delivery corridor for freight transfer service in the multi-modal transportation network. In the multi-objective analysis, authors include safety components, the number of accidents a year, and freight delivery time in the multi-modal transportation network. The proposed methodology has practical value in the management of multi-modal transportation processes.

Keywords: Multi-objective decision support, analysis, data validation, freight delivery, multi-modal transportation, genetic programming methods.

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Authors: E. H. N. Gashti, J. Razzaghi, K. Kujala

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In general, codes and regulations consider seismic loads only for completed structures of the bridges while, evaluation of incomplete structure of bridges, especially those constructed by free cantilever method, under these loads is also of great importance. Hence, this research tried to study the behavior of incomplete structure of common bridge type (box girder bridge), in construction phase under vertical seismic loads. Subsequently, the paper provided suitable guidelines and solutions to resist this destructive phenomenon. Research results proved that use of preventive methods can significantly reduce the stresses resulted from vertical seismic loads in box cross sections to an acceptable range recommended by design codes.

Keywords: Box girder bridges, Prestress loads, Free cantilever method, Seismic loads, Construction phase.

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Authors: T.C. Manjunath

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This paper deals with the design of a moving sliding surface in a variable structure plant for a second order system. The chattering phenomena is also dealt with during the switching process for an unstable sliding surface condition. The simulation examples considered in this paper shows the effectiveness of the sliding mode control method used for the design of the moving sliding surfaces. A simulink model of the continuous system was also developed in MATLAB-SIMULINK for the design and hence demonstrated. The phase portraits and the state plots shows the demonstration of the powerful control technique which can be applied for second order systems.

Keywords: Sliding mode control, VSC, Reaching phase, Sliding phase, Moving surfaces, Chattering, Trajectories.

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Authors: Susanta Banerjee, Sanjaya Kumar Patro

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Buildings with floating column are highly undesirable built in seismically active areas. Many urban multi-storey buildings today have floating column buildings which are adopted to accommodate parking at ground floor or reception lobbies in the first storey. The earthquake forces developed at different floor levels in a building need to be brought down along the height to the ground by the shortest path; any deviation or discontinuity in this load transfer path results in poor performance of the building. Floating column buildings are severely damaged during earthquake. Damage on this structure can be reduce by taking the effect of infill wall. This paper presents the effect of stiffness of infill wall to the damage occurred in floating column building when ground shakes. Modelling and analysis are carried out by non linear analysis programme IDARC-2D. Damage occurred in beams, columns, storey are studied by formulating modified Park & Ang model to evaluate damage indices. Overall structural damage indices in buildings due to shaking of ground are also obtained. Dynamic response parameters i.e. lateral floor displacement, storey drift, time period, base shear of buildings are obtained and results are compared with the ordinary moment resisting frame buildings. Formation of cracks, yield, plastic hinge, are also observed during analysis.

Keywords: Floating column, Infill Wall, Park-Ang Damage Index, Damage State.

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Authors: Tapan Trivedi, Pramod Agarwal, Rajendrasinh Jadeja, Pragnesh Bhatt

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Space Vector Pulse Width Modulation is popular for variable frequency drives. The method has several advantages over carried based PWM and is computation intensive. The implementation of SVPWM for multilevel inverter requires special attention and at the same time consumes considerable resources. Due to faster processing power and reduced over all computational burden, FPGAs are being investigated as an alternative for other controllers. In this paper, a space vector PWM algorithm is implemented using FPGA which requires less computational area and is modular in structure. The algorithm is verified experimentally for Neutral Point Clamped inverter using FPGA development board xc3s5000-4fg900.

Keywords: Modular structure, Multilevel inverter, Space Vector PWM, Switching States.

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Authors: Ahmet C. Kutlu, Seçkin Polat

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Organizational structure of the Turkish state universities is a form of bureaucracy, a high efficient system in rational and formal control. According to the dimensional approach bureaucracy can occur in an organization in a degree, as some bureaucracy characteristics can be stronger than others. In addition, the units of an organization due to their different specific characteristic properties can perceive the bureaucracy differently. In the study, Hall-s Organizational Inventory, which was developed for evaluating the degree of bureaucratization from the dimensional perspective, is used to find out if there is a difference in the perception of the bureaucracy between the academicians working in three different departments and two faculties in the same university.

Keywords: Degree of bureaucratization, Hall's Organizational Inventory, perceived bureaucracy.

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Authors: Gil Hwan Na , Woo Young Jung , Tae Kwon Ha

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Most buildings have been using anchor bolts commonly for installing outdoor advertising structures. Anchor bolts of common carbon steel are widely used and often installed indiscriminately by inadequate installation standards. In the area where strong winds frequently blow, falling accidents of outdoor advertising structures can occur and cause a serious disaster, which is very dangerous and to be prevented. In this regard, the development of high-performance anchor bolts is urgently required. In the present study, 25Cr-8Ni-1.5Si-1Mn-0.4C alloy was produced by traditional vacuum induction melting (VIM) for the application of anchor bolt. The alloy composition is revealed as a duplex microstructure from thermodynamic phase analysis by FactSage® and confirmed by metallographic experiment. Addition of Nitrogen to the alloy was found to reduce the ferritic phase domain and significantly increase the hardness and the tensile strength. Microstructure observation revealed mixed structure of austenite and ferrite with fine carbide distributed along the grain and phase boundaries.

Keywords: Anchor bolt, Duplex stainless steel, FactSage®, Hardness, Thermodynamic phase analysis.

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Authors: Radu Dobrescu, Matei Dobrescu, Daniela Hossu

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The paper proposes a unified model for multimedia data retrieval which includes data representatives, content representatives, index structure, and search algorithms. The multimedia data are defined as k-dimensional signals indexed in a multidimensional k-tree structure. The benefits of using the k-tree unified model were demonstrated by running the data retrieval application on a six networked nodes test bed cluster. The tests were performed with two retrieval algorithms, one that allows parallel searching using a single feature, the second that performs a weighted cascade search for multiple features querying. The experiments show a significant reduction of retrieval time while maintaining the quality of results.

Keywords: balancing strategies, multimedia databases, parallelprocessing, retrieval algorithms

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Authors: Chetan Mahawar, Sarath Chandran, Sridhar Panigrahi, V. P. Shaji

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The ever-growing advancement in space exploration has led to an alarming concern for space debris removal as it restricts further launch operations and adventurous space missions; hence various technologies and methods are explored for re-entry predictions and material selection processes for mitigating space debris. The selection of material and operating conditions is determined with the objective of lightweight structure and ability to demise faster subject to spacecraft survivability during its mission. The various evolving thermal material properties such as emissivity, specific heat capacity, thermal conductivity, radiation intensity, etc. affect demisability of spacecraft. Thus, this paper presents the analysis of evolving thermal material properties of spacecraft, which affect the demisability process and thus estimate demise time using the demisability model by incorporating evolving thermal properties for sensible heating followed by the complete or partial break-up of spacecraft. The demisability analysis thus concludes that the best suitable spacecraft material is based on the least estimated demise time, which fulfills the criteria of design-for-survivability and as well as of design-for-demisability.

Keywords: Demisability, emissivity, lightweight, re-entry, survivability.

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Authors: Ahmed A. D. Sarhan, Chong Feng Duan, Mum Wai Yip, M. Sayuti

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Rapid Prototyping (RP) technologies enable physical parts to be produced from various materials without depending on the conventional tooling. Fused Deposition Modeling (FDM) is one of the famous RP processes used at present. Tensile strength and compressive strength resistance will be identified for different sample structures and different layer orientations of ABS rapid prototype solid models. The samples will be fabricated by a FDM rapid prototyping machine in different layer orientations with variations in internal geometrical structure. The 0° orientation where layers were deposited along the length of the samples displayed superior strength and impact resistance over all the other orientations. The anisotropic properties were probably caused by weak interlayer bonding and interlayer porosity.

Keywords: Building orientation, compression strength, rapid prototyping, tensile strength.

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Authors: Alexander Y. Vaninsky

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The objective of this paper is finding the way of economic restructuring - that is, change in the shares of sectoral gross outputs - resulting in the maximum possible increase in the gross domestic product (GDP) combined with decreases in energy consumption and CO₂ emissions. It uses an input-output model for the GDP and factorial models for the energy consumption and CO₂ emissions to determine the projection of the gradient of GDP, and the antigradients of the energy consumption and CO₂ emissions, respectively, on a subspace formed by the structure-related variables. Since the gradient (antigradient) provides a direction of the steepest increase (decrease) of the objective function, and their projections retain this property for the functions' limitation to the subspace, each of the three directional vectors solves a particular problem of optimal structural change. In the next step, a type of factor analysis is applied to find a convex combination of the projected gradient and antigradients having maximal possible positive correlation with each of the three. This convex combination provides the desired direction of the structural change. The national economy of the United States is used as an example of applications.

Keywords: Economic restructuring, Input-Output analysis, Divisia index, Factorial decomposition, E3 models.

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Authors: Seung-Won Lee, Jong Soo Lee, Won-Jik Yang, Hyung-Joon Kim

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A capacity spectrum method (CSM), one of methodologies to evaluate seismic fragilities of building structures, has been long recognized as the most convenient method, even if it contains several limitations to predict the seismic response of structures of interest. This paper proposes the procedure to estimate seismic fragility curves using an incremental dynamic analysis (IDA) rather than the method adopting a CSM. To achieve the research purpose, this study compares the seismic fragility curves of a 5-story reinforced concrete (RC) moment frame obtained from both methods; an IDA method and aCSM. Both seismic fragility curves are similar in slight and moderate damage states whereas the fragility curve obtained from the IDA method presents less variation (or uncertainties) in extensive and complete damage states. This is due to the fact that the IDA method can properly capture the structural response beyond yielding rather than the CSM and can directly calculate higher mode effects. From these observations, the CSM could overestimate seismic vulnerabilities of the studied structure in extensive or complete damage states.

Keywords: Seismic fragility curve, Incremental dynamic analysis, Capacity spectrum method, Reinforced concrete moment frame.

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Authors: Zahra Ghiabaklou

Abstract:

Ventilation is a fundamental requirement for occupant health and indoor air quality in buildings. Natural ventilation can be used as a design strategy in free-running buildings to: • Renew indoor air with fresh outside air and lower room temperatures at times when the outdoor air is cooler. • Promote air flow to cool down the building structure (structural cooling). • Promote occupant physiological cooling processes (comfort cooling). This paper focuses on ways in which ventilation can provide the mechanism for heat dissipation and cooling of the building structure..It also discusses use of ventilation as a means of increasing air movement to improve comfort when indoor air temperatures are too high. The main influencing factors and design considerations and quantitative guidelines to help meet the design objectives are also discussed.

Keywords: Natural Ventilation, Sustainable Building, Passive Cooling, Energy Saving

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Authors: Sima Ziaee, Khosro Jafarpur

Abstract:

Among all mechanical joining processes, welding has been employed for its advantage in design flexibility, cost saving, reduced overall weight and enhanced structural performance. However, for structures made of relatively thin components, welding can introduce significant buckling distortion which causes loss of dimensional control, structural integrity and increased fabrication costs. Different parameters can affect buckling behavior of welded thin structures such as, heat input, welding sequence, dimension of structure. In this work, a 3-D thermo elastic-viscoplastic finite element analysis technique is applied to evaluate the effect of shell dimensions on buckling behavior and entropy generation of welded thin shells. Also, in the present work, the approximated longitudinal transient stresses which produced in each time step, is applied to the 3D-eigenvalue analysis to ratify predicted buckling time and corresponding eigenmode. Besides, the possibility of buckling prediction by entropy generation at each time is investigated and it is found that one can predict time of buckling with drawing entropy generation versus out of plane deformation. The results of finite element analysis show that the length, span and thickness of welded thin shells affect the number of local buckling, mode shape of global buckling and post-buckling behavior of welded thin shells.

Keywords: Buckling behavior, Elastic viscoplastic model, Entropy generation, Finite element method, Shell dimensions.

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Authors: YongXian, JIN

Abstract:

Introducing survivability into embedded real-time system (ERTS) can improve the survivability power of the system. This paper mainly discusses about the survivability of ERTS. The first is the survivability origin of ERTS. The second is survivability analysis. According to the definition of survivability based on survivability specification and division of the entire survivability analysis process for ERTS, a survivability analysis profile is presented. The quantitative analysis model of this profile is emphasized and illuminated in detail, the quantifying analysis of system was showed helpful to evaluate system survivability more accurate. The third is platform design of survivability analysis. In terms of the profile, the analysis process is encapsulated and assembled into one platform, on which quantification, standardization and simplification of survivability analysis are all achieved. The fourth is survivability design. According to character of ERTS, strengthened design method is selected to realize system survivability design. Through the analysis of embedded mobile video-on-demand system, intrusion tolerant technology is introduced in whole survivability design.

Keywords: ERTS (embedded real-time system), survivability, quantitative analysis, survivability specification, intrusion tolerant

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Authors: Sannikumar Patel, Brian Nolan, Markus Hofmann, Philip Owende, Kunjan Patel

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Sentiment analysis and opinion mining have become emerging topics of research in recent years but most of the work is focused on data in the English language. A comprehensive research and analysis are essential which considers multiple languages, machine translation techniques, and different classifiers. This paper presents, a comparative analysis of different approaches for multilingual sentiment analysis. These approaches are divided into two parts: one using classification of text without language translation and second using the translation of testing data to a target language, such as English, before classification. The presented research and results are useful for understanding whether machine translation should be used for multilingual sentiment analysis or building language specific sentiment classification systems is a better approach. The effects of language translation techniques, features, and accuracy of various classifiers for multilingual sentiment analysis is also discussed in this study.

Keywords: Cross-language analysis, machine learning, machine translation, sentiment analysis.

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Authors: Chalise Kiran

Abstract:

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.

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Authors: Seema Chopra, R. Mitra, Vijay Kumar

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In this paper, a neural network tuned fuzzy controller is proposed for controlling Multi-Input Multi-Output (MIMO) systems. For the convenience of analysis, the structure of MIMO fuzzy controller is divided into single input single-output (SISO) controllers for controlling each degree of freedom. Secondly, according to the characteristics of the system-s dynamics coupling, an appropriate coupling fuzzy controller is incorporated to improve the performance. The simulation analysis on a two-level mass–spring MIMO vibration system is carried out and results show the effectiveness of the proposed fuzzy controller. The performance though improved, the computational time and memory used is comparatively higher, because it has four fuzzy reasoning blocks and number may increase in case of other MIMO system. Then a fuzzy neural network is designed from a set of input-output training data to reduce the computing burden during implementation. This control strategy can not only simplify the implementation problem of fuzzy control, but also reduce computational time and consume less memory.

Keywords: Fuzzy Control, Neural Network, MIMO System, Optimization of Membership functions.

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Authors: E. Farshidi

Abstract:

This paper presents a new general technique for analysis of noise in static log-domain translinear circuits. It is demonstrated that employing this technique, leads to a general, simple and routine method of the noise analysis. The circuit has been simulated by HSPICE. The simulation results are seen to conform to the theoretical analysis and shows benefits of the proposed circuit.

Keywords: Noise analysis, log-domain, static, dynamic, translinear loop, companding.

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Authors: N. Utaberta, N. Sharifi, M. Surat, A. I. Che-Ani, N.M. Tawil

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Iran has diverse climates and each have established distinct properties in their area. The extent and intensity of climatic factors effects on the lives of people living in various regions of Iran is so great that it cannot be simply ignored. In a large part of Iran known as the Central Plateau there is no precipitation for more than half of the year and dry weather and scarcity of fresh water pose an ever present problem for the people of these regions while in north of Iran upon the southern shores of the Caspian Sea the people face 80% humidity caused by the sea and 2 meters of annual precipitation. This article tries to review the past experiences of local architecture of Iran-s various regions so that they can be used to reshape and redirect the urban areas and structure of Iran-s current cities to provide environmental comfort by minimum use of fossil fuels.

Keywords: Urban Passage, Architecture in Iran, Urban Structure, Climatic Comfort

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Authors: Elena B. Cherepetskaya, Vladimir A. Makarov, Dmitry V. Morozov, Ivan E. Sas

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Laboratory studies of the stress-strain behavior of rocks specimens were conducted by using acoustic emission and laser-ultrasonic diagnostics. The sensitivity of the techniques allowed changes in the internal structure of the specimens under uniaxial compressive load to be examined at micro- and macro scales. It was shown that microcracks appear in geologic materials when the stress level reaches about 50% of breaking strength. Also, the characteristic stress of the main crack formation was registered in the process of single-stage compression of rocks. On the base of laser-ultrasonic echoscopy, 2D visualization of the internal structure of rocky soil specimens was realized, and the microcracks arising during uniaxial compression were registered.

Keywords: Acoustic emission, geomaterial, laser ultrasound, uniaxial compression.

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Authors: Moussa Hamdan, Abdulati Abdullah

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This paper presents an investigation of the fabrication of the optical devices in terms of their characteristics based on the use of the electromagnetic waves. Planar waveguides are used to examine the field modes (bound modes) and the parameters required for this structure. The modifications are conducted on surface plasmons based waveguides. Simple symmetric dielectric slab structure is used and analyzed in terms of transverse electric mode (TE-Mode) and transverse magnetic mode (TM-Mode. The paper presents mathematical and numerical solutions for solving simple symmetric plasmons and provides simulations of surface plasmons for field confinement. Asymmetric TM-mode calculations for dielectric surface plasmons are also provided.

Keywords: Surface plasmons, optical waveguides, semiconductor lasers, refractive index, slab dialectical.

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Authors: Alan Luo, Hunter N. B. Moseley

Abstract:

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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Authors: K.Tavzarashvili, G.Ghvedashili

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A semi-analytic boundary discretization method, the Method of Auxiliary Sources (MAS) is used to analyze Optical Antennas consisting of metallic parts. In addition to standard dipoletype antennas, consisting of two pieces of metal, a new structure consisting of a single metal piece with a tiny groove in the center is analyzed. It is demonstrated that difficult numerical problems are caused because optical antennas exhibit strong material dispersion, loss, and plasmon-polariton effects that require a very accurate numerical simulation. This structure takes advantage of the Channel Plasmon-Polariton (CPP) effect and exhibits a strong enhancement of the electric field in the groove. Also primitive 3D antenna model with spherical nano particles is analyzed.

Keywords: optical antenna, channel plasmon-polariton, computational physics, Method of Auxiliary Sources

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Authors: Shervin Khazaeli, Shahab Haj-zamani

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

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

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Authors: Zulkufly Ramly

Abstract:

This paper attempts to investigate the effect of corporate governance and shareholder monitoring mechanisms on cost of debt of Malaysian listed firms. We assess the quality of corporate governance using comprehensive corporate governance index, which consists of 139 items in six broad categories. We classify shareholder monitoring mechanisms into concentrated ownership, family, insider and government ownerships. Using panel sample from 2003 to 2007, regression results show that high corporate governance quality and concentrated ownership lower firm cost of debt. Debt issuers consider board structure and procedures, board compensation practices, accountability and audit, transparency and social and environmental activities as integral components of a good corporate governance framework.

Keywords: Corporate governance index, cost of debt, ownership structure, Malaysia.

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