Search results for: Integrated biology and chemistry

Authors: Babak H. Tabrizi, Seyed Farid Ghaderi

Abstract:

Concurrent planning of project scheduling and material ordering can provide more flexibility to the project scheduling problem, as the project execution costs can be enhanced. Hence, the issue has been taken into account in this paper. To do so, a mixed-integer mathematical model is developed which considers the aforementioned flexibility, in addition to the materials quantity discount and space availability restrictions. Moreover, the activities duration has been treated as decision variables. Finally, the efficiency of the proposed model is tested by different instances. Additionally, the influence of the aforementioned parameters is investigated on the model performance.

Keywords: Material ordering, project scheduling, quantity discount, space availability.

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Authors: Joel Arrais, João E. Pereira, João Fernandes, José Luís Oliveira

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The scientific achievements coming from molecular biology depend greatly on the capability of computational applications to analyze the laboratorial results. A comprehensive analysis of an experiment requires typically the simultaneous study of the obtained dataset with data that is available in several distinct public databases. Nevertheless, developing a centralized access to these distributed databases rises up a set of challenges such as: what is the best integration strategy, how to solve nomenclature clashes, how to solve database overlapping data and how to deal with huge datasets. In this paper we present GeNS, a system that uses a simple and yet innovative approach to address several biological data integration issues. Compared with existing systems, the main advantages of GeNS are related to its maintenance simplicity and to its coverage and scalability, in terms of number of supported databases and data types. To support our claims we present the current use of GeNS in two concrete applications. GeNS currently contains more than 140 million of biological relations and it can be publicly downloaded or remotely access through SOAP web services.

Keywords: Data integration, biological databases

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Authors: Vimala Balakrishnan, Mohammad R. Shakouri, Hooman Hoodeh, Loo, Huck-Soo

Abstract:

Diabetes is one of the high prevalence diseases worldwide with increased number of complications, with retinopathy as one of the most common one. This paper describes how data mining and case-based reasoning were integrated to predict retinopathy prevalence among diabetes patients in Malaysia. The knowledge base required was built after literature reviews and interviews with medical experts. A total of 140 diabetes patients- data were used to train the prediction system. A voting mechanism selects the best prediction results from the two techniques used. It has been successfully proven that both data mining and case-based reasoning can be used for retinopathy prediction with an improved accuracy of 85%.

Keywords: Case-Based Reasoning, Data Mining, Prediction, Retinopathy.

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Authors: Kuan-Yu Chiu, Yin-Hsuan Chen, Tung-Han Chuang

Abstract:

Ti/Ni/Ag/Sn-metallized Si chips were bonded to Ni/Pd/Au-surface finished DBC (Direct Bonding Copper) alumina substrate through the formation of an Ag3Sn intermetallic interlayer by solid–liquid interdiffusion bonding method. The results indicated that the holes and gaps at the bonding interface could be effectively prevented. The intermetallic phases at the bonding interface between the Si/Ti/Ni/Ag/Sn wafer and the DBC substrate were identified as Ag3Sn, Ni3Sn4, and Ni3Sn2. The average bonding strength was about 19.75 MPa, and the maximum bonding strength reached 35.24 MPa.

Keywords: BGBM, Backside Grinding and Backside Metallization, SLID bonding, Solid–liquid Interdiffusion Bonding, Si/Ti/Ni/Sn, Si/Ti/Ni/Ag/Sn, intermetallic compound.

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Authors: Rio G. L. D'Souza, K. Chandra Sekaran, A. Kandasamy

Abstract:

The goal of Gene Expression Analysis is to understand the processes that underlie the regulatory networks and pathways controlling inter-cellular and intra-cellular activities. In recent times microarray datasets are extensively used for this purpose. The scope of such analysis has broadened in recent times towards reconstruction of gene networks and other holistic approaches of Systems Biology. Evolutionary methods are proving to be successful in such problems and a number of such methods have been proposed. However all these methods are based on processing of genotypic information. Towards this end, there is a need to develop evolutionary methods that address phenotypic interactions together with genotypic interactions. We present a novel evolutionary approach, called Phenomic algorithm, wherein the focus is on phenotypic interaction. We use the expression profiles of genes to model the interactions between them at the phenotypic level. We apply this algorithm to the yeast sporulation dataset and show that the algorithm can identify gene networks with relative ease.

Keywords: Evolutionary computing, gene expression analysis, gene networks, microarray data analysis, phenomic algorithms.

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Authors: Tom Snir, Eitan Rubin

Abstract:

Mendelian Disease Genes represent a collection of single points of failure for the various systems they constitute. Such genes have been shown, on average, to encode longer proteins than 'non-disease' proteins. Existing models suggest that this results from the increased likeli-hood of longer genes undergoing mutations. Here, we show that in saturated mutagenesis experiments performed on model organisms, where the likelihood of each gene mutating is one, a similar relationship between length and the probability of a gene being lethal was observed. We thus suggest an extended model demonstrating that the likelihood of a mutated gene to produce a severe phenotype is length-dependent. Using the occurrence of conserved domains, we bring evidence that this dependency results from a correlation between protein length and the number of functions it performs. We propose that protein length thus serves as a proxy for protein cardinality in different networks required for the organism's survival and well-being. We use this example to argue that the collection of Mendelian Disease Genes can, and should, be used to study the rules governing systems vulnerability in living organisms.

Keywords: Systems Biology, Protein Length

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Authors: Adil Salam, Nadia Bhuiyan, Gerard J. Gouw

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The Canadian aerospace industry faces many challenges. One of them is the difficulty in estimating costs. In particular, the design effort required in a project impacts resource requirements and lead-time, and consequently the final cost. This paper presents the findings of a case study conducted for recognized global leader in the design and manufacturing of aircraft engines. The study models parametric cost estimation relationships to estimate the design effort of integrated blade-rotor low-pressure compressor fans. Several effort drivers are selected to model the relationship. Comparative analyses of three types of models are conducted. The model with the best accuracy and significance in design estimation is retained.

Keywords: Effort estimation, design, aerospace.

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Authors: R. Chanajaree, D. Luanwiset, K. Pongpratea

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Dye removal is an environmental concern because the textile industries have been increasing by world population and industrialization. Adsorption is the technique to find adsorbents to remove dyes from wastewater. This method is low-cost and effective for dye removal. This work tries to develop effective adsorbents using the computational approach because it will be able to predict the possibility of the adsorbents for specific dyes in terms of binding free energies. The computational approach is faster and cheaper than the experimental approach in case of finding the best adsorbents. All starting structures of dyes and adsorbents are optimized by quantum calculation. The complexes between dyes and adsorbents are generated by the docking method. The obtained binding free energies from docking are compared to binding free energies from the experimental data. The calculated energies can be ranked as same as the experimental results. In addition, this work also shows the possible orientation of the complexes. This work used two experimental groups of the complexes of the dyes and adsorbents. In the first group, there are chitosan (adsorbent) and two dyes (reactive red (RR) and direct sun yellow (DY)). In the second group, there are poly(1,2-epoxy-3-phenoxy) propane (PEPP), which is the adsorbent, and 2 dyes of bromocresol green (BCG) and alizarin yellow (AY).

Keywords: Dye removal, binding free energies, quantum calculation, docking.

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Authors: Sumit Tiwari, Rohit Tripathi, G. N. Tiwari

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Present study focused on the utilization of solar energy by the help of photovoltaic greenhouse solar dryer under forced mode. A single slope photovoltaic greenhouse solar dryer has been proposed and thermal modelling has been developed. Various parameters have been calculated by thermal modelling such as greenhouse room temperature, cell temperature, crop temperature and air temperature at exit of greenhouse. Further cell efficiency, thermal efficiency, and overall thermal efficiency have been calculated for a typical day of May and November. It was found that system can generate equivalent thermal energy up to 7.65 kW and 6.66 kW per day for clear day of May and November respectively.

Keywords: Characteristics curve, Photovoltaic, Thermal modelling, Thermal efficiency.

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Authors: Valeria M. Pequeno, Joao Carlos G. M. Pires

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Data Warehouses (DWs) are repositories which contain the unified history of an enterprise for decision support. The data must be Extracted from information sources, Transformed and integrated to be Loaded (ETL) into the DW, using ETL tools. These tools focus on data movement, where the models are only used as a means to this aim. Under a conceptual viewpoint, the authors want to innovate the ETL process in two ways: 1) to make clear compatibility between models in a declarative fashion, using correspondence assertions and 2) to identify the instances of different sources that represent the same entity in the real-world. This paper presents the overview of the proposed framework to model the ETL process, which is based on the use of a reference model and perspective schemata. This approach provides the designer with a better understanding of the semantic associated with the ETL process.

Keywords: conceptual data model, correspondence assertions, data warehouse, data integration, ETL process, object relational database.

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Authors: M. Samaka

Abstract:

This paper presents the development of a software application for Off-line robot task programming and simulation. Such application is designed to assist in robot task planning and to direct manipulator motion on sensor based programmed motion. The concept of the designed programming application is to use the power of the knowledge base for task accumulation. In support of the programming means, an interactive graphical simulation for manipulator kinematics was also developed and integrated into the application as the complimentary factor to the robot programming media. The simulation provides the designer with useful, inexpensive, off-line tools for retain and testing robotics work cells and automated assembly lines for various industrial applications.

Keywords: Robot programming, task-level programming, robot languages, robot simulation, robotics software.

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Authors: Nurcan Tuncbag, Turkan Haliloglu, Ozlem Keskin

Abstract:

Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In the light of the clustering data, we have verified some interactions which were not identified as core interactions in DIP and also, we have characterized some functionally unknown proteins according to the interaction data and functional correlation. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins, also to predict new interactions and to characterize functions of unknown proteins.

Keywords: Pair-wise protein interactions, DIP database, functional correlations, biclustering.

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Authors: Saman M. Siddiqui, Fang Jiancheng

Abstract:

Micro electromechanical sensors (MEMS) play a vital role along with global positioning devices in navigation of autonomous vehicles .These sensors are low cost ,easily available but depict colored noises and unpredictable discontinuities .Conventional filters like Kalman filters and Sigma point filters are not able to cope with nonwhite noises. This research has utilized H∞ filter in nonlinear frame work both with Kalman filter and Unscented filter for navigation and self alignment of an airborne vehicle. The system is simulated for colored noises and discontinuities and results are compared with not robust nonlinear filters. The results are found 40%-70% more robust against colored noises and discontinuities.

Keywords: filtering, integrated navigation, MEMS, nonlinearfiltering, self alignment

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Authors: Yingjie Zhang

Abstract:

This paper is concerned with an improved algorithm based on the piecewise-smooth Mumford and Shah (MS) functional for an efficient and reliable segmentation. In order to speed up convergence, an additional force, at each time step, is introduced further to drive the evolution of the curves instead of only driven by the extensions of the complementary functions u + and u - . In our scheme, furthermore, the piecewise-constant MS functional is integrated to generate the extra force based on a temporary image that is dynamically created by computing the union of u + and u - during segmenting. Therefore, some drawbacks of the original algorithm, such as smaller objects generated by noise and local minimal problem also are eliminated or improved. The resulting algorithm has been implemented in Matlab and Visual Cµ, and demonstrated efficiently by several cases.

Keywords: Active contours, energy minimization, image segmentation, level sets.

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Authors: Nazar Zaki, Safaai Deris

Abstract:

The amount of the information being churned out by the field of biology has jumped manifold and now requires the extensive use of computer techniques for the management of this information. The predominance of biological information such as protein sequence similarity in the biological information sea is key information for detecting protein evolutionary relationship. Protein sequence similarity typically implies homology, which in turn may imply structural and functional similarities. In this work, we propose, a learning method for detecting remote protein homology. The proposed method uses a transformation that converts protein sequence into fixed-dimensional representative feature vectors. Each feature vector records the sensitivity of a protein sequence to a set of amino acids substrings generated from the protein sequences of interest. These features are then used in conjunction with support vector machines for the detection of the protein remote homology. The proposed method is tested and evaluated on two different benchmark protein datasets and it-s able to deliver improvements over most of the existing homology detection methods.

Keywords: Protein homology detection; support vectormachine; string kernel.

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Authors: H. Buluthan Cetintas

Abstract:

Corporate identity, which has several advantages such that the employees become integrated with their corporations, corporation is distinguished from its competitors and it is recognized by the masses, is the total of the distinctive corporate features that and corporation has. That the information takes part in production as a more important component than labor and capital has required that the corporations are reorganized as information-based. Therefore, information and its management have reached a basic and prevalent position in having sustainable competitive advantage. Thanks to the information management which regulates the information and makes it reachable and available, information will be produced in line with a specific purpose in the corporations and be used in all the corporate processes. As an auxiliary power for increase in the economic potential, efficiency and productivity of the corporation, corporate identity consists of four components. These are corporate philosophy, corporate design, corporate behavior and corporate communication. In this study, the effects of the information management on corporate identity are discussed from the point of these four elements.

Keywords: Corporate identity, information management.

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Authors: Y. Harold Robinson, E. Golden Julie, S. Balaji

Abstract:

The scheduling based routing scheme is presented in this paper to avoid link failure. The main objective of this system is to introduce a cross-layer protocol framework that integrates routing with priority-based traffic management and distributed transmission scheduling. The reservation scheme is based on ID. The presented scheme guarantees that bandwidth reserved time slot is used by another packet in which end-to-end reservation is achieved. The Bandwidth and Delay Aware Routing Protocol with Scheduling Algorithm is presented to allocate channels efficiently. The experimental results show that the presented schemes performed well in various parameters compared to existing methods.

Keywords: Integrated routing, scheduling, MAC layer, IEEE 802.11.

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Authors: Mohamad Saab, Sidi Souvi

Abstract:

In a major nuclear accident, the released fission products (FPs) and the structural materials are likely to influence the transport of iodine in the reactor coolant system (RCS) of a pressurized water reactor (PWR). So far, the thermodynamic data on cesium and silver species used to estimate the magnitude of FP release show some discrepancies, data are scarce and not reliable. For this reason, it is crucial to review the thermodynamic values related to cesium and silver materials. To this end, we have used state-of-the-art quantum chemical methods to compute the formation enthalpies and entropies of AgHMoO₄, CsHMoO₄, and AgCsMoO₄ in the gas phase. Different quantum chemical methods have been investigated (DFT and CCSD(T)) in order to predict the geometrical parameters and the energetics including the correlation energy. The geometries were optimized with TPSSh-5%HF method, followed by a single point calculation of the total electronic energies using the CCSD(T) wave function method. We thus propose with a final uncertainty of about 2 kJmol⁻¹ standard enthalpies of formation of AgHMoO₄, CsHMoO₄, and AgCsMoO₄.

Keywords: ASTEC, Accident Source Term Evaluation Code, quantum chemical methods, severe nuclear accident, thermochemical database.

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Authors: Romuald Synak, Wlodzimierz Lipinski, Marcin Pawelczak

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An area-integrating method that uses the technique of total integrated light scatter for evaluating the root mean square height of the surface Sq has been presented in the paper. It is based on the measurement of the scatter power using a flat photodiode integrator rather than an optical sphere or a hemisphere. By this means, one can obtain much less expensive and smaller instruments than traditional ones. Thanks to this, they could find their application for surface control purposes, particularly in small and medium size enterprises. A description of the functioning of the measuring unit as well as the impact caused by different factors on its properties is presented first. Next, results of measurements of the Sq values performed for optical, silicon and metal samples have been shown. It has been also proven that they are in a good agreement with the results obtained using the Ulbricht sphere instrument.

Keywords: ISO 25178 Standard, scatterometry, surface metrology, surface roughness

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Authors: Ararat Khachatryan, Davit Mirzoyan

Abstract:

In sub micrometer technology, the aging phenomenon starts to have a significant impact on the reliability of integrated circuits by bringing performance degradation. For that reason, it is important to have a capability to evaluate the aging effects accurately. This paper presents an accurate aging measurement approach based on phase-locked loop (PLL) and voltage-controlled oscillator (VCO) circuit. The architecture is rejecting the circuit self-aging effect from the characteristics of PLL, which is generating the frequency without any aging phenomena affects. The aging monitor is implemented in low power 32 nm CMOS technology, and occupies a pretty small area. Aging simulation results show that the proposed aging measurement circuit improves accuracy by about 2.8% at high temperature and 19.6% at high voltage.

Keywords: Nanoscale, aging, effect, NBTI, HCI.

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Authors: Meisam Moghadasi, Hassan Ali Ozgoli, Foad Farhani

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In this research, firstly, a commercial gas sweetening unit with methyl-di-ethanol-amine (MDEA) solution is simulated and comprised in an integrated model in accordance with Aspen HYSYS software. For evaluation purposes, in the second step, the results of the simulation are compared with operating data gathered from South Pars Gas Complex (SPGC). According to the simulation results, the considerable energy potential contributed to the pressure difference between absorber and regenerator columns causes this energy driving force to be applied in power recovery turbine (PRT). In the last step, the amount of waste hydraulic energy is calculated, and its recovery methods are investigated.

Keywords: Gas sweetening unit, simulation, MDEA, power recovery turbine, waste-to-energy.

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Authors: Rosalba D'onofrio

Abstract:

It is not easy to imagine how the existing city can be converted to the principles of sustainability, however, the need for innovation, requires a pioneering phase which must address the main problems of rehabilitation of the operating models of the city. Today, however, there is a growing awareness that the identification and implementation of policies and measures to promote the adaptation, resilience and reversibility of the city, require the contribution of our discipline. This breakthrough is present in some recent international experiences of Climate Plans, in which the envisaged measures are closely interwoven with those of urban planning. These experiences, provide some answers principle questions, such as: how the strategies to combat climate can be integrated in the instruments of the local government; what new and specific analysis must be introduced in urban planning in order to understand the issues of urban sustainability, and how the project compares with different spatial scales.

Keywords: Climate change, urban sustainability, urban planning

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Authors: S. Yordchim, G. Anugkakul, T. Gibbs

Abstract:

The English competence of Thai people was examined in the context of knowledge of English in everyday life for Small and Medium Entrepreneurs (SMEs), and also integrated with Second language acquisition (SLA) students’ classroom. Second language acquisition was applied to the results of the questionnaires and interview forms. Levels of the need on English used for SME entrepreneurs in Thailand, satisfaction on joining the street classroom project were shown to be significantly high for some certain language functions and satisfaction. Finding suggests that the language functions on etiquette for professional use is essential and useful because lesson learned can be used in the real situation for their career. Implications for the climate of the street classroom are discussed.

Keywords: English classroom, second language acquisition, Small and Medium Entrepreneurs, Thai students.

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Authors: F. Allag, S. Bouharati, M. Belmahdi, R. Zegadi

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The rapid expansion of deserts in recent decades as a result of human actions combined with climatic changes has highlighted the necessity to understand biological processes in arid environments. Whereas physical processes and the biology of flora and fauna have been relatively well studied in marginally used arid areas, knowledge of desert soil micro-organisms remains fragmentary. The objective of this study is to conduct a diversity analysis of bacterial communities in unvegetated arid soils. Several biological phenomena in hot deserts related to microbial populations and the potential use of micro-organisms for restoring hot desert environments. Dry land ecosystems have a highly heterogeneous distribution of resources, with greater nutrient concentrations and microbial densities occurring in vegetated than in bare soils. In this work, we found it useful to use techniques of artificial intelligence in their treatment especially artificial neural networks (ANN). The use of the ANN model, demonstrate his capability for addressing the complex problems of uncertainty data.

Keywords: Desert soil, Climatic changes, Bacteria, Vegetation, Artificial neural networks.

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Authors: A. Mobini, K. Saghafi, V. Ahmadi

Abstract:

in this paper we modified a simple two-dimensional photonic crystal waveguide by creating micro cavity resonators in order to increase the output light emission which can be applicable to photonic integrated circuits. The micro cavity resonators are constructed by removing two tubes close to the waveguide output. Coupling emitted light from waveguide with those micro cavities, results increasing intensity of waveguide output light. Inserting a tube in last row of waveguide, we have improved directionality of output light beam.

Keywords: photonic crystal, waveguide, micro cavity resonators, directional emission

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Authors: Mei-Hsiu Chi, Jyh-Yang Wu, Sheng-Gwo Chen

Abstract:

The diffusion-reaction equations are important Partial Differential Equations in mathematical biology, material science, physics, and so on. However, finding efficient numerical methods for diffusion-reaction systems on curved surfaces is still an important and difficult problem. The purpose of this paper is to present a convergent geometric method for solving the reaction-diffusion equations on closed surfaces by an O(r)-LTL configuration method. The O(r)-LTL configuration method combining the local tangential lifting technique and configuration equations is an effective method to estimate differential quantities on curved surfaces. Since estimating the Laplace-Beltrami operator is an important task for solving the reaction-diffusion equations on surfaces, we use the local tangential lifting method and a generalized finite difference method to approximate the Laplace-Beltrami operators and we solve this reaction-diffusion system on closed surfaces. Our method is not only conceptually simple, but also easy to implement.

Keywords: Close surfaces, high-order approach, numerical solutions, reaction-diffusion systems.

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Authors: M. Chen, S-Q. Zhang, X. Wang, D. Tate

Abstract:

This paper presents a numerical solution, namely limit and shakedown analysis, to predict the safety state of smart structures made of heterogeneous materials under unknown cyclic loadings, for instance, the flexure hinge in the micro-positioning stage driven by piezoelectric actuator. In combination of homogenization theory and finite-element method (FEM), the safety evaluation problem is converted to a large-scale nonlinear optimization programming for an acceptable bounded loading as the design reference. Furthermore, a general numerical scheme integrated with the FEM and interior-point-algorithm based optimization tool is developed, which makes the practical application possible.

Keywords: Limit state, shakedown analysis, homogenization, heterogeneous structure.

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Authors: Germán Santos-Boada, Jordi Domingo-Pascual

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Recently, in some places, optical-fibre access networks have been used with GPON technology belonging to organizations (in most cases public bodies) that act as neutral operators. These operators simultaneously provide network services to various telecommunications operators that offer integrated voice, data and television services. This situation creates new problems related to quality of service, since the interests of the users are intermingled with the interests of the operators. In this paper, we analyse this problem and consider solutions that make it possible to provide guaranteed quality of service for voice over IP, data services and interactive digital television.

Keywords: GPON networks, multioperator, quality of service, triple-play services.

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Authors: A. Tellaeche, R. Arana

Abstract:

Injection molding is a very complicated process to monitor and control. With its high complexity and many process parameters, the optimization of these systems is a very challenging problem. To meet the requirements and costs demanded by the market, there has been an intense development and research with the aim to maintain the process under control. This paper outlines the latest advances in necessary algorithms for plastic injection process and monitoring, and also a flexible data acquisition system that allows rapid implementation of complex algorithms to assess their correct performance and can be integrated in the quality control process. This is the main topic of this paper. Finally, to demonstrate the performance achieved by this combination, a real case of use is presented.

Keywords: Plastic injection, machine learning, rapid complex algorithm prototyping.

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Authors: B. G. Sampath, K. C. R. Perera, W. A. S. I. Wijesuriya, V. P. C. Dassanayake

Abstract:

In this paper the design, development and testing of a stabilizer control system for a Quad-rotor is presented which is focused on the maneuverability. The mechanical design is performed along with the design of the controlling algorithm which is devised using fuzzy logic controller. The inputs for the system are the angular positions and angular rates of the Quad-rotor relative to three axes. Then the output data is filtered from an accelerometer and a gyroscope through a Kalman filter. In the development of the stability controlling system Mandani fuzzy model is incorporated. The results prove that the fuzzy based stabilizer control system is superior in high dynamic disturbances compared to the traditional systems which use PID integrated stabilizer control systems.

Keywords: Fuzzy stabilizer, maneuverability, PID, Quad-rotor.

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