Search results for: LUDI de novo design method

Authors: Shaila Ahmed, Raghu Prasad Rao Metpally, Sreedhara Sangadala, Boojala Vijay B Reddy

Abstract:

Bone growth factors, such as Bone Morphogenic Protein-2 (BMP-2) have been approved by the FDA to replace grafting for some surgical interventions, but the high dose requirement limits its use in patients. Noggin, an extracellular protein, blocks the effect of BMP-2 by binding to BMP. Preventing the BMP-2/noggin interaction will help increase the free concentration of BMP-2 and therefore should enhance its efficacy to induce bone formation. The work presented here involves computational design of novel small molecule inhibitory agents of BMP-2/noggin interaction, based on our current understanding of BMP-2, and its known putative ligands (receptors and antagonists). A successful acquisition of such an inhibitory agent of BMP-2/noggin interaction would allow clinicians to reduce the dose required of BMP-2 protein in clinical applications to promote osteogenesis. The available crystal structures of the BMPs, its receptors, and the binding partner noggin were analyzed to identify the critical residues involved in their interaction. In presenting this study, LUDI de novo design method was utilized to perform virtual screening of a large number of compounds from a commercially available library against the binding sites of noggin to identify the lead chemical compounds that could potentially block BMP-noggin interaction with a high specificity.

Keywords: Transforming growth factor-beta, Bone morphogenic proteins, Noggin, LUDI de novo design method, CAP small molecules.

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Authors: Z. Babic, I. Veza, A. Balic, M. Crnjac

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The linear programming model is sometimes difficult to apply in real business situations due to its assumption of proportionality. This paper shows an example of how to use De Novo programming approach instead of linear programming. In the De Novo programming, resources are not fixed like in linear programming but resource quantities depend only on available budget. Budget is a new, important element of the De Novo approach. Two different production situations are presented: increasing costs and quantity discounts of raw materials. The focus of this paper is on advantages of the De Novo approach in the optimization of production plan for production company which produces souvenirs made from famous stone from the island of Brac, one of the greatest islands from Croatia.

Keywords: De Novo Programming, production plan, stone souvenirs, variable prices.

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Authors: Mohamed Hafez, Georg Hausner

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The full length mitochondrial small subunit ribosomal (mt-rns) gene has been characterized for Ophiostoma novo-ulmi subspecies americana. The gene was also characterized for Ophiostoma ulmi and a group II intron was noted in the mt-rns gene of O. ulmi. The insertion in the mt-rns gene is at position S952 and it is a group IIB1 intron that encodes a double motif LAGLIDADG homing endonuclease from an open reading frame located within a loop of domain III. Secondary structure models for the mt-rns RNA of O. novo-ulmi subsp. americana and O. ulmi were generated to place the intron within the context of the ribosomal RNA. The in vivo splicing of the O.ul-mS952 group II intron was confirmed with reverse transcription-PCR. A survey of 182 strains of Dutch Elm Diseases causing agents showed that the mS952 intron was absent in what is considered to be the more aggressive species O. novo-ulmi but present in strains of the less aggressive O. ulmi. This observation suggests that the O.ul-mS952 intron can be used as a PCR-based molecular marker to discriminate between O. ulmi and O. novo-ulmi subsp. americana.

Keywords: Dutch Elm Disease, group II introns, mtDNA, species identification

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Authors: Chien-Ju Li, Chun-Hui Yu, Chi-Chuan Hwang, Tsunglin Liu , Darby Tien-Hao Chang

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De novo genome assembly is always fragmented. Assembly fragmentation is more serious using the popular next generation sequencing (NGS) data because NGS sequences are shorter than the traditional Sanger sequences. As the data throughput of NGS is high, the fragmentations in assemblies are usually not the result of missing data. On the contrary, the assembled sequences, called contigs, are often connected to more than one other contigs in a complicated manner, leading to the fragmentations. False connections in such complicated connections between contigs, named a contig graph, are inevitable because of repeats and sequencing/assembly errors. Simplifying a contig graph by removing false connections directly improves genome assembly. In this work, we have developed a tool, SIMGraph, to resolve ambiguous connections between contigs using NGS data. Applying SIMGraph to the assembly of a fungus and a fish genome, we resolved 27.6% and 60.3% ambiguous contig connections, respectively. These results can reduce the experimental efforts in resolving contig connections.

Keywords: Contig graph, NGS, de novo assembly, scaffold.

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Authors: John R. Rose, James P. Cleveland, Alvin Fox

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Tandem mass spectrometry (MS/MS) is the engine driving high-throughput protein identification. Protein mixtures possibly representing thousands of proteins from multiple species are treated with proteolytic enzymes, cutting the proteins into smaller peptides that are then analyzed generating MS/MS spectra. The task of determining the identity of the peptide from its spectrum is currently the weak point in the process. Current approaches to de novo sequencing are able to compute candidate peptides efficiently. The problem lies in the limitations of current scoring functions. In this paper we introduce the concept of proteome signature. By examining proteins and compiling proteome signatures (amino acid usage) it is possible to characterize likely combinations of amino acids and better distinguish between candidate peptides. Our results strongly support the hypothesis that a scoring function that considers amino acid usage patterns is better able to distinguish between candidate peptides. This in turn leads to higher accuracy in peptide prediction.

Keywords: Tandem mass spectrometry, proteomics, scoring, peptide, de novo, mutual information

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Authors: Yunbin Yang, Liangli He, Fengjun Wang

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The essentiality of maintenance assessment and maintenance optimization in design stage is analyzed, and the existent problems of conventional maintenance design method are illuminated. MDMVM (Maintenance Design Method based Virtual Maintenance) is illuminated, and the process of MDMVM established, and the MDMVM architecture is given out. The key techniques of MDMVM are analyzed, and include maintenance design based KBE (Knowledge Based Engineering) and virtual maintenance based physically attribute. According to physical property, physically based modeling, visual object movement control, the simulation of operation force and maintenance sequence planning method are emphatically illuminated. Maintenance design system based virtual maintenance is established in foundation of maintenance design method.

Keywords: Digital mock-up, virtual maintenance, knowledge engineering, maintenance sequence planning.

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Authors: Tianchai Suksri, U-thai Sritheeravirojana, Arjin Numsomran, Viriya Kongrattana, Thongchai Werataweemart

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A control system design with Characteristic Ratio Assignment (CRA) is proven that effective for SISO control design. But the control system design for MIMO via CRA is not concrete procedure. In this paper presents the control system design method for quadruple-tank process via CRA. By using the decentralized method for both minimum phase and non-minimum phase are made. The results from PI and PID controller design via CRA can be illustrated the validity of our approach by MATLAB.

Keywords: CRA, Quadruple-Tank.

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Authors: Wenjuan Du

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The phase compensation method was proposed based on the concept of the damping torque analysis (DTA). It is a method for the design of a PSS (power system stabilizer) to suppress local-mode power oscillations in a single-machine infinite-bus power system. This paper presents the application of the phase compensation method for the design of a PSS in a multi-machine power system. The application is achieved by examining the direct damping contribution of the stabilizer to the power oscillations. By using linearized equal area criterion, a theoretical proof to the application for the PSS design is presented. Hence PSS design in the paper is an example of stable tending control by localized method.

Keywords: Phase compensation method, power system small-signal stability, power system stabilizer.

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Authors: Wei-Der Chang, Dai-Ming Chang, Eri-Wei Chiang, Chia-Hung Lin, Jian-Liung Chen

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In this paper, a fractional-order FIR differentiator design method using the differential evolution (DE) algorithm is presented. In the proposed method, the FIR digital filter is designed to meet the frequency response of a desired fractal-order differentiator, which is evaluated in the frequency domain. To verify the design performance, another design method considered in the time-domain is also provided. Simulation results reveal the efficiency of the proposed method.

Keywords: Fractional-order differentiator, FIR digital filter, Differential evolution algorithm.

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Authors: G. Kehl, P. Wagner

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A novel simulation method to determine the displacements of machine tools due to thermal factors is presented. The specific characteristic of this method is the employment of original CAD data from the design process chain, which is interpreted by an algorithm in terms of geometry-based allocation of convection and radiation parameters. Furthermore analogous models relating to the thermal behaviour of machine elements are automatically implemented, which were gained by extensive experimental testing with thermography imaging. With this a transient simulation of the thermal field and in series of the displacement of the machine tool is possible simultaneously during the design phase. This method was implemented and is already used industrially in the design of machining centres in order to improve the quality of herewith manufactured workpieces.

Keywords: Accuracy, design process, finite element analysis, machine tools, thermal simulation.

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Authors: Pavel Y. Tabakov

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An accurate optimal design of laminated composite structures may present considerable difficulties due to the complexity and multi-modality of the functional design space. The Big Bang – Big Crunch (BB-BC) optimization method is a relatively new technique and has already proved to be a valuable tool for structural optimization. In the present study the exceptional efficiency of the method is demonstrated by an example of the lay-up optimization of multilayered anisotropic cylinders based on a three-dimensional elasticity solution. It is shown that, due to its simplicity and speed, the BB-BC is much more efficient for this class of problems when compared to the genetic algorithms.

Keywords: Big Bang – Big Crunch method, optimization, composite laminates, pressure vessel.

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Authors: Yasunori Sugita, Toshinori Yoshikawa

Abstract:

The design problem of Infinite Impulse Response (IIR) digital filters is usually expressed as the minimization problem of the complex magnitude error that includes both the magnitude and phase information. However, the group delay of the filter obtained by solving such design problem may be far from the desired group delay. In this paper, we propose a design method of stable IIR digital filters with prespecified maximum group delay errors. In the proposed method, the approximation problems of the magnitude-phase and group delay are separately defined, and these two approximation problems are alternately solved using successive projections. As a result, the proposed method can design the IIR filters that satisfy the prespecified allowable errors for not only the complex magnitude but also the group delay by alternately executing the coefficient update for the magnitude-phase and the group delay approximation. The usefulness of the proposed method is verified through some examples.

Keywords: Filter design, Group delay approximation, Stable IIRfilters, Successive projection method.

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Authors: K.Ramesh, A.Nirmalkumar, G.Gurusamy

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In this paper, a new model order reduction phenomenon is introduced at the design stage of linear phase digital IIR filter. The complexity of a system can be reduced by adopting the model order reduction method in their design. In this paper a mixed method of model order reduction is proposed for linear IIR filter. The proposed method employs the advantages of factor division technique to derive the reduced order denominator polynomial and the reduced order numerator is obtained based on the resultant denominator polynomial. The order reduction technique is used to reduce the delay units at the design stage of IIR filter. The validity of the proposed method is illustrated with design example in frequency domain and stability is also examined with help of nyquist plot.

Keywords: Error index (J), Factor division method, IIR filter, Nyquist plot, Order reduction.

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Authors: P. Johansson, S. Mardh

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The present study proposes a usability test method, Atmosphere, to assess the fitness of components and interaction patterns of design systems. The method covers the user’s perception of the components of the system, the efficiency of the logic of the interaction patterns, perceived ease of use as well as the user’s understanding of the intended outcome of interactions. These aspects are assessed by combining measures of first impression, visual affordance and expectancy. The method was applied to a design system developed for the design of an electronic health record system. The study was conducted involving 15 healthcare personnel. It could be concluded that the Atmosphere method provides tangible data that enable human-computer interaction practitioners to analyze and categorize components and patterns based on perceived usability, success rate of identifying interactive components and success rate of understanding components and interaction patterns intended outcome.

Keywords: atomic design, atmosphere methodology, design system, expectancy testing, first impression testing, usability testing, visual affordance testing

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Authors: Chaoraingern J., Trisuwannawat T., Numsomran A.

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The author present PID controller design for following control of hard disk drive by characteristic ratio assignment method. The study in this paper concerns design of a PID controller which sufficiently robust to the disturbances and plant perturbations on following control of hard disk drive. Characteristic Ratio Assignment (CRA) is shown to be an efficient control technique to serve this requirement. The controller design by CRA is based on the choice of the coefficients of the characteristic polynomial of the closed loop system according to the convenient performance criteria such as equivalent time constant and ration of characteristic coefficient. Hence, in this study, CRA method is applied in PID controller design for following control of hard disk drive. Matlab simulation results shown that CRA design is fairly stable and robust whilst giving the convenience in controller-s parameters adjustment.

Keywords: Following Control, Hard Disk Drive, PID, CRA

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Authors: Ahmad Darabi, Hassan Moradi, Hossein Azarinfar

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In this paper presented initial design of Low Speed Axial Flux Permanent Magnet (AFPM) Machine with Non-Slotted TORUS topology type by use of certain algorithm (Appendix). Validation of design algorithm studied by means of selected data of an initial prototype machine. Analytically design calculation carried out by means of design algorithm and obtained results compared with results of Finite Element Method (FEM).

Keywords: Axial Flux Permanent Magnet (AFPM) Machine, Design Algorithm, Finite Element Method (FEM), TORUS

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Authors: Ö. Şenyiğit, A. Çolak

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It is of great importance for an architectural student to know the parameters through which he/she can conduct his/her design and makes his/her design effective in architectural education. Therefore; an empirical application study was carried out through the designing activity using the emulation model to support the design and design approaches of architectural students. During the investigation period, studies were done on the basic design elements and principles of the fall semester, and the emulation model, one of the designing methods that constitute the subject of the study, was fictionalized as three phased “recognition-interpretation-application”. As a result of the study, it was observed that when students were given a key method during the design process, their awareness increased and their aspects improved as well.

Keywords: Basic design, design education, design methods, emulation.

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Authors: Yasunori Sugita, Toshinori Yoshikawa, Naoyuki Aikawa

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Variable digital filters are useful for various signal processing and communication applications where the frequency characteristics, such as fractional delays and cutoff frequencies, can be varied. In this paper, we propose a design method of variable FIR digital filters with an approximate linear phase characteristic in the passband. The proposed variable FIR filters have some large attenuation in stopband and their large attenuation can be varied by spectrum parameters. In the proposed design method, a quasi-equiripple characteristic can be obtained by using an iterative weighted least square method. The usefulness of the proposed design method is verified through some examples.

Keywords: Weighted Least Squares Approximation, Variable FIR Filters, Low-Delay, Quasi-Equiripple

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Authors: Mohammadreza Vafaei, Amirali Moradi, Sophia C. Alih

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The method selected for the design of structures not only can affect their seismic vulnerability but also can affect their construction cost. For the design of steel structures, two distinct methods have been introduced by existing codes, namely allowable stress design (ASD) and load resistant factor design (LRFD). This study investigates the effect of using the aforementioned design methods on the seismic vulnerability and construction cost of steel structures. Specifically, a 20-story building equipped with special moment resisting frame and an eccentrically braced system was selected for this study. The building was designed for three different intensities of peak ground acceleration including 0.2 g, 0.25 g, and 0.3 g using the ASD and LRFD methods. The required sizes of beams, columns, and braces were obtained using response spectrum analysis. Then, the designed frames were subjected to nine natural earthquake records which were scaled to the designed response spectrum. For each frame, the base shear, story shears, and inter-story drifts were calculated and then were compared. Results indicated that the LRFD method led to a more economical design for the frames. In addition, the LRFD method resulted in lower base shears and larger inter-story drifts when compared with the ASD method. It was concluded that the application of the LRFD method not only reduced the weights of structural elements but also provided a higher safety margin against seismic actions when compared with the ASD method.

Keywords: Allowable stress design, load resistant factor design, nonlinear time history analysis, seismic vulnerability, steel structures.

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Authors: Johan Segeborn, Johan S. Carlson, Robert Bohlin, Rikard Söderberg

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This paper presents a method to support dynamic packing in cases when no collision-free path can be found. The method, which is primarily based on path planning and shrinking of geometries, suggests a minimal geometry design change that results in a collision-free assembly path. A supplementing approach to optimize geometry design change with respect to redesign cost is described. Supporting this dynamic packing method, a new method to shrink geometry based on vertex translation, interweaved with retriangulation, is suggested. The shrinking method requires neither tetrahedralization nor calculation of medial axis and it preserves the topology of the geometry, i.e. holes are neither lost nor introduced. The proposed methods are successfully applied on industrial geometries.

Keywords: Dynamic packing, path planning, shrinking.

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Authors: Chiung-Hui Chen

Abstract:

With the approaching of digital era, various interactive service platforms and systems support human beings- needs in lives by different contents and measures. Design strategies have gradually turned from function-based to user-oriented, and are often customized. In other words, how designers include users- value reaction in creation becomes the goal. Creative design service of interior design requires positive interaction and communication to allow users to obtain full design information, recognize the style and process of personal needs, develop creative service design, lower communication time and cost and satisfy users- sense of achievement. Thus, by constructing a co-design method, based on the communication between interior designers and users, this study recognizes users- real needs and provides the measure of co-design for designers and users.

Keywords: Co-Design, Customized, Design Service, Interactive Genetic Algorithm, Interior Design.

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Authors: Muniyasamy Kalanchiam, Baskar Mannai

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Topology Optimization is a defined as the method of determining optimal distribution of material for the assumed design space with functionality, loads and boundary conditions [1]. Topology optimization can be used to optimize shape for the purposes of weight reduction, minimizing material requirements or selecting cost effective materials [2]. Topology optimization has been implemented through the use of finite element methods for the analysis, and optimization techniques based on the method of moving asymptotes, genetic algorithms, optimality criteria method, level sets and topological derivatives. Case study of Typical “Fuselage design" is considered for this paper to explain the benefits of Topology Optimization in the design cycle. A cylindrical shell is assumed as the design space and aerospace standard pay loads were applied on the fuselage with wing attachments as constraints. Then topological optimization is done using Finite Element (FE) based software. This optimization results in the structural concept design which satisfies all the design constraints using minimum material.

Keywords: Fuselage, Topology optimization, payloads, designoptimization, Finite Element Analysis.

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Authors: A. Jabbari, M. Shakeri, A. Nabavi

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In this paper, a tooth shape optimization method for cogging torque reduction in Permanent Magnet (PM) motors is developed by using the Reduced Basis Technique (RBT) coupled by Finite Element Analysis (FEA) and Design of Experiments (DOE) methods. The primary objective of the method is to reduce the enormous number of design variables required to define the tooth shape. RBT is a weighted combination of several basis shapes. The aim of the method is to find the best combination using the weights for each tooth shape as the design variables. A multi-level design process is developed to find suitable basis shapes or trial shapes at each level that can be used in the reduced basis technique. Each level is treated as a separated optimization problem until the required objective – minimum cogging torque – is achieved. The process is started with geometrically simple basis shapes that are defined by their shape co-ordinates. The experimental design of Taguchi method is used to build the approximation model and to perform optimization. This method is demonstrated on the tooth shape optimization of a 8-poles/12-slots PM motor.

Keywords: PM motor, cogging torque, tooth shape optimization, RBT, FEA, DOE.

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Authors: Didier Casner, Jean Renaud, Remy Houssin, Dominique Knittel

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In this paper, a novel approach for the multidisciplinary design optimization (MDO) of complex mechatronic systems. This approach, which is a part of a global project aiming to include the MDO aspect inside an innovative design process. As a first step, the paper considers the MDO as a redesign approach which is limited to the parametric optimization. After defining and introducing the different keywords, the proposed method which is based on the V-Model which is commonly used in mechatronics.

Keywords: mechatronics, Multidisciplinary Design Optimization (MDO), multiobjective optimization, engineering design.

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Authors: N. Azadi-Tinat, H. Oraizi

Abstract:

Design of compact UWB multilayered microstrip filter with E-shape resonator is presented, which provides wide stopband up to 20 GHz and arbitrary impedance matching. The design procedure is developed based on the method of least squares and theory of N-coupled transmission lines. The dimensions of designed filter are about 11 mm × 11 mm and the three E-shape resonators are placed among four dielectric layers. The average insertion loss in the passband is less than 1 dB and in the stopband is about 30 dB up to 20 GHz. Its group delay in the UWB region is about 0.5 ns. The performance of the optimized filter design perfectly agrees with the microwave simulation softwares.

Keywords: Ultra-wideband, method of least square, multilayer microstrip filter, n-coupled transmission lines.

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Authors: Yael Dubinsky, Orit Hazzan

Abstract:

There is a constant need for hi-tech innovation to be decentralized to peripheral regions. This work describes how we applied Design Science Research (DSR) principles to define what we refer to as the Sea of Galilee (SoG) method. The goal of the SoG method is to harness existing and new technological initiatives in peripheral regions to create a socio-technological network that can initiate and maintain hi-tech activities. The SoG method consists of a set of principles, a stakeholder network, and actual hi-tech business initiatives, including their infrastructure and practices. The three cycles of DSR, the Relevance, Design, and Rigor cycles, lay out a research framework to sharpen the requirements, collect data from case studies, and iteratively refine the SoG method based on the existing knowledge base. We propose that the SoG method can be deployed by regional authorities that wish to be considered as smart regions (an extension of the notion of smart cities).

Keywords: Design Science Research, socio-technological initiatives, Sea of Galilee method, periphery stakeholder network, hi-tech initiatives.

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Authors: Jun-Oh Kim, Seol-Min Yang, Seok-Heum Baek, Sangmo Kang

Abstract:

In this paper, the shape design process is briefly discussed emphasizing the use of topology optimization in the conceptual design stage. The basic idea is to view feasible domains for sensitivity region concepts. In this method, the main process consists of two steps: as the design moves further inside the feasible domain using Taguchi method, and thus becoming more successful topology optimization, the sensitivity region becomes larger. In designing a double-eccentric butterfly valve, related to hydrodynamic performance and disc structure, are discussed where the use of topology optimization has proven to dramatically improve an existing design and significantly decrease the development time of a shape design. Computational Fluid Dynamics (CFD) analysis results demonstrate the validity of this approach.

Keywords: Double-eccentric butterfly valve, CFD, Topology optimization

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Authors: Jong-Jy Shyu, Soo-Chang Pei, Min-Han Chang

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In this paper, the least-squares design of variable fractional-delay (VFD) finite impulse response (FIR) digital differentiators is proposed. The used transfer function is formulated so that Farrow structure can be applied to realize the designed system. Also, the symmetric characteristics of filter coefficients are derived, which leads to the complexity reduction by saving almost a half of the number of coefficients. Moreover, all the elements of related vectors or matrices for the optimal process can be represented in closed forms, which make the design easier. Design example is also presented to illustrate the effectiveness of the proposed method.

Keywords: Differentiator, variable fractional-delay filter, FIR filter, least-squares method, Farrow structure.

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Authors: Sunil S. Mayengbam, S. Choudhury

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A method to predict the column size for displacement based design of reinforced concrete frame buildings with higher target inter storey drift is reported here. The column depth derived from empirical relation as a function of given beam section, target inter-story drift, building plan features and common displacement based design parameters is used. Regarding the high drift requirement, a minimum column-beam moment capacity ratio is maintained during capacity design. The method is used in designing four, eight and twelve story frame buildings with displacement based design for three percent target inter storey drift. Non linear time history analysis of the designed buildings are performed under five artificial ground motions to show that the columns are found elastic enough to avoid column sway mechanism assuring that for the design the column size can be used with or without minor changes.

Keywords: Column size, point of contra flexure, displacement based design, capacity design.

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Authors: Michal Polanský, C. Ardil

Abstract:

This paper shows a new method for design of fuzzy observers for Takagi-Sugeno systems. The method is based on Linear matrix inequalities (LMIs) and it allows to insert H constraint into the design procedure. The speed of estimation can tuned be specification of a decay rate of the observer closed loop system. We discuss here also the influence of parametric uncertainties at the output control system stability.

Keywords: H norm, Linear Matrix Inequalities, Observers, Takagi-Sugeno Systems, Parallel Distributed Compensation

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