Search results for: self-impinging secondary supersonic jet

Authors: Rabah Haoui

Abstract:

The aim of this work is to analyze a viscous flow around the axisymmetric blunt body taken into account the mesh size both in the free stream and into the boundary layer. The resolution of the Navier-Stokes equations is realized by using the finite volume method to determine the flow parameters and detached shock position. The numerical technique uses the Flux Vector Splitting method of Van Leer. Here, adequate time stepping parameter, CFL coefficient and mesh size level are selected to ensure numerical convergence. The effect of the mesh size is significant on the shear stress and velocity profile. The best solution is obtained with using a very fine grid. This study enabled us to confirm that the determination of boundary layer thickness can be obtained only if the size of the mesh is lower than a certain value limits given by our calculations.

Keywords: Supersonic flow, viscous flow, finite volume, blunt body.

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Authors: Rabah Haoui

Abstract:

Hypersonic flows around spatial vehicles during their reentry phase in planetary atmospheres are characterized by intense aerothermal phenomena. The aim of this work is to analyze high temperature flows around an axisymmetric blunt body taking into account chemical and vibrational non-equilibrium for air mixture species. For this purpose, a finite volume methodology is employed to determine the supersonic flow parameters around the axisymmetric blunt body, especially at the stagnation point and along the wall of spacecraft for several altitudes. This allows the capture shock wave before a blunt body placed in supersonic free stream. The numerical technique uses the Flux Vector Splitting method of Van Leer. Here, adequate time stepping parameter, along with CFL coefficient and mesh size level are selected to ensure numerical convergence, sought with an order of 10-8

Keywords: Chemical kinetic, dissociation, finite volumes, frozen, hypersonic flow, non-equilibrium, Reactive flow, supersonicflow , vibration.

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Authors: Rabah Haoui

Abstract:

The aim of this work is to analyze a viscous flow in the axisymmetric nozzle taken into account the mesh size both in the free stream and into the boundary layer. The resolution of the Navier- Stokes equations is realized by using the finite volume method to determine the supersonic flow parameters at the exit of convergingdiverging nozzle. The numerical technique uses the Flux Vector Splitting method of Van Leer. Here, adequate time stepping parameter, along with CFL coefficient and mesh size level is selected to ensure numerical convergence. The effect of the boundary layer thickness is significant at the exit of the nozzle. The best solution is obtained with using a very fine grid, especially near the wall, where we have a strong variation of velocity, temperature and shear stress. This study enabled us to confirm that the determination of boundary layer thickness can be obtained only if the size of the mesh is lower than a certain value limits given by our calculations.

Keywords: Supersonic flow, viscous flow, finite volume, nozzle

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Authors: Muhammad Yamin Younis, Muhammad Amjad Sohail, Tawfiqur Rahman, Zaka Muhammad, Saifur Rahman Bakaul

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The performance of Advection Upstream Splitting Method AUSM schemes are evaluated against experimental flow fields at different Mach numbers and results are compared with experimental data of subsonic, supersonic and hypersonic flow fields. The turbulent model used here is SST model by Menter. The numerical predictions include lift coefficient, drag coefficient and pitching moment coefficient at different mach numbers and angle of attacks. This work describes a computational study undertaken to compute the Aerodynamic characteristics of different air vehicles configurations using a structured Navier-Stokes computational technique. The CFD code bases on the idea of upwind scheme for the convective (convective-moving) fluxes. CFD results for GLC305 airfoil and cone cylinder tail fined missile calculated on above mentioned turbulence model are compared with the available data. Wide ranges of Mach number from subsonic to hypersonic speeds are simulated and results are compared. When the computation is done by using viscous turbulence model the above mentioned coefficients have a very good agreement with the experimental values. AUSM scheme is very efficient in the regions of very high pressure gradients like shock waves and discontinuities. The AUSM versions simulate the all types of flows from lower subsonic to hypersonic flow without oscillations.

Keywords: Subsonic, supersonic, Hypersonic, AUSM+, Drag Coefficient, lift Coefficient, Pitching moment coefficient, pressure Coefficient, turbulent flow.

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Authors: Nikol Žižková, Šárka Keprdová, Rostislav Drochytka

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The paper focuses on the study of the properties of cement-based composites produced using secondary crystallization (crystalline additive). In this study, cement mortar made with secondary crystallization was exposed to an aggressive environment and the influence of secondary crystallization on the degradation of the cementitious composite was investigated. The results indicate that the crystalline additive contributed to increasing the resistance of the cement-based composite to the attack of the selected environments (sodium sulphate solution and ammonium chloride solution).

Keywords: Secondary crystallization, cement-based composites, durability.

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Authors: N. Kulakova

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Thisresearch paper is dedicated to an actual issue in Latvia and in the whole European Union – development of the secondary materials management. The goal of this paper is to research the development of the secondary materials management in Latvia as a result to point out its main positive aspects and problems. In this research paper the author regards following issues: significance of the secondary materials management, current situation of the waste generation and utilization in Latvia comparing with other EU Member States, main problems and positive aspects of the secondary materials management in Latvia. The research author concludes that in last ten years a great work is done to develop the secondary materials market. Nevertheless following improvements are necessary: implementation of the packaging deposit system, development of the separate waste collection, increasing of the recycling capacity.

Keywords: sustainable development, secondary materials, separate waste collection, packaging deposit system.

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Authors: M. J. Park, S. H. Lee, C. H. Lee, O. M. Kwon

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This paper studies a secondary voltage control framework of the microgrids based on the consensus for a communication network of multiagent. The proposed control is designed by the communication network with one-way links. The communication network is modeled by a directed graph. At this time, the concept of sampling is considered as the communication constraint among each distributed generator in the microgrids. To analyze the sampling effects on the secondary voltage control of the microgrids, by using Lyapunov theory and some mathematical techniques, the sufficient condition for such problem will be established regarding linear matrix inequality (LMI). Finally, some simulation results are given to illustrate the necessity of the consideration of the sampling effects on the secondary voltage control of the microgrids.

Keywords: Microgrids, secondary control, multiagent, sampling, LMI.

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Authors: A. Haddad, H. Kbab

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A supersonic expansion cannot be achieved within a convergent-divergent nozzle if the flow velocity does not reach that of the sound at the throat. The computation of the flow field characteristics at the throat is thus essential to the nozzle developed thrust value and therefore to the aircraft or rocket it propels. Several approaches were developed in order to describe the transonic expansion, which takes place through the throat of a De-Laval convergent-divergent nozzle. They all allow reaching good results but showing a major shortcoming represented by their inability to describe the transonic flow field for nozzles having a small throat radius. The approach initially developed by Kliegel & Levine uses the velocity series development in terms of the normalized throat radius added to unity instead of solely the normalized throat radius or the traditional small disturbances theory approach. The present investigation carries out the application of these three approaches for different throat radiuses of curvature. The method using the normalized throat radius added to unity shows better results when applied to geometries integrating small throat radiuses.

Keywords: De-Laval nozzles, transonic calculations, transonic flow, supersonic nozzle.

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Authors: Shih-Yi Chao

Abstract:

The similarity comparison of RNA secondary structures is important in studying the functions of RNAs. In recent years, most existing tools represent the secondary structures by tree-based presentation and calculate the similarity by tree alignment distance. Different to previous approaches, we propose a new method based on maximum clique detection algorithm to extract the maximum common structural elements in compared RNA secondary structures. A new graph-based similarity measurement and maximum common subgraph detection procedures for comparing purely RNA secondary structures is introduced. Given two RNA secondary structures, the proposed algorithm consists of a process to determine the score of the structural similarity, followed by comparing vertices labelling, the labelled edges and the exact degree of each vertex. The proposed algorithm also consists of a process to extract the common structural elements between compared secondary structures based on a proposed maximum clique detection of the problem. This graph-based model also can work with NC-IUB code to perform the pattern-based searching. Therefore, it can be used to identify functional RNA motifs from database or to extract common substructures between complex RNA secondary structures. We have proved the performance of this proposed algorithm by experimental results. It provides a new idea of comparing RNA secondary structures. This tool is helpful to those who are interested in structural bioinformatics.

Keywords: Clique detection, labeled vertices, RNA secondary structures, subgraph, similarity.

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Authors: J. Kosikova, B. Vacenovska, M. Vyhnankova

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The paper reports on the subject of recycling and further use of secondary raw materials obtained from solar panels, which is becoming a very up to date topic in recent years. Recycling these panels is very difficult and complex, and the use of resulting secondary raw materials is still not fully resolved. Within the research carried out at the Brno University of Technology, new polymer materials used for industrial floors are being developed. Secondary raw materials are incorporated into these polymers as fillers. One of the tested filler materials was glass obtained from solar panels. The following text describes procedures and results of the tests that were performed on these materials, confirming the possibility of the use of solar panel glass in industrial polymer flooring systems.

Keywords: Fillers, industrial floors, recycling, secondary raw material, solar panel.

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Authors: Hezlina Mohd Hashim, Abdul Mutalib Embong, Zullina H. Shaari

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This study analyses the perceptions of secondary school students about the accounting profession in Malaysia. Fifty five form three and form four students who are taking accounting/commerce subjects were met. Individual-s perception data were collected through questionnaires. The results at the secondary school level suggest that the stereotypical negative image of the accountant ends, with students expressing the positive view of the work of an accountant. There were also gender differences in perceiving the accounting profession. Overall, the results of the study suggest that we are now in line in projecting positive and accurate perceptions of the accounting profession to secondary school students.

Keywords: Perceptions, secondary school students, accounting profession, Malaysia.

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Authors: Verónica Diaz Quezada

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This research examines the teaching models used by secondary math teachers when teaching logarithmic, quadratic and exponential functions. For this, descriptive case studies have been carried out on 5 secondary teachers. These teachers have been chosen from 3 scientific-humanistic and technical schools, in Chile. Data have been obtained through non-participant class observation and the application of a questionnaire and a rubric to teachers. According to the results, the didactic model that prevails is the one that starts with an interactive strategy, moves to a more content-based structure, and ends with a reinforcement stage. Nonetheless, there is always influence from teachers, their methods, and the group of students.

Keywords: Teaching models, math teachers, functions, secondary education.

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Authors: Douangmala Kounsana, Xiang Wen, Toru Takahashi

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After a strong earthquake occurs, a secondary disaster due to strong aftershocks, flood, landslide or heavy snow can possible to occur and the secondary disaster due to resident-s action also can possible to happen. However, until now seldom researchers have paid attention at it. This paper focused on the Inhabitant-s action after the strong earthquake occurs when a terrible even becomes calm. An inappropriate behavior of people with disadvantaged climate after the worse earthquake can bring a tragedy to their life.

Keywords: Sichuan Earthquake, Secondary Disaster, Inhabitant's Action, inappropriate behavior.

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Authors: Pamela L. Knox, Linda R. Guthrie

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Trauma in early life is widely regarded as a cause for adult mental health problems. This study explores the role of secondary trauma on later functioning in a sample of 359 university students enrolled in undergraduate psychology classes in the United States. Participants were initially divided into four groups based on 1) having directly experienced trauma (assaultive violence), 2) having directly experienced trauma and secondary traumatization through the unanticipated death of a close friend or family member or witnessing of an injury or shocking even), 3) having no experience of direct trauma but having experienced indirect trauma (secondary trauma), or 4) reporting no exposure. Participants completed a battery of measures on concepts associated with psychological functioning which included measures of psychological well-being, problem solving, coping and resiliency. Findings discuss differences in psychological functioning and resilience based on participants who experienced secondary traumatization and assaultive violence versus secondary traumatization alone.

Keywords: Psychological Functioning, Resiliency, Trauma, Abuse

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Authors: Ellen. A. Kalinga

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Moodle is an open source learning management system that enables creation of a powerful and flexible learning environment. Many organizations, especially learning institutions have customized Moodle open source LMS for their own use. In general open source LMSs are of great interest due to many advantages they offer in terms of cost, usage and freedom to customize to fit a particular context. Tanzania Secondary School e- Learning (TanSSe-L) system is the learning management system for Tanzania secondary schools. TanSSe-L system was developed using a number of methods, one of them being customization of Moodle Open Source LMS. This paper presents few areas on the way Moodle OS LMS was customized to produce a functional TanSSe-L system fitted to the requirements and specifications of Tanzania secondary schools’ context.

Keywords: LMS, Moodle, e-Learning, Tanzania, Secondary school.

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Authors: Rakesh Arasu, Sasitharan Ambicapathy, Sivaraj Ponnusamy, Mohanraj Murugesan, V. R. Sanal Kumar

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The flow field within the combustor of scramjet engine is very complex and poses a considerable challenge in the design and development of a supersonic combustor with an optimized geometry. In this paper comprehensive numerical studies on flow field characteristics of different cavity based scramjet combustors with transverse injection of hydrogen have been carried out for both non-reacting and reacting flows. The numerical studies have been carried out using a validated 2D unsteady, density based 1st-order implicit k-omega turbulence model with multi-component finite rate reacting species. The results show a wide variety of flow features resulting from the interactions between the injector flows, shock waves, boundary layers, and cavity flows. We conjectured that an optimized cavity is a good choice to stabilize the flame in the hypersonic flow, and it generates a recirculation zone in the scramjet combustor. We comprehended that the cavity based scramjet combustors having a bearing on the source of disturbance for the transverse jet oscillation, fuel/air mixing enhancement, and flameholding improvement. We concluded that cavity shape with backward facing step and 45o forward ramp is a good choice to get higher temperatures at the exit compared to other four models of scramjet combustors considered in this study.

Keywords: Flame holding, Hypersonic flow, Scramjet combustor, Supersonic combustor.

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Authors: Cory A. Bennett

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Teaching and learning through the use of discourse support students’ conceptual understanding by attending to key concepts and relationships. One discourse structure used in primary classrooms is number talks wherein students mentally calculate, discuss, and reason about the appropriateness and efficiency of their strategies. In the secondary mathematics classroom, the mathematics understudy does not often lend itself to mental calculations yet learning to reason, and articulate reasoning, is central to learning mathematics. This qualitative case study discusses how one secondary school in the Middle East adapted the number talk protocol for secondary mathematics classrooms. Several challenges in implementing ‘reasoning talks’ became apparent including shifting current discourse protocols and practices to a more student-centric model, accurately recording and probing student thinking, and specifically attending to reasoning rather than computations.

Keywords: Discourse, reasoning, secondary mathematics, teacher development.

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Authors: Leong Lee, Cyriac Kandoth, Jennifer L. Leopold, Ronald L. Frank

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Protein 3D structure prediction has always been an important research area in bioinformatics. In particular, the prediction of secondary structure has been a well-studied research topic. Despite the recent breakthrough of combining multiple sequence alignment information and artificial intelligence algorithms to predict protein secondary structure, the Q3 accuracy of various computational prediction algorithms rarely has exceeded 75%. In a previous paper [1], this research team presented a rule-based method called RT-RICO (Relaxed Threshold Rule Induction from Coverings) to predict protein secondary structure. The average Q3 accuracy on the sample datasets using RT-RICO was 80.3%, an improvement over comparable computational methods. Although this demonstrated that RT-RICO might be a promising approach for predicting secondary structure, the algorithm-s computational complexity and program running time limited its use. Herein a parallelized implementation of a slightly modified RT-RICO approach is presented. This new version of the algorithm facilitated the testing of a much larger dataset of 396 protein domains [2]. Parallelized RTRICO achieved a Q3 score of 74.6%, which is higher than the consensus prediction accuracy of 72.9% that was achieved for the same test dataset by a combination of four secondary structure prediction methods [2].

Keywords: data mining, protein secondary structure prediction, parallelization.

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Authors: O. Ali Alghtani, Y. Abdul-Ekhalq Ali, A. Abdul-Ekhalq Ali, A. Al Sadiq Abdul Majeed, N. Attian Al-Mohammadi, O. Mozel Alharbi, S. Mohamed Ismail, O. Ibrahim Asiri

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This study assessed the curricula of secondary schools given requirements to enhance the quality of life of students. The components of quality of life were described to build a list of standards and indicators. A questionnaire assessing the dimensions of mental (cognitive and emotional), physical, digital, and social health, and environmental awareness was prepared. A descriptive-analytical approach was used on a sample of 258 teachers and educational supervisors in Tabuk. The results indicated shortcomings in the secondary school curricula regarding developing standards and indicators of components of quality of life. Results also indicated that secondary school curricula incorporated few practices to improve student’s quality of life. No significant differences were found regarding the core subject, job, gender, and years of experience.

Keywords: Assessing curricula, teacher practices, quality of life, Secondary School.

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Authors: A. Ellen Kalinga, R. B. Burchard Bagile, Lena Trojer

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Information and Communications Technologies (ICT) has been integrated in education in many developing and developed countries alike, but the use of ICT in Tanzanian schools is dismal. Many Tanzanian secondary schools have no computers. The few schools with computers use them primarily for secretarial services and computer literacy training. The Tanzanian education system at other levels like secondary school level has to undergo substantial transformation, underscored by the growing application of new information and communication technology. This paper presents the e-readiness survey result from secondary schools in Tanzania. The paper also suggests how Tanzania can make use of the few present ICT resources to support and improve teaching and learning functions to improve performance and acquisition of knowledge by using e-Learning Management System (e-LMS).

Keywords: e-Learning, ICT, Object-Oriented, Participatorydesign.

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Authors: Manpreet Singh, Parvinder Singh Sandhu, Reet Kamal Kaur

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Protein structure determination and prediction has been a focal research subject in the field of bioinformatics due to the importance of protein structure in understanding the biological and chemical activities of organisms. The experimental methods used by biotechnologists to determine the structures of proteins demand sophisticated equipment and time. A host of computational methods are developed to predict the location of secondary structure elements in proteins for complementing or creating insights into experimental results. However, prediction accuracies of these methods rarely exceed 70%.

Keywords: Protein, Secondary Structure, Prediction, DNA, RNA.

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Authors: Payam Haghparast, Mikhail V. Sorin, Hakim Nesreddine

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The complex oblique shock phenomenon can be simply assumed as a normal shock at the constant area section to simulate a sharp pressure increase and velocity decrease in 1-D thermodynamic models. The assumed normal shock location is one of the greatest sources of error in ejector thermodynamic models. Most researchers consider an arbitrary location without justifying it. Our study compares the effect of normal shock place on ejector dimensions in 1-D models. To this aim, two different ejector experimental test benches, a constant area-mixing ejector (CAM) and a constant pressure-mixing (CPM) are considered, with different known geometries, operating conditions and working fluids (R245fa, R141b). In the first step, in order to evaluate the real value of the efficiencies in the different ejector parts and critical back pressure, a CFD model was built and validated by experimental data for two types of ejectors. These reference data are then used as input to the 1D model to calculate the lengths and the diameters of the ejectors. Afterwards, the design output geometry calculated by the 1D model is compared directly with the corresponding experimental geometry. It was found that there is a good agreement between the ejector dimensions obtained by the 1D model, for both CAM and CPM, with experimental ejector data. Furthermore, it is shown that normal shock place affects only the constant area length as it is proven that the inlet normal shock assumption results in more accurate length. Taking into account previous 1D models, the results suggest the use of the assumed normal shock location at the inlet of the constant area duct to design the supersonic ejectors.

Keywords: 1D model, constant area-mixing, constant pressure-mixing, normal shock location, ejector dimensions.

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Authors: Petri Vaattovaara, Zoran D. Ristovski, Martin Graus, Marcus Müller, EijaAsmi, Luca Di Liberto, StaffanSjögren, Douglas Orsini, Caroline Leck, Ari Laaksonen

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Due to climate warming and consequently due to ice and snow melting of the Arctic Ocean, the highly biologically active ocean surface area has been expanding quickly making possible longer marine biota growth seasons during polar summers. That increase the probability of the remote marine environment secondary contribution, especially secondary organic contribution, to the particle production and particle growth events and particle properties, consequently effecting on the open ocean, pack ice and ground based regions radiation budget and thus on the feedbacks between arctic biota, particles, clouds, and climate.

Keywords: Arctic Ocean, ice melting, nucleation, secondary organics, clouds, climate.

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Authors: Esam I. Jassim, Mohamed M. Awad

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Natural gas flow contains undesirable solid particles, liquid condensation, and/or oil droplets and requires reliable removing equipment to perform filtration. Recent natural gas processing applications are demanded compactness and reliability of process equipment. Since conventional means are sophisticated in design, poor in efficiency, and continue lacking robust, a supersonic nozzle has been introduced as an alternative means to meet such demands. A 3-D Convergent-Divergent Nozzle is simulated using commercial Code for pressure ratio (NPR) varies from 1.2 to 2. Six different shapes of nozzle are numerically examined to illustrate the position of shock-wave as such spot could be considered as a benchmark of particle separation. Rectangle, triangle, circular, elliptical, pentagon, and hexagon nozzles are simulated using Fluent Code with all have same cross-sectional area. The simple one-dimensional inviscid theory does not describe the actual features of fluid flow precisely as it ignores the impact of nozzle configuration on the flow properties. CFD Simulation results, however, show that nozzle geometry influences the flow structures including location of shock wave. The CFD analysis predicts shock appearance when p01/pa>1.2 for almost all geometry and locates at the lower area ratio (Ae/At). Simulation results showed that shock wave in Elliptical nozzle has the farthest distance from the throat among the others at relatively small NPR. As NPR increases, hexagon would be the farthest. The numerical result is compared with available experimental data and has shown good agreement in terms of shock location and flow structure.

Keywords: CFD, Particle Separation, Shock wave, Supersonic Nozzle.

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Authors: Lenka Hurtalová, Eva Tillová, Mária Chalupová, Juraj Belan, Milan Uhríčik

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The secondary alloy A226 is used for many automotive casting produced by mould casting and high pressure die casting. This alloy has excellent castability, good mechanical properties and cost-effectiveness. Production of primary aluminium alloys belong to heavy source fouling of life environs. The European Union calls for the emission reduction and reduction in energy consumption therefore increase production of recycled (secondary) aluminium cast alloys. The contribution is deal with influence of recycling on the quality of the casting made from A226 in automotive industry. The properties of the casting made from secondary aluminium alloys were compared with the required properties of primary aluminium alloys. The effect of recycling on microstructure was observed using combination different analytical techniques (light microscopy upon black-white etching, scanning electron microscopy - SEM upon deep etching and energy dispersive X-ray analysis - EDX). These techniques were used for the identification of the various structure parameters, which was used to compare secondary alloy microstructure with primary alloy microstructure.

Keywords: A226 secondary aluminium alloy, deep etching, mechanical properties, recycling foundry aluminium alloy.

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Authors: Muhammad Ridhuan Tony Lim Abdullah, Saedah Siraj

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The learning society has currently transformed from 'wired society' to become 'mobile society' which is facilitated by wireless network. To suit to this new paradigm, m-learning was given birth and rapidly building its prospect to be included in the future curriculum. Research and studies on m-learning spruced up in numerous aspects but there is still scarcity in studies on curriculum design of m-learning. This study is a part of an ongoing bigger study probing into the m-learning curriculum for secondary schools. The paper reports on the first phase of the study which aims to probe into the needs of curriculum design for m-learning at the secondary school level and the researcher adopted the needs analysis method. Data accrued from responses on survey questionnaires based on Lickert-point scale were analyzed statistically. The findings from this preliminary study serve as a basis for m-learning curriculum development for secondary schools.

Keywords: curriculum design, e-learning, future curriculum, m-learning

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Authors: G. M. Arun Prasath, N. Arthi

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This work proposed a multi-objective mathematical programming approach to select the appropriate supply network elements. The multi-item multi-objective production-distribution inventory model is formulated with possible constraints under fuzzy environment. The unit cost has taken under fuzzy environment. The inventory model and warehouse location model has combined to formulate the production-distribution inventory model. Warehouse location is important in supply chain network. Particularly, if a company maintains more selling stores it cannot maintain individual secondary warehouse near to each selling store. Hence, maintaining the optimum number of secondary warehouses is important. Hence, the combined mathematical model is formulated to reduce the total expenditure of the organization by arranging the network of minimum number of secondary warehouses. Numerical example has been taken to illustrate the proposed model.

Keywords: Fuzzy inventory model, warehouse location model, triangular fuzzy number, secondary warehouse, LINGO software.

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Authors: Minh Tuan Nguyen, Sang-Wook Lee

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In this study, numerical simulations on laminar flow in sinusoidal wavy shaped tubes were conducted for mean Reynolds number of 250, which is in the range of physiological flow-rate and investigated flow structures, pressure distribution and particle trajectories both in steady and periodic inflow conditions. For extensive comparisons, various wave lengths and amplitudes of sine function for geometry of tube models were employed. The results showed that small amplitude secondary curvature has significant influence on the nature of flow patterns and particle mixing mechanism. This implies that characterizing accurate geometry is essential in accurate predicting of in vivo hemodynamics and may motivate further study on any possibility of reflection of secondary flow on vascular remodeling and pathophysiology.

Keywords: Secondary curvature, Sinusoidal wavy tubes, Mixing Characteristics, Pulsatile flow, Hemodynamics.

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Authors: Maurizio Dapor, Isabel Abril, Pablo de Vera, Rafael Garcia-Molina

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The ionization yield of ion tracks in polymers and bio-molecular systems reaches a maximum, known as the Bragg peak, close to the end of the ion trajectories. Along the path of the ions through the materials, many electrons are generated, which produce a cascade of further ionizations and, consequently, a shower of secondary electrons. Among these, very low energy secondary electrons can produce damage in the biomolecules by dissociative electron attachment. This work deals with the calculation of the energy distribution of electrons produced by protons in a sample of polymethylmethacrylate (PMMA), a material that is used as a phantom for living tissues in hadron therapy. PMMA is also of relevance for microelectronics in CMOS technologies and as a photoresist mask in electron beam lithography. We present a Monte Carlo code that, starting from a realistic description of the energy distribution of the electrons ejected by protons moving through PMMA, simulates the entire cascade of generated secondary electrons. By following in detail the motion of all these electrons, we find the radial distribution of the energy that they deposit in PMMA for several initial proton energies characteristic of the Bragg peak.

Keywords: Monte Carlo method, secondary electrons, energetic ions, ion-beam cancer therapy, ionization cross section, polymethylmethacrylate, proton beams, secondary electrons, radial energy distribution.

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Authors: Rafał Adamczak

Abstract:

State-of-the-art methods for secondary structure (Porter, Psi-PRED, SAM-T99sec, Sable) and solvent accessibility (Sable, ACCpro) predictions use evolutionary profiles represented by the position specific scoring matrix (PSSM). It has been demonstrated that evolutionary profiles are the most important features in the feature space for these predictions. Unfortunately applying PSSM matrix leads to high dimensional feature spaces that may create problems with parameter optimization and generalization. Several recently published suggested that applying feature extraction for the PSSM matrix may result in improvements in secondary structure predictions. However, none of the top performing methods considered here utilizes dimensionality reduction to improve generalization. In the present study, we used simple and fast methods for features selection (t-statistics, information gain) that allow us to decrease the dimensionality of PSSM matrix by 75% and improve generalization in the case of secondary structure prediction compared to the Sable server.

Keywords: Secondary structure prediction, feature selection, position specific scoring matrix.

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