Search results for: computational fluid dynamics (CFD)

Authors: Hiroshi Yamaguchi, Phillip C.-Y. Sheu, Ryo Fujita, Shigeo Tsujii

Abstract:

In this paper, the secure BioSemantic Scheme is presented to bridge biological/biomedical research problems and computational solutions via semantic computing. Due to the diversity of problems in various research fields, the semantic capability description language (SCDL) plays and important role as a common language and generic form for problem formalization. SCDL is expected the essential for future semantic and logical computing in Biosemantic field. We show several example to Biomedical problems in this paper. Moreover, in the coming age of cloud computing, the security problem is considered to be crucial issue and we presented a practical scheme to cope with this problem.

Keywords: Biomedical applications, private information retrieval (PIR), semantic capability description language (SCDL), semantic computing.

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Authors: I. Abuiziah, A. Oulhaj, K. Sebari, D. Ouazar, A. A. Saber

Abstract:

Fluid transient analysis is one of the more challenging and complicated flow problems in the design and the operation of water pipeline systems (wps). When transient conditions "water hammer" exists, the life expectancy of the wps can be adversely impacted, resulting in pump and valve failures and catastrophic pipe ruptures. Transient control has become an essential requirement for ensuring safe operation of wps. An accurate analysis and suitable protection devices should be used to protect wps. This paper presents the problem of modeling and simulation of transient phenomena in wps based on the characteristics method. Also, it provides the influence of using the protection devices to control the adverse effects due to excessive and low pressure occur in the transient. The developed model applied for main wps: pump combined with closed surge tank connected to a reservoir. The results obtained provide that the model is an efficient tool for water hammer analysis. Moreover; using the closed surge tank reduces the unfavorable effects of transients.

Keywords: Flow Transient, Water hammer, Pipeline System, Closed Surge Tank, Simulation Model, Protection Devices, Characteristics Method.

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Authors: Shadi Janbabaei, Hossein Gharaee Garakani, Naser Mohammadzadeh

Abstract:

Internet of things is a new concept that its emergence has caused ubiquity of sensors in human life, so that at any time, all data are collected, processed and transmitted by these sensors. In order to establish a secure connection, the first challenge is authentication between sensors. However, this challenge also requires some features so that the authentication is done properly. Anonymity, untraceability, and being lightweight are among the issues that need to be considered. In this paper, we have evaluated the authentication protocols and have analyzed the security vulnerabilities found in them. Then an improved light weight authentication protocol for sensor-to-sensor communications is presented which uses the hash function and logical operators. The analysis of protocol shows that security requirements have been met and the protocol is resistant against various attacks. In the end, by decreasing the number of computational cost functions, it is argued that the protocol is lighter than before.

Keywords: Anonymity, authentication, Internet of Things, lightweight, untraceablity.

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Authors: Tai-Hsi Wu, Jinn-Yi Yeh, Chin-Chih Chang

Abstract:

Cell formation is the first step in the design of cellular manufacturing systems. In this study, a general purpose computational scheme employing a hybrid tabu search algorithm as the core is proposed to solve the cell formation problem and its variants. In the proposed scheme, great flexibilities are left to the users. The core solution searching algorithm embedded in the scheme can be easily changed to any other meta-heuristic algorithms, such as the simulated annealing, genetic algorithm, etc., based on the characteristics of the problems to be solved or the preferences the users might have. In addition, several counters are designed to control the timing of conducting intensified solution searching and diversified solution searching strategies interactively.

Keywords: Cell formation problem, Tabu search

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Authors: S. Balaji, V. Swaminathan, K. Kannan

Abstract:

The Minimum Weighted Vertex Cover (MWVC) problem is a classic graph optimization NP - complete problem. Given an undirected graph G = (V, E) and weighting function defined on the vertex set, the minimum weighted vertex cover problem is to find a vertex set S V whose total weight is minimum subject to every edge of G has at least one end point in S. In this paper an effective algorithm, called Support Ratio Algorithm (SRA), is designed to find the minimum weighted vertex cover of a graph. Computational experiments are designed and conducted to study the performance of our proposed algorithm. Extensive simulation results show that the SRA can yield better solutions than other existing algorithms found in the literature for solving the minimum vertex cover problem.

Keywords: Weighted vertex cover, vertex support, approximation algorithms, NP-complete problem.

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Authors: Bhaveshkumar P. Patel, J. M. Prajapati

Abstract:

Excavators are high power machines used in the mining, agricultural and construction industry whose principal functions are digging (material removing), ground leveling and material transport operations. During the digging task there are certain unknown forces exerted by the bucket on the soil and the digging operation is repetitive in nature. Automation of the digging task can be performed by an automatically controlled excavator system, which is not only control the forces but also follow the planned digging trajectories. To develop such a controller for automated excavation, it is required to develop a dynamic model to describe the behavior of the control system during digging operation and motion of excavator with time. The presented work described a dynamic model needed for controller design and which is derived by applying Lagrange-Euler approach. The developed dynamic model is intended for further development of an automated excavation control system for light duty construction work and can be applied for heavy duty or all types of backhoe excavators.

Keywords: Backhoe excavator, controller, digging, excavation, trajectory.

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Authors: Chansiri Singhtaun

Abstract:

This paper proposes a mathematical model and examines the performance of an exact algorithm for a location– transportation problems in humanitarian relief. The model determines the number and location of distribution centers in a relief network, the amount of relief supplies to be stocked at each distribution center and the vehicles to take the supplies to meet the needs of disaster victims under capacity restriction, transportation and budgetary constraints. The computational experiments are conducted on the various sizes of problems that are generated. Branch and bound algorithm is applied for these problems. The results show that this algorithm can solve problem sizes of up to three candidate locations with five demand points and one candidate location with up to twenty demand points without premature termination.

Keywords: Disaster response, facility location, humanitarian relief, transportation.

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Authors: A.H.M.A.Rahim

Abstract:

The impact of fixed speed squirrel cage type as well as variable speed doubly fed induction generators (DFIG) on dynamic performance of a multimachine power system has been investigated. Detailed models of the various components have been presented and the integration of asynchronous and synchronous generators has been carried out through a rotor angle based transform. Simulation studies carried out considering the conventional dynamic model of squirrel cage asynchronous generators show that integration, as such, could degrade to the AC system performance transiently. This article proposes a frequency or power controller which can effectively control the transients and restore normal operation of fixed speed induction generator quickly. Comparison of simulation results between classical cage and doubly-fed induction generators indicate that the doubly fed induction machine is more adaptable to multimachine AC system. Frequency controller installed in the DFIG system can also improve its transient profile.

Keywords: Doubly-fed generator, Induction generator, Multimachine system modeling, Wind energy systems

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Authors: Gamal Abd El-Nasser A. Said, El-Sayed M. El-Horbaty

Abstract:

Container handling problems at container terminals are NP-hard problems. This paper presents an approach using discrete-event simulation modeling to optimize solution for storage space allocation problem, taking into account all various interrelated container terminal handling activities. The proposed approach is applied on a real case study data of container terminal at Alexandria port. The computational results show the effectiveness of the proposed model for optimization of storage space allocation in container terminal where 54% reduction in containers handling time in port is achieved.

Keywords: Container terminal, discrete-event simulation, optimization, storage space allocation.

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Authors: Mikhail Strongin

Abstract:

The mixing of two or more liquids is very common in many industrial applications from automotive to food processing. CFD simulations of these processes require comparison with test results. In many cases it is practically impossible. Therefore, comparison provides with scalable tests.  So, parameterization of the problem is sufficient to capture the performance of the mixer.

However, the influence of geometrical and thermo-physical parameters on the mixing is not well understood.

In this work influence of geometrical and thermal parameters was studied. It was shown that for full developed turbulent flows (Re > 10⁴⁾, Pe_t»const and concentration of secondary fluid ~ F(r/l).

In other words, the mixing is practically independent of total flow rate and scale for a given geometry and ratio of flow rates of mixing flows. This statement was proved in present work for different geometries and mixtures such as EGR and water-urea mixture.

Present study has been shown that the best way to improve the mixing is to establish geometry with the lowest Pe_t number possible by intensifying the turbulence in the domain. This is achievable by using step geometry, impinging flow EGR on a wall, or EGR jets, with a strong change in the flow direction, or using swirler like flow in the domain or combination all of these factors. All of these results are applicable to any mixtures of no compressible fluids.  

Keywords: CFD, mixing, fluids, parameterization, scalability.

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Authors: S. Khali, R. Nebbali, K. Bouhadef

Abstract:

A numerical investigation is performed for non Newtonian fluids flow between two concentric cylinders. The D2Q9 lattice Boltzmann model developed from the Bhatangar-Gross-Krook (LBGK) approximation is used to obtain the flow field for fluids obeying to the power-law model. The inner and outer cylinders rotate in the same and the opposite direction while the end walls are maintained at rest. The combined effects of the Reynolds number (Re) of the inner and outer cylinders, the radius ratio (η) as well as the power-law index (n) on the flow characteristics are analyzed for an annular space of a finite aspect ratio (Γ). Two flow modes are obtained: a primary mode (laminar stable regime) and a secondary mode (laminar unstable regime). The so obtained flow structures are different from one mode to another. The transition critical Reynolds number Re_c from the primary to the secondary mode is analyzed for the co-courant and counter-courant flows. This critical value increases as n increases. The prediction of the swirling flow of non Newtonians fluids in axisymmetric geometries is shown in the present work.

Keywords: Taylor-Couette flows, non Newtonian fluid, Lattice Boltzmann method.

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Authors: M. Heydari, S. A. Torabi

Abstract:

The problem of lot sizing, sequencing and scheduling multiple products in flow line production systems has been studied by several authors. Almost all of the researches in this area assumed that setup times and costs are sequence –independent even though sequence dependent setups are common in practice. In this paper we present a new mixed integer non linear program (MINLP) and a heuristic method to solve the problem in sequence dependent case. Furthermore, a genetic algorithm has been developed which applies this constructive heuristic to generate initial population. These two proposed solution methods are compared on randomly generated problems. Computational results show a clear superiority of our proposed GA for majority of the test problems.

Keywords: Economic lot scheduling problem, finite horizon, genetic algorithm, mixed zero-one nonlinear programming, sequence-dependent.

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Authors: Lei Shi, Zhibin Yu, Artur J. Jaworski, Abdulrahman S. Abduljalil

Abstract:

This paper investigates vortex shedding processes occurring at the end of a stack of parallel plates, due to an oscillating flow induced by an acoustic standing wave within an acoustic resonator. Here, Particle Image Velocimetry (PIV) is used to quantify the vortex shedding processes within an acoustic cycle phase-by-phase, in particular during the “ejection" of the fluid out of the stack. Standard hot-wire anemometry measurement is also applied to detect the velocity fluctuations near the end of the stack. Combination of these two measurement techniques allowed a detailed analysis of the vortex shedding phenomena. The results obtained show that, as the Reynolds number varies (by varying the plate thickness and drive ratio), different flow patterns of vortex shedding are observed by the PIV measurement. On the other hand, the time-dependent hot-wire measurements allow obtaining detailed frequency spectra of the velocity signal, used for calculating characteristic Strouhal numbers. The impact of the plate thickness and the Reynolds number on the vortex shedding pattern has been discussed. Furthermore, a detailed map of the relationship between the Strouhal number and Reynolds number has been obtained and discussed.

Keywords: Oscillatory flow, Parallel-plate thermoacoustic stack, Strouhal numbers, Vortex shedding.

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Authors: S. Balaji, N. Revathi

Abstract:

Connected dominating set (CDS) problem in unit disk graph has signi£cant impact on an ef£cient design of routing protocols in wireless sensor networks, where the searching space for a route is reduced to nodes in the set. A set is dominating if all the nodes in the system are either in the set or neighbors of nodes in the set. In this paper, a simple and ef£cient heuristic method is proposed for £nding a minimum connected dominating set (MCDS) in ad hoc wireless networks based on the new parameter support of vertices. With this parameter the proposed heuristic approach effectively £nds the MCDS of a graph. Extensive computational experiments show that the proposed approach outperforms the recently proposed heuristics found in the literature for the MCD

Keywords: ad hoc wireless networks, dominating sets, unit disk graphs, heuristic.

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Authors: E. N. Hasanov, K. Y. Yusifova, M. A. Ali

Abstract:

Rabies is a zoonotic disease that causes acute encephalitis in domestic and wild carnivores. The goal of this investigation was to analyze the data on oral vaccination of wild canids and stray dogs in Azerbaijan. Before the start of vaccination campaign conducted by the IDEA (International Dialogue for Environmental Action) Animal Care Center (IACC), all rabies cases in Azerbaijan for the period of 2017-2020 were analyzed. So, 30 regions for oral immunization with the Rabadrop vaccine were selected. In total, 95.9 thousand doses of baits were scattered in 30 regions, 970 (0.97%) remained intact. In addition, a campaign to sterilize and vaccinate stray dogs and cats undoubtedly had a positive impact on reducing the dynamics of rabies incidence. During the period 2017-2020, 2,339 dogs and 2,962 cats were sterilized and vaccinated under this program. It can be noted that the risk of rabies infection can be reduced through special preventive measures against disease reservoirs, which include oral immunization of wild and stray animals.

Keywords: Rabies, vaccination, oral immunization, wild canids, stray dogs, vaccine, disease reservoirs.

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Authors: Ahmad Forouzantabar

Abstract:

this paper presents a novel neural network controller with composite adaptation low to improve the trajectory tracking problems of biped robots comparing with classical controller. The biped model has 5_link and 6 degrees of freedom and actuated by Plated Pneumatic Artificial Muscle, which have a very high power to weight ratio and it has large stoke compared to similar actuators. The proposed controller employ a stable neural network in to approximate unknown nonlinear functions in the robot dynamics, thereby overcoming some limitation of conventional controllers such as PD or adaptive controllers and guarantee good performance. This NN controller significantly improve the accuracy requirements by retraining the basic PD/PID loop, but adding an inner adaptive loop that allows the controller to learn unknown parameters such as friction coefficient, therefore improving tracking accuracy. Simulation results plus graphical simulation in virtual reality show that NN controller tracking performance is considerably better than PD controller tracking performance.

Keywords: Biped robot, Neural network, Plated Pneumatic Artificial Muscle, Composite adaptation

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Authors: A. Shahsavari, M. Nili-Ahmadabadi

Abstract:

This paper presents an innovative one-dimensional optimization of a transonic compressor based on the radial equilibrium theory by means of increasing blade loading. Firstly, the rotor blade of the transonic compressor is redesigned based on the constant span-wise deHaller number and diffusion. The code is applied to extract compressor meridional plane and blade to blade geometry containing rotor and stator in order to design blade three-dimensional view. A structured grid is generated for the numerical domain of fluid. Finer grids are used for regions near walls to capture boundary layer effects and behavior. RANS equations are solved by finite volume method for rotating zones (rotor) and stationary zones (stator). The experimental data, available for the performance map of NASA Rotor67, is used to validate the results of simulations. Then, the capability of the design method is validated by CFD that is capable of predicting the performance map. The numerical results of new geometry show about 19% increase in pressure ratio and 11% improvement in overall efficiency of the transonic stage; however, the design point mass flow rate of the new compressor is 5.7% less than that of the original compressor.

Keywords: One dimensional design, deHaller number, radial equilibrium, transonic compressor.

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Authors: Henry Hexmoor, Kailash Yelasani

Abstract:

We present vehicular platooning as a special case of crowd-sensing framework where sharing sensory information among a crowd is used for their collective benefit. After offering an abstract policy that governs processes involving a vehicular platoon, we review several common scenarios and components surrounding vehicular platooning. We then present a simulated prototype that illustrates efficiency of road usage and vehicle travel time derived from platooning. We have argued that one of the paramount benefits of platooning that is overlooked elsewhere, is the substantial computational savings (i.e., economizing benefits) in acquisition and processing of sensory data among vehicles sharing the road. The most capable vehicle can share data gathered from its sensors with nearby vehicles grouped into a platoon.

Keywords: Cloud network, collaboration, Internet of Things, social network.

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Authors: Akram Khaleghei Ghosheh Balagh, Viliam Makis, Leila Jafari

Abstract:

In this paper, we present a new maintenance model for a partially observable system subject to two failure modes, namely a catastrophic failure and a failure due to the system degradation. The system is subject to condition monitoring and the degradation process is described by a hidden Markov model. A cost-optimal Bayesian control policy is developed for maintaining the system. The control problem is formulated in the semi-Markov decision process framework. An effective computational algorithm is developed, illustrated by a numerical example.

Keywords: Partially observable system, hidden Markov model, competing risks, multivariate Bayesian control.

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Authors: Zane Turner, Kevin Labille, Susan Gauch

Abstract:

Sentiment analysis is a broad and expanding field that aims to extract and classify opinions from textual data. Lexicon-based approaches are based on the use of a sentiment lexicon, i.e., a list of words each mapped to a sentiment score, to rate the sentiment of a text chunk. Our work focuses on predicting stock price change using a sentiment lexicon built from financial conference call logs. We present a method to generate a sentiment lexicon based upon an existing probabilistic approach. By using a domain-specific lexicon, we outperform traditional techniques and demonstrate that domain-specific sentiment lexicons provide higher accuracy than generic sentiment lexicons when predicting stock price change.

Keywords: Lexicon, sentiment analysis, stock movement prediction., computational finance.

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Authors: Kew Lee Ming, Norhashidah Hj. Mohd. Ali

Abstract:

In a previous work, we presented the numerical solution of the two dimensional second order telegraph partial differential equation discretized by the centred and rotated five-point finite difference discretizations, namely the explicit group (EG) and explicit decoupled group (EDG) iterative methods, respectively. In this paper, we utilize a domain decomposition algorithm on these group schemes to divide the tasks involved in solving the same equation. The objective of this study is to describe the development of the parallel group iterative schemes under OpenMP programming environment as a way to reduce the computational costs of the solution processes using multicore technologies. A detailed performance analysis of the parallel implementations of points and group iterative schemes will be reported and discussed.

Keywords: Telegraph equation, explicit group iterative scheme, domain decomposition algorithm, parallelization.

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Authors: S. Chonsatidjamroen , K-N. Areerak, K-L. Areerak

Abstract:

This paper presents the averaging model of a buck converter derived from the generalized state-space averaging method. The sliding mode control is used to regulate the output voltage of the converter and taken into account in the model. The proposed model requires the fast computational time compared with those of the full topology model. The intensive time-domain simulations via the exact topology model are used as the comparable model. The results show that a good agreement between the proposed model and the switching model is achieved in both transient and steady-state responses. The reported model is suitable for the optimal controller design by using the artificial intelligence techniques.

Keywords: Generalized state-space averaging method, buck converter, sliding mode control, modeling, simulation.

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Authors: A. Kumar, V. Devadas

Abstract:

India has the most year-round favorable sunny conditions along with the second-highest solar irradiation in the world, the country holds the potential to become the global solar hub. The solar and wind-based generation capacity has skyrocketed in India with the successful effort of the Ministry of Renewable Energy, whereas the potential of rooftop based solar power generation has yet to be explored for proposed solar cities in India. The research aims to analyze the gap in the energy scenario in Jodhpur City and proposes interventions of solar energy generation systems as a catalyst for urban development. The research is based on the system concept which deals with simulation between the city system as a whole and its interactions between different subsystems. A system-dynamics based mathematical model is developed by identifying the control parameters using regression and correlation analysis to assess the gap in energy sector. The base model validation is done using the past 10 years timeline data collected from secondary sources. Further, energy consumption and solar energy generation-based projection are made for testing different scenarios to conclude the feasibility for maintaining the city level energy independence till 2031.

Keywords: City, consumption, energy, generation.

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Authors: Brahim Brahmi, Mohammed Hamza Laraki, Mohammad Habibur Rahman, Islam M. Rasedul, M. Assad Uz-Zaman

Abstract:

The humanoid robot, specifically the NAO robot must be able to provide a highly dynamic performance on the soccer field. Maintaining the balance of the humanoid robot during the required motion is considered as one of a challenging problems especially when the robot is subject to external disturbances, as contact with other robots. In this paper, a dynamic controller is proposed in order to ensure a robust walking (stabilization) and to improve the dynamic balance of the robot during its contact with the environment (external disturbances). The generation of the trajectory of the center of mass (CoM) is done by a model predictive controller (MPC) conjoined with zero moment point (ZMP) technique. Taking into account the properties of the rotational dynamics of the whole-body system, a modified previous control mixed with feedback control is employed to manage the angular momentum and the CoM’s acceleration, respectively. This latter is dedicated to provide a robust gait of the robot in the presence of the external disturbances. Simulation results are presented to show the feasibility of the proposed strategy.

Keywords: Preview control, walking, stabilization, humanoid robot.

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Authors: G. Quiroga-Cubides, A. Díaz, M. Gómez

Abstract:

The genus Azotobacter has been widely used as bio-fertilizer due to its significant effects on the stimulation and promotion of plant growth in various agricultural species of commercial interest. In order to obtain significantly viable cellular concentration, a scale-up strategy for a liquid fermentation process (SmF) with two strains of A. chroococcum (named Ac1 and Ac10) was validated and adjusted at laboratory and pilot scale. A batch fermentation process under previously defined conditions was carried out on a biorreactor Infors®, model Minifors of 3.5 L, which served as a baseline for this research. For the purpose of increasing process efficiency, the effect of the reduction of stirring speed was evaluated in combination with a fed-batch-type fermentation laboratory scale. To reproduce the efficiency parameters obtained, a scale-up strategy with geometric and fluid dynamic behavior similarities was evaluated. According to the analysis of variance, this scale-up strategy did not have significant effect on cellular concentration and in laboratory and pilot fermentations (Tukey, p > 0.05). Regarding air consumption, fermentation process at pilot scale showed a reduction of 23% versus the baseline. The percentage of reduction related to energy consumption reduction under laboratory and pilot scale conditions was 96.9% compared with baseline.

Keywords: Azotobacter chroococcum, scale-up, liquid fermentation, fed-batch process.

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Authors: E. Kharaishvili, M. Chavleishvili, M. Natsvaladze

Abstract:

The article presents the trends in Georgian wine market development and evaluates the competitive advantages of Georgia to enter the wine market based on its customs, traditions and historical practices combined with modern technologies. In order to analyze the supply of wine, dynamics of vineyard land area and grape varieties are discussed, trends in wine production are presented, trends in export and import are evaluated, local wine market, its micro and macro environments are studied and analyzed based on the interviews with experts and analysis of initial recording materials. For strengthening its position on the international market, the level of competitiveness of Georgian wine is defined, which is evaluated by “ex-ante” and “ex-post” methods, as well as by four basic and two additional factors of the Porter’s diamond method; potential advantages and disadvantages of Georgian wine are revealed. Conclusions are made by identifying the factors that hinder the development of Georgian wine market. Based on the conclusions, relevant recommendations are developed.

Keywords: Georgian wine market, competitive advantage, bio wine, export-import, Porter's diamond model.

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Authors: Zane Turner, Kevin Labille, Susan Gauch

Abstract:

Sentiment analysis is a broad and expanding field that aims to extract and classify opinions from textual data. Lexicon-based approaches are based on the use of a sentiment lexicon, i.e., a list of words each mapped to a sentiment score, to rate the sentiment of a text chunk. Our work focuses on predicting stock price change using a sentiment lexicon built from financial conference call logs. We introduce a method to generate a sentiment lexicon based upon an existing probabilistic approach. By using a domain-specific lexicon, we outperform traditional techniques and demonstrate that domain-specific sentiment lexicons provide higher accuracy than generic sentiment lexicons when predicting stock price change.

Keywords: Computational finance, sentiment analysis, sentiment lexicon, stock movement prediction.

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Authors: Hiroki Yoshikai, Shin’ichi Arakawa, Tetsuya Takine, Masayuki Murata

Abstract:

API (Application Programming Interface) economy is expected to create new value by converting corporate services such as information processing and data provision into APIs and using these APIs to connect services. Understanding dynamics of a market of API economy under strategies of participants is crucial to fully maximize the values of API economy. To capture the behavior of a market in which the number of participants changes over time, we present a time-evolving market model for a platform in which API providers who provide APIs to service providers participate in addition to service providers and consumers. Then, we use the market model to clarify the role API providers play in expanding market participants and forming ecosystems. The results show that the platform with API providers increased the number of market participants by 67% and decreased the cost to develop services by 25% compared to the platform without API providers. Furthermore, during the expansion phase of the market, it is found that the profits of participants are mostly the same when 70% of the revenue from consumers is distributed to service providers and API providers. It is also found that, when the market is mature, the profits of the service provider and API provider will decrease significantly due to their competitions and the profit of the platform increases.

Keywords: API Economy, ecosystem, platform, API providers.

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Authors: Keun Woo Lee, Minky Son, Chanin Park, Ayoung Baek

Abstract:

Certain tRNA synthetases have developed highly accurate molecular machinery to discriminate their cognate amino acids. Those aaRSs achieve their goal via editing reaction in the Connective Polypeptide 1 (CP1). Recently mutagenesis studies have revealed the critical importance of residues in the CP1 domain for editing activity and X-ray structures have shown binding mode of noncognate amino acids in the editing domain. To pursue molecular mechanism for amino acid discrimination, molecular modeling studies were performed. Our results suggest that aaRS bind the noncognate amino acid more tightly than the cognate one. Finally, by comparing binding conformations of the amino acids in three systems, the amino acid binding mode was elucidated and a discrimination mechanism proposed. The results strongly reveal that the conserved threonines are responsible for amino acid discrimination. This is achieved through side chain interactions between T252 and T247/T248 as well as between those threonines and the incoming amino acids.

Keywords: Amino acid discrimination, Binding free energy Leucyl-tRNAsynthetase, Molecular dynamics.

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Authors: Yunxia Zhang, Jiti Zhou, Jianbo Guo, Xiuhong Zhang, Lihong Zhao, Shouzhi Yuan

Abstract:

Novel nitrogen removal technologies via nitrite pathway attract increasing interest in recent years. In this study, batch experiments were performed to investigate nitrite accumulation characteristics and shifts in nitrifying community structure at different growth environments including ammonia concentration, pH and alkalinity. It was found that nitrite accumulation ratios were maintained at around 95% at studied conditions, and the optimum pH and Alk/N (ratio between alkalinity and nitrogen) for ammonium oxidization were 8.5 and 8.33, respectively. Fluorescence in situ hybridization analysis of nitrifying bacteria showed that high free ammonia (from influent ammonium or caused by high pH) significantly altered the structure of nitrifying community, leading to abundance of ammonia-oxidizing bacteria (AOB), especially Nitrososmonas, and inhibition of nitrite-oxidizing bacteria (NOB). The results suggest that free ammonia plays more important role than other studied conditions on nitrite accumulation.

Keywords: Partial nitrification, Nitrite accumulation, Nitrifyingbacteria, Fluorescence in situ hybridization (FISH).

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