Search results for: Markov switching GARCH model

Authors: Zainab Magaji Musa, Nordin M. A. Rahman, Julaily Aida Jusoh

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The web services applications for digital reference service (WSDRS) of LIS model is an informal model that claims to reduce the problems of digital reference services in libraries. It uses web services technology to provide efficient way of satisfying users’ needs in the reference section of libraries. The formal WSDRS model consists of the Z specifications of all the informal specifications of the model. This paper discusses the formal validation of the Z specifications of WSDRS model. The authors formally verify and thus validate the properties of the model using Z/EVES theorem prover.

Keywords: validation, verification, formal, theorem prover

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Authors: Matthew C. Best

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Linear Multi-Input Multi-Output (MIMO) dynamic models can be identified, with no a priori knowledge of model structure or order, using a new Generalised Identifying Filter (GIF). Based on an Extended Kalman Filter, the new filter identifies the model iteratively, in a continuous modal canonical form, using only input and output time histories. The filter’s self-propagating state error covariance matrix allows easy determination of convergence and conditioning, and by progressively increasing model order, the best fitting reduced-order model can be identified. The method is shown to be resistant to noise and can easily be extended to identification of smoothly nonlinear systems.

Keywords: system identification, Kalman filter, linear model, MIMO, model order reduction

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Authors: Tejush Badal, Sanaa Alwidian

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Class diagrams are useful tools within the Unified Modelling Language (UML) to model and visualize the relationships between, and properties of objects within a system. As a system evolves over time and space (e.g., products), a series of models with several commonalities and variabilities create what is known as a model family. In circumstances where there are several versions of a model, examining each model individually, becomes expensive in terms of computation resources. To avoid performing redundant operations, this paper proposes an approach for representing a family of class diagrams into Union Models to represent model families using a single generic model. The paper aims to analyze and reason about a family of class diagrams using union models as opposed to individual analysis of each member model in the family. The union algorithm provides a holistic view of the model family, where the latter cannot be otherwise obtained from an individual analysis approach, this in turn, enhances the analysis performed in terms of speeding up the time needed to analyze a family of models together as opposed to analyzing individual models, one model at a time.

Keywords: analysis, class diagram, model family, unified modeling language, union model

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Authors: Mudavath Raju, Bhaskar Gugulothu, B. Rajendra Naik

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The rapid advances in Very Large Scale Integration (VLSI) technology has resulted in the reduction of minimum feature size to sub-quarter microns and switching time in tens of picoseconds or even less. As a result, the degradation of high-speed digital circuits due to signal integrity issues such as coupling effects, clock feedthrough, crosstalk noise and delay uncertainty noise. Crosstalk noise in VLSI interconnects is a major concern and reduction in VLSI interconnect has become more important for high-speed digital circuits. It is the most effectively considered in Deep Sub Micron (DSM) and Ultra Deep Sub Micron (UDSM) technology. Increasing spacing in-between aggressor and victim line is one of the technique to reduce the crosstalk. Guard trace or shield insertion in-between aggressor and victim is also one of the prominent options for the minimization of crosstalk. In this paper, far end crosstalk noise is estimated with mutual inductance and capacitance RLC interconnect model. Also investigated the extent of crosstalk in capacitive and inductively coupled interconnects to minimizes the same through shield insertion technique.

Keywords: VLSI, interconnects, signal integrity, crosstalk, shield insertion, guard trace, deep sub micron

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Authors: Pengcheng Xiang Jr., Xueqing Sun, Dong Ngoduy

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In the context of rapid urbanization, urban sprawl has brought about extensive negative impacts on ecosystems and the environment, resulting in a gradual shift from "incremental growth" to ‘stock growth’ in cities. A detailed urban growth boundary is a prerequisite for urban renewal and management. This study takes Shenyang City, China, as the study area and evaluates the spatial distribution of urban spatial suitability in the study area from the perspective of spatial constraints-suitability using multi-source data and simulates the future rigid and elastic growth boundaries of the city in the study area using the CA-Markov model. The results show that (1) the suitable construction area and moderate construction area in the study area account for 8.76% and 19.01% of the total area, respectively, and the suitable construction area and moderate construction area show a trend of distribution from the urban centre to the periphery, mainly in Shenhe District, the southern part of Heping District, the western part of Dongling District, and the central part of Dadong District; (2) the area of expansion of construction land in the study area in the period of 2023-2030 is 153274.6977hm2, accounting for 44.39% of the total area of the study area; (3) the rigid boundary of the study area occupies an area of 153274.6977 hm2, accounting for 44.39% of the total area of the study area, and the elastic boundary of the study area contains an area of 75362.61 hm2, accounting for 21.69% of the total area of the study area. The study constructed a method for urban growth boundary delineation, which helps to apply remote sensing to guide future urban spatial growth management and urban renewal.

Keywords: urban growth boundary, spatial constraints, spatial suitability, urban sprawl

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Authors: D. Thawinkarn, S. Wongbutlee

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The Social Change Leadership model is strongly aligned with administration’s mission. This research aims to examine the elements of social change leadership, build and develop leadership for social change, and evaluate effectiveness of leadership development model for social change. The research operation has 3 phases: model studies by in-depth interviews and survey research; drafting and creating model which verified by the experts; and trial of model in schools. The results showed that administrators and teachers have the elements of leadership for social change in moderate level. These elements are ranged descending from consciousness of self, common purpose, congruence, collaboration, commitment, citizenship, and controversy with civility. Model of leadership for social change is included the principles, objectives, content, process. Workshop process: Results show that the model of leadership development for social change in administrators and teachers leads to higher score in leadership evaluation prior to administering the operation.

Keywords: leadership, social change model, organization, administrators

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Authors: A. Lakrim, D. Tahri

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This paper sets out a behavioral macro-model of a Merged PiN and Schottky (MPS) diode based on silicon carbide (SiC). This model holds good for both static and dynamic electrothermal simulations for industrial applications. Its parameters have been worked out from datasheets curves by drawing on the optimization method: Simulated Annealing (SA) for the SiC MPS diodes made available in the industry. The model also adopts the Analog Behavioral Model (ABM) of PSPICE in which it has been implemented. The thermal behavior of the devices was also taken into consideration by making use of Foster’ canonical network as figured out from electro-thermal measurement provided by the manufacturer of the device.

Keywords: SiC MPS diode, electro-thermal, SPICE model, behavioral macro-model

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Authors: Funda Kul, İsmail Gür

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Pension scheme providers have to price mortality risk by accurate mortality forecasting method. There are many mortality-forecasting methods constructed and used in literature. The Lee-Carter model is the first model to consider stochastic improvement trends in life expectancy. It is still precisely used. Mortality forecasting is done by mortality index in the Lee-Carter model. It is assumed that mortality index fits ARIMA time series model. In this paper, we propose and use dynamic normal inverse gaussian distribution to modeling mortality indes in the Lee-Carter model. Using population mortality data for Italy, France, and Turkey, the model is forecasting capability is investigated, and a comparative analysis with other models is ensured by some well-known benchmarking criterions.

Keywords: mortality, forecasting, lee-carter model, normal inverse gaussian distribution

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Authors: C. Shih, J. R. Wang, H. C. Chang, S. W. Chen, S. C. Chiang, T. Y. Yu

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After the measurement uncertainty recapture (MUR) power uprates, Kuosheng nuclear power plant (NPP) was uprated the power from 2894 MWt to 2943 MWt. For power upgrade, several codes (e.g., TRACE, RELAP5, etc.) were applied to assess the safety of Kuosheng NPP. Hence, the main work of this research is to establish a RELAP5/MOD3.3 model of Kuosheng NPP with SNAP interface. The establishment of RELAP5/SNAP model was referred to the FSAR, training documents, and TRACE model which has been developed and verified before. After completing the model establishment, the startup test scenarios would be applied to the RELAP5/SNAP model. With comparing the startup test data and TRACE analysis results, the applicability of RELAP5/SNAP model would be assessed.

Keywords: RELAP5, TRACE, SNAP, BWR

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Authors: Hoda Ghavamipoor, S. Alireza Hashemi Golpayegani

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An approach to model the customer interaction with e-commerce websites is presented. Considering the service quality level as a predictive feature, we offer an improved method based on the Customer Behavior Model Graph (CBMG), a state-transition graph model. To derive the Quality of Service sensitive-CBMG (QoS-CBMG) model, process-mining techniques is applied to pre-processed website server logs which are categorized as ‘buy’ or ‘visit’. Experimental results on an e-commerce website data confirmed that the proposed method outperforms CBMG based method.

Keywords: customer behavior model, electronic commerce, quality of service, customer behavior model graph, process mining

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Authors: Ishit Sheth, Chandrasekhar Jinendran, Chinmaya Ranjan Sahu

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A fourteen degree of freedom (DOF) ride and handling control mathematical model is developed for a car using generalized boltzmann hamel equation which will create a basis for design of ride and handling controller. Mathematical model developed yield equations of motion for non-holonomic constrained systems in quasi-coordinates. The governing differential equation developed integrates ride and handling control of car. Model-based systems engineering approach is implemented for simulation using matlab/simulink, vehicle’s response in different DOF is examined and later validated using commercial software (ADAMS). This manuscript involves detailed derivation of full car vehicle model which provides response in longitudinal, lateral and yaw motion to demonstrate the advantages of the developed model over the existing dynamic model. The dynamic behaviour of the developed ride and handling model is simulated for different road conditions.

Keywords: Full Vehicle Model, MBSE, Non Holonomic Constraints, Boltzmann Hamel Equation

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Authors: Jolanta Tamošaitienė

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The article focuses on a developed comprehensive model to be used in an agile environment for the risk assessment and selection based on multi-attribute methods. The model is based on a multi-attribute evaluation of risk in construction, and the determination of their optimality criterion values are calculated using complex Multiple Criteria Decision-Making methods. The model may be further applied to risk assessment in an agile construction environment. The attributes of risk in a construction project are selected by applying the risk assessment condition to the construction sector, and the construction process efficiency in the construction industry accounts for the agile environment. The paper presents the comprehensive risk assessment model in an agile construction environment. It provides a background and a description of the proposed model and the developed analysis of the comprehensive risk assessment model in an agile construction environment with the criteria.

Keywords: assessment, environment, agile, model, risk

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Authors: Guowei Hou, Lixin Yu, Wei Zhuang, Hui Qin, Xue Yang

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Formal verification is proposed to ensure the correctness of the design and make functional verification more efficient. As cache plays a vital role in the design of System on Chip (SoC), and cache with Memory Management Unit (MMU) and cache memory unit makes the state space too large for simulation to verify, then a formal verification is presented for such system design. In the paper, a formal model checking verification flow is suggested and a new cache memory model which is called “exhaustive search model” is proposed. Instead of using large size ram to denote the whole cache memory, exhaustive search model employs just two cache blocks. For cache system contains data cache (Dcache) and instruction cache (Icache), Dcache memory model and Icache memory model are established separately using the same mechanism. At last, the novel model is employed to the verification of a cache which is module of a custom-built SoC system that has been applied in practical, and the result shows that the cache system is verified correctly using the exhaustive search model, and it makes the verification much more manageable and flexible.

Keywords: cache system, formal verification, novel model, system on chip (SoC)

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Authors: Owamah Hilary, O. C. Izinyon

Abstract:

Many existing biogas kinetic models are difficult to apply to substrates they were not developed for, as they are substrate specific. Biodegradability kinetic (BIK) model and maximum biogas production potential and stability assessment (MBPPSA) model were therefore developed in this study for the anaerobic co-digestion of food waste and maize husk. Biodegradability constant (k) was estimated as 0.11d-1 using the BIK model. The results of maximum biogas production potential (A) obtained using the MBPPSA model corresponded well with the results obtained using the popular but complex modified Gompertz model for digesters B-1, B-2, B-3, B-4, and B-5. The (If) value of MBPPSA model also showed that digesters B-3, B-4, and B-5 were stable, while B-1 and B-2 were unstable. Similar stability observation was also obtained using the modified Gompertz model. The MBPPSA model can therefore be used as alternative model for anaerobic digestion feasibility studies and plant design.

Keywords: biogas, inoculum, model development, stability assessment

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Authors: Chui Ka Shing

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This case study research attempts to examine the use of the Bar Model Method approach in learning and teaching mathematics in a primary school in Hong Kong. The objectives of the study are to find out to what extent (a) the Bar Model Method approach enhances the construction of students’ mathematics concepts, and (b) the school-based mathematics curriculum development with adopting the Bar Model Method approach. This case study illuminates the effectiveness of using the Bar Model Method to solve mathematics problems from Primary 1 to Primary 6. Some effective pedagogies and assessments were developed to strengthen the use of the Bar Model Method across year levels. Suggestions including school-based curriculum development for using Bar Model Method and further study were discussed.

Keywords: bar model method, curriculum development, mathematics education, problem solving

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Authors: B. H. Lee

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Nowadays, a grid-connected photovoltaic (PV) inverter is adopted in various places like as home, factory, because grid-connected PV inverter can reduce total power consumption by supplying electricity from PV array. In this paper, design and implementation of a 300 W grid-connected PV inverter are described. It is implemented with TI Piccolo DSP core and operated at 100 kHz switching frequency in order to reduce harmonic contents. The maximum operating input voltage is up to 45 V. The characteristics of the designed system that include maximum power point tracking (MPPT), single operation and battery charging are verified by simulation and experimental results.

Keywords: design, grid-connected, implementation, photovoltaic

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Authors: Irtaza M. Syed, Kaamran Raahemifar

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This paper presents modeling of a Alternating Current (AC) Photovoltaic (PV) module using Matlab/Simulink. The proposed AC-PV module model is simple, realistic, and application oriented. The model is derived on module level as compared to cell level directly from the information provided by the manufacturer data sheet. DC-PV module, MPPT control, BC, VSI and LC filter, all were treated as a single unit. The model accounts for changes in variations of both irradiance and temperature. The AC-PV module proposed model is simulated and the results are compared with the datasheet projected numbers to validate model’s accuracy and effectiveness. Implementation and results demonstrate simplicity and accuracy, as well as reliability of the model.

Keywords: PV modeling, AC PV Module, datasheet, VI curves irradiance, temperature, MPPT, Matlab/Simulink

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Authors: Pham Van Nha, Le Cam Binh

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Particle swarm optimization (PSO) is a population-based stochastic optimization algorithm. PSO was inspired by the natural behavior of birds and fish in migration and foraging for food. PSO is considered as a multidisciplinary optimization model that can be applied in various optimization problems. PSO’s ideas are simple and easy to understand but PSO is only applied in simple model problems. We think that in order to expand the applicability of PSO in complex problems, PSO should be described more explicitly in the form of a mathematical model. In this paper, we represent PSO in a mathematical model and apply in the multivariate data classification. First, PSOs general mathematical model (MPSO) is analyzed as a universal optimization model. Then, Model of Optimal Centroids (MOC) is proposed for the multivariate data classification. Experiments were conducted on some benchmark data sets to prove the effectiveness of MOC compared with several proposed schemes.

Keywords: analysis of optimization, artificial intelligence based optimization, optimization for learning and data analysis, global optimization

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Authors: Catherine Maware, Olufemi Adetunji

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The paper is aimed at developing a model to measure the impact of Lean manufacturing deployment on organizational performance. The model will help industry practitioners to assess the impact of implementing Lean constructs on organizational performance. It will also harmonize the measurement models of Lean performance with the house of Lean that seems to have become the industry standard. The sheer number of measurement models for impact assessment of Lean implementation makes it difficult for new adopters to select an appropriate assessment model or deployment methodology. A literature review is conducted to classify the Lean performance model. Pareto analysis is used to select the Lean constructs for the development of the model. The model is further formalized through the use of Structural Equation Modeling (SEM) in defining the underlying latent structure of a Lean system. An impact assessment measurement model developed can be used to measure Lean performance and can be adopted by different industries.

Keywords: impact measurement model, lean bundles, lean manufacturing, organizational performance

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Authors: Nada Poropat Jeletic, Gordana Hrzica

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Bilingual conversational corpora represent a meaningful and the most comprehensive data source for investigating the genuine contact phenomena in non-monitored bi-lingual speech productions. They can be particularly useful for bilingual research since some features of bilingual interaction can hardly be accessed with more traditional methodologies (e.g., elicitation tasks). The method of language sampling provides the resources for describing language interaction in a bilingual community and/or in bilingual situations (e.g. code-switching, amount of languages used, number of languages used, etc.). To capture these phenomena in genuine communication situations, such sampling should be as close as possible to spontaneous communication. Bilingual spoken corpus design is methodologically demanding. Therefore this paper aims at describing the methodological challenges that apply to the corpus design of the conversational corpus design of the Istrian Istrovenetian-Croatian Bilingual Corpus. Croatian is the first official language of the Croatian-Italian officially bilingual Istria County, while Istrovenetian is a diatopic subvariety of Venetian, a longlasting lingua franca in the Istrian peninsula, the mother tongue of the members of the Italian National Community in Istria and the primary code of informal everyday communication among the Istrian Italophone population. Within the CLARIN infrastructure, TalkBank is being used, as it provides relevant procedures for designing and analyzing bilingual corpora. Furthermore, it allows public availability allows for easy replication of studies and cumulative progress as a research community builds up around the corpus, while the tools developed within the field of corpus linguistics enable easy retrieval and analysis of information. The method of language sampling employed is kept at the level of spontaneous communication, in order to maximise the naturalness of the collected conversational data. All speakers have provided written informed consent in which they agree to be recorded at a random point within the period of one month after signing the consent. Participants are administered a background questionnaire providing information about the socioeconomic status and the exposure and language usage in the participants social networks. Recording data are being transcribed, phonologically adapted within a standard-sized orthographic form, coded and segmented (speech streams are being segmented into communication units based on syntactic criteria) and are being marked following the CHAT transcription system and its associated CLAN suite of programmes within the TalkBank toolkit. The corpus consists of transcribed sound recordings of 36 bilingual speakers, while the target is to publish the whole corpus by the end of 2020, by sampling spontaneous conversations among approximately 100 speakers from all the bilingual areas of Istria for ensuring representativeness (the participants are being recruited across three generations of native bilingual speakers in all the bilingual areas of the peninsula). Conversational corpora are still rare in TalkBank, so the Corpus will contribute to BilingBank as a highly relevant and scientifically reliable resource for an internationally established and active research community. The impact of the research of communities with societal bilingualism will contribute to the growing body of research on bilingualism and multilingualism, especially regarding topics of language dominance, language attrition and loss, interference and code-switching etc.

Keywords: conversational corpora, bilingual corpora, code-switching, language sampling, corpus design methodology

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Authors: T. Sahbani, M. Bouteraa, R. Wamkeue

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Wind Turbine are considered to be one of the more efficient system of energy production nowadays, a reason that leads the main industrial companies in wind turbine construction and researchers in over the world to look for better performance and one of the ways for that is the use of the synchronous permanent magnet generator. In this context, this work is about developing an analytical model that could simulate different situation in which the synchronous generator may go through, and of course this model match perfectly with the numerical and experimental model.

Keywords: MATLAB, synchronous permanent magnet generator, wind turbine, analytical model

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Authors: Hui Hsin Huang

Abstract:

The downstream manufactures will order their materials from different upstream suppliers to maintain a certain level of the demand. This paper proposes a bivariate model to portray this phenomenon of material demand. We use empirical data to estimate the parameters of model and evaluate the RMSD of model calibration. The results show that the model has better fitness.

Keywords: recency, ordering time, materials demand quantity, multi-source ordering

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Authors: Paul Han, Jun-Geol Baek

Abstract:

In the flat panel display industry, the scheduler and dispatching system to meet production target quantities and the deadline of production are the major production management system which controls each facility production order and distribution of WIP (Work in Process). In dispatching system, delivery time is a key factor for the time when a lot can be supplied to the facility. In this paper, we use survival analysis methods to identify main factors and a forecasting model of delivery time. Of survival analysis techniques to select important explanatory variables, the cox proportional hazard model is used to. To make a prediction model, the Accelerated Failure Time (AFT) model was used. Performance comparisons were conducted with two other models, which are the technical statistics model based on transfer history and the linear regression model using same explanatory variables with AFT model. As a result, the Mean Square Error (MSE) criteria, the AFT model decreased by 33.8% compared to the existing prediction model, decreased by 5.3% compared to the linear regression model. This survival analysis approach is applicable to implementing a delivery time estimator in display manufacturing. And it can contribute to improve the productivity and reliability of production management system.

Keywords: delivery time, survival analysis, Cox PH model, accelerated failure time model

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Authors: Aziz Ahmad, Guillermo Ramirez-Prado

Abstract:

Governments around the world encourage the use of solar water heating in residential houses due to the low maintenance requirements and efficiency of the solar collector water heating systems. The aim of this work is to study a domestic solar water heating system in a residential building to develop a model of the entire solar water heating system including flat-plate solar collector and storage tank. The proposed model is adaptable to any households and location. The model can be used to test different types of controllers and can provide efficiency as well as economic analysis. The proposed model is based on the heat and mass transfer equations along with assumptions applied in the model which can be modified for a variety of different solar water heating systems and sizes. Simulation results of the model were compared with the actual system which shows similar trends.

Keywords: solar thermal systems, solar water heating, solar collector model, hot water tank model, solar controllers

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Authors: Chakib Jerry, Mounir Jerry

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In this paper, a mathematical model of infested honey bees colonies is formulated in order to investigate Colony Collapse Disorder in a honeybee colony. CCD, as it is known, is a major problem on honeybee farms because of the massive decline in colony numbers. We introduce to the model a control variable which represents forager protection. We study the controlled model to derive conditions under which the bee colony can fight off epidemic. Secondly we study the problem of minimizing prevention cost under model’s dynamics constraints.

Keywords: honey bee, disease transmission model, disease control honeybees, optimal control

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Authors: T. Benazzouz, K. Auhmani

Abstract:

This paper presents a Hospital 4.0 Maturity Assessment Model based on the Industry 4.0 concepts. The self-assessment model defines current and target states of digital transformation by considering multiple aspects of a hospital and a healthcare supply chain. The developed model was validated and evaluated on real-life cases. The resulting model consisted of 5 domains: Technology, Strategy 4.0, Human resources 4.0 & Culture 4.0, Supply chain 4.0 management, and Patient journeys management. Each domain is further divided into several sub-domains, totally 34 sub-domains are identified, that reflect different facets of a hospital 4.0 mature organization.

Keywords: hospital 4.0, Industry 4.0, maturity assessment model, supply chain 4.0, patient

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Authors: Huilan Yao, Huaixin Zhang

Abstract:

Simulations of the transition flow of model propellers are important for predicting hydrodynamic performance and studying scale effects. In this paper, the transition flow of a model propeller under different loadings are simulated using a transition model provided by STAR-CCM+, and the influence of turbulence intensity (TI) on the transition, especially friction and pressure components of propeller performance, was studied. Before that, the transition model was applied to simulate the transition flow of a flat plate and an airfoil. Predicted transitions agree well with experimental results. Then, the transition model was applied for propeller simulations in open water, and the influence of TI was studied. Under the heavy and moderate loadings, thrust and torque of the propeller predicted by the transition model (different TI) and two turbulence models are very close and agree well with measurements. However, under the light loading, only the transition model with low TI predicts the most accurate results. Above all, the friction components of propeller performance predicted by the transition model with different TI have obvious difference.

Keywords: transition flow, model propellers, hydrodynamic performance, numerical simulation

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Authors: Mohamed Jama Madar, Oso Wilis

Abstract:

E-learning is the application of information technology in the teaching and learning process. This paper presents the Funnel model as a solution for the problems of implementation of e-learning in tertiary education institutions. While existing models such as TAM, theory-based e-learning and pedagogical model have been used over time, they have generally been found to be inadequate because of their tendencies to treat materials development, instructional design, technology, delivery and governance as separate and isolated entities. Yet it is matching components that bring framework of e-learning strategic implementation. The Funnel model enhances all these into one and applies synchronously and asynchronously to e-learning implementation where the only difference is modalities. Such a model for e-learning implementation has been lacking. The proposed Funnel model avoids ad-ad-hoc approach which has made other systems unused or inefficient, and compromised educational quality. Therefore, the proposed Funnel model should help tertiary education institutions adopt and develop effective and efficient e-learning system which meets users’ requirements.

Keywords: e-learning, pedagogical, technology, strategy

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Authors: Amir Deljoo

Abstract:

The endeavor to comprehend the existence have been the center of thought for human in form of different disciplines and now basically in physics as the theory of everything. Here, after a brief review of the basic frameworks of thought, and a history of thought since ancient up to present, a logical methodology is presented based on a core axiom after which a function, a proto-field and then a coordinates are explained. Afterwards a generalization to Standard Model is proposed as General Standard Model which is believed to be the base of the Unified Theory of Everything.

Keywords: general relativity, grand unified theory, quantum mechanics, standard model, theory of everything

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Authors: Danny Barash

Abstract:

Riboswitches are RNA genetic control elements that were originally discovered in bacteria and provide a unique mechanism of gene regulation. They work without the participation of proteins and are believed to represent ancient regulatory systems in the evolutionary timescale. One of the biggest challenges in riboswitch research is that many are found in prokaryotes but only a small percentage of known riboswitches have been found in certain eukaryotic organisms. The few examples of eukaryotic riboswitches were identified using sequence-based bioinformatics search methods that include some slight structural considerations. These pattern-matching methods were the first ones to be applied for the purpose of riboswitch detection and they can also be programmed very efficiently using a data structure called affix arrays, making them suitable for genome-wide searches of riboswitch patterns. However, they are limited by their ability to detect harder to find riboswitches that deviate from the known patterns. Several methods have been developed since then to tackle this problem. The most commonly used by practitioners is Infernal that relies on Hidden Markov Models (HMMs) and Covariance Models (CMs). Profile Hidden Markov Models were also carried out in the pHMM Riboswitch Scanner web application, independently from Infernal. Other computational approaches that have been developed include RMDetect by the use of 3D structural modules and RNAbor that utilizes Boltzmann probability of structural neighbors. We have tried to incorporate more sophisticated secondary structure considerations based on RNA folding prediction using several strategies. The first idea was to utilize window-based methods in conjunction with folding predictions by energy minimization. The moving window approach is heavily geared towards secondary structure consideration relative to sequence that is treated as a constraint. However, the method cannot be used genome-wide due to its high cost because each folding prediction by energy minimization in the moving window is computationally expensive, enabling to scan only at the vicinity of genes of interest. The second idea was to remedy the inefficiency of the previous approach by constructing a pipeline that consists of inverse RNA folding considering RNA secondary structure, followed by a BLAST search that is sequence-based and highly efficient. This approach, which relies on inverse RNA folding in general and our own in-house fragment-based inverse RNA folding program called RNAfbinv in particular, shows capability to find attractive candidates that are missed by Infernal and other standard methods being used for riboswitch detection. We demonstrate attractive candidates found by both the moving-window approach and the inverse RNA folding approach performed together with BLAST. We conclude that structure-based methods like the two strategies outlined above hold considerable promise in detecting riboswitches and other conserved RNAs of functional importance in a variety of organisms.

Keywords: riboswitches, RNA folding prediction, RNA structure, structure-based methods

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