Search results for: system dynamics modelling

Authors: Seyed Ali Jafari, Mohammad Ghomi Avili, Emad Benhelal

Abstract:

In this study, a mathematical model was proposed and the accuracy of this model was assessed to predict the growth of Pseudomonas aeruginosa and rhamnolipid production under nitrogen limiting (sodium nitrate) fed-batch fermentation. All of the parameters used in this model were achieved individually without using any data from the literature. The overall growth kinetic of the strain was evaluated using a dual-parallel substrate Monod equation which was described by several batch experimental data. Fed-batch data under different glycerol (as the sole carbon source, C/N=10) concentrations and feed flow rates were used to describe the proposed fed-batch model and other parameters. In order to verify the accuracy of the proposed model several verification experiments were performed in a vast range of initial glycerol concentrations. While the results showed an acceptable prediction for rhamnolipid production (less than 10% error), in case of biomass prediction the errors were less than 23%. It was also found that the rhamnolipid production by P. aeruginosa was more sensitive at low glycerol concentrations. Based on the findings of this work, it was concluded that the proposed model could effectively be employed for rhamnolipid production by this strain under fed-batch fermentation on up to 80 g l- 1 glycerol.

Keywords: Fed-batch culture, glycerol, kinetic parameters, modelling, Pseudomonas aeruginosa, rhamnolipid.

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Authors: Toru Murayama, Akinori Nagano, Zhi-Wei Luo

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In this research, we study a control method of a multivehicle system while considering the limitation of communication range for each vehicles. When we control networked vehicles with limitation of communication range, it is important to control the communication network structure of a multi-vehicle system in order to keep the network-s connectivity. From this, we especially aim to control the network structure to the target structure. We formulate the networked multi-vehicle system with some disturbance and the communication constraints as a hybrid dynamical system, and then we study the optimal control problems of the system. It is shown that the system converge to the objective network structure in finite time when the system is controlled by the receding horizon method. Additionally, the optimal control probrems are convertible into the mixed integer problems and these problems are solvable by some branch and bound algorithm.

Keywords: Hybrid system, multi-vehicle system, receding horizon control, topology control.

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Authors: Ramin Javadzadeh, Zahra Afsahi, MohammadReza Meybodi

Abstract:

The hybridization of artificial immune system with cellular automata (CA-AIS) is a novel method. In this hybrid model, the cellular automaton within each cell deploys the artificial immune system algorithm under optimization context in order to increase its fitness by using its neighbor-s efforts. The hybrid model CA-AIS is introduced to fix the standard artificial immune system-s weaknesses. The credibility of the proposed approach is evaluated by simulations and it shows that the proposed approach achieves better results compared to standard artificial immune system.

Keywords: Artificial Immune System, Cellular Automat, neighborhood

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Authors: L. C. Gómez-Pavón, M. A. Rojas Aparicio, E. Juárez Ruiz, M. A. Flores Guerrero, and O. Gómez-de la Fuente

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In this work the design and characterization of an optoelectronic automated measurement system it is presented. The optoelectronic devices of this system are an optical transmitter, the optical components and the optical receiver, which were selected for a great precision of the system. The mechanical system allows free displacement of the components as well as the devices that generate the movement. The results, length and profile of the objects are display in Lab View.

Keywords: Automated, optoelectronic, triangulation method.

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Authors: Tofigh Hamidavi, Sepehr Abrishami, Pasquale Ponterosso, David Begg

Abstract:

Structural design and analysis is an important and time-consuming process, particularly at the conceptual design stage. Decisions made at this stage can have an enormous effect on the entire project, as it becomes ever costlier and more difficult to alter the choices made early on in the construction process. Hence, optimisation of the early stages of structural design can provide important efficiencies in terms of cost and time. This paper suggests a structural design optimisation (SDO) framework in which Genetic Algorithms (GAs) may be used to semi-automate the production and optimisation of early structural design alternatives. This framework has the potential to leverage conceptual structural design innovation in Architecture, Engineering and Construction (AEC) projects. Moreover, this framework improves the collaboration between the architectural stage and the structural stage. It will be shown that this SDO framework can make this achievable by generating the structural model based on the extracted data from the architectural model. At the moment, the proposed SDO framework is in the process of validation, involving the distribution of an online questionnaire among structural engineers in the UK.

Keywords: Building Information Modelling, BIM, Genetic Algorithm, GA, architecture-engineering-construction, AEC, Optimisation, structure, design, population, generation, selection, mutation, crossover, offspring.

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Authors: J. Rizk, Y. Chaiko

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This paper shows the potential system benefits of simple tracking solar system using a stepper motor and light sensor. This method is increasing power collection efficiency by developing a device that tracks the sun to keep the panel at a right angle to its rays. A solar tracking system is designed, implemented and experimentally tested. The design details and the experimental results are shown.

Keywords: Renewable Energy, Power Optimization.

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Authors: Jamaiah H. Yahaya, Aziz Deraman, Abdul Razak Hamdan, Yusmadi Yah Jusoh

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One of the most essential issues in software products is to maintain it relevancy to the dynamics of the user’s requirements and expectation. Many studies have been carried out in quality aspect of software products to overcome these problems. Previous software quality assessment models and metrics have been introduced with strengths and limitations. In order to enhance the assurance and buoyancy of the software products, certification models have been introduced and developed. From our previous experiences in certification exercises and case studies collaborating with several agencies in Malaysia, the requirements for user based software certification approach is identified and demanded. The emergence of social network applications, the new development approach such as agile method and other varieties of software in the market have led to the domination of users over the software. As software become more accessible to the public through internet applications, users are becoming more critical in the quality of the services provided by the software. There are several categories of users in web-based systems with different interests and perspectives. The classifications and metrics are identified through brain storming approach with includes researchers, users and experts in this area. The new paradigm in software quality assessment is the main focus in our research. This paper discusses the classifications of users in web-based software system assessment and their associated factors and metrics for quality measurement. The quality model is derived based on IEEE structure and FCM model. The developments are beneficial and valuable to overcome the constraints and improve the application of software certification model in future.

Keywords: Software certification model, user centric approach, software quality factors, metrics and measurements, web-based system.

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Authors: Hema Nair

Abstract:

This paper presents a new system developed in Java® for pattern recognition and pattern summarisation in multi-band (RGB) satellite images. The system design is described in some detail. Results of testing the system to analyse and summarise patterns in SPOT MS images and LANDSAT images are also discussed.

Keywords: Pattern recognition, image analysis, feature extraction, blackboard component, linguistic summary.

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Authors: Rattanathip Rattanachai, Piyachai Petchyen, Kunyanuth Kularbphettong

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This paper describes the development of a Weight- Balancing Control System based on the Android Operating System and it provides recommendations on ways of balancing of user’s weight based on daily metabolism process and need so that user can make informed decisions on his or her weight controls. The system also depicts more information on nutrition details. Furthermore, it was designed to suggest to users what kinds of foods they should eat and how to exercise in the right ways. We describe the design methods and functional components of this prototype. To evaluate the system performance, questionnaires for system usability and Black Box Testing were used to measure expert and user satisfaction. The results were satisfactory as followed: Means for experts and users were 3.94 and 4.07 respectively.

Keywords: Weight-Balancing Control, Android Operating System, daily metabolism, Black Box Testing.

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Authors: Daiming Wang

Abstract:

In this paper, a neutral impulsive competition system with distributed delays is studied by using Mawhin-s coincidence degree theory and the mean value theorem of differential calculus. Sufficient conditions on the existence of positive periodic solution of the system are obtained.

Keywords: Neutral impulsive delay system, competitive system, coincidence degree, periodic solution, existence.

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Authors: Goodarz Sabetian, Sajjad Moshfe

Abstract:

Control system for hi-tech industries could be realized generally and deeply by a special document. Vast heavy industries such as power plants with a large number of I/O signals are controlled by a distributed control system (DCS). This system comprises of so many parts from field level to high control level, and junior instrument engineers may be confused by this enormous information. The key document which can solve this problem is “control configuration system diagram” for each type of DCS. This is a road map that covers all of activities respect to control system in each industrial plant and inevitable to be studied by whom corresponded. It plays an important role from designing control system start point until the end; deliver the system to operate. This should be inserted in bid documents, contracts, purchasing specification and used in different periods of project EPC (engineering, procurement, and construction). Separate parts of DCS are categorized here in order of importance and a brief description and some practical plan is offered. This article could be useful for all instrument and control engineers who worked is EPC projects.

Keywords: Control, configuration, DCS, power plant, bus.

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Authors: Hideyuki Shintani, Ichiro Koshijima

Abstract:

In Cyber Physical System (CPS), if there are a large number of persons in the process, a role of person in CPS might be different comparing with the one-man system. It is also necessary to consider how Human-in-The-Loop Cyber Physical Systems (HiTLCPS) ensure safety of each person in the loop process. In this paper, the authors discuss a system safety framework with an illustrative example with STAMP model to clarify what point for safety should be considered and what role of person in the should have.

Keywords: Cyber Physical System, Human-in-The-Loop, Safety, STAMP model.

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Authors: Bhupeshwaran Mani, S. Radha, A. Jawahar, A. Sivasubramanian

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Here, we study the characteristic feature of conventional (ON-OFF keying) and soliton based transmission system. We consider 20Gbps transmission system implemented with Conventional Single Mode Fiber (C-SMF) to examine the role of Gaussian pulse which is the characteristic of conventional propagation and Hyperbolic-secant pulse which is the characteristic of soliton propagation in it. We note the influence of these pulses with respect to different dispersion lengths and soliton period in conventional and soliton system respectively and evaluate the system performance in terms of Quality factor. From the analysis, we could prove that the soliton pulse has the consistent performance even for long distance without dispersion compensation than the conventional system as it is robust to dispersion. For the length of transmission of 200Km, soliton system yielded Q of 33.958 while the conventional system totally exhausted with Q=0.

Keywords: Soliton, dispersion length, Soliton period, Return-tozero (RZ), Q-factor.

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Authors: T. Delval, C. Sauvage, Q. Jullien, R. Viano, T. Diallo, B. Collignan, G. Picinbono

Abstract:

In the context of the international spread of COVID-19, the Centre Scientifique et Technique du Bâtiment (CSTB) has led a joint research with the French government authorities Hauts-de-Seine department, to analyse the risk in school spaces according to their configuration, ventilation system and spatial segmentation strategy. This paper describes the main results of this joint research. A multidisciplinary team involving experts in indoor air quality/ventilation, pedestrian movements and IT domains was established to develop a COVID risk analysis tool based on Building Information Model. The work started with specific analysis on two pilot schools in order to provide for the local administration specifications to minimize the spread of the virus. Different recommendations were published to optimize/validate the use of ventilation systems and the strategy of student occupancy and student flow segmentation within the building. This COVID expertise has been digitized in order to manage a quick risk analysis on the entire building that could be used by the public administration through an easy user interface implemented in a free BIM Management software. One of the most interesting results is to enable a dynamic comparison of different ventilation system scenarios and space occupation strategy inside the BIM model. This concurrent engineering approach provides users with the optimal solution according to both ventilation and pedestrian flow expertise.

Keywords: BIM, knowledge management, system expert, risk management, indoor ventilation, pedestrian movement, integrated design.

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Authors: M. Belén Prendes-Gero, Celestino González-Nicieza, M. Inmaculada Alvarez-Fernández

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Roof collapse is one of the problems with a higher frequency in most of the mines of all countries, even now. There are many reasons that may cause the roof to collapse, namely the mine stress activities in the mining process, the lack of vigilance and carelessness or the complexity of the geological structure and irregular operations. This work is the result of the analysis of one accident produced in the “Mary” coal exploitation located in northern Spain. In this accident, the roof of a crossroad of excavated galleries to exploit the “Morena” Layer, 700 m deep, collapsed. In the paper, the work done by the forensic team to determine the causes of the incident, its conclusions and recommendations are collected. Initially, the available documentation (geology, geotechnics, mining, etc.) and accident area were reviewed. After that, laboratory and on-site tests were carried out to characterize the behaviour of the rock materials and the support used (metal frames and shotcrete). With this information, different hypotheses of failure were simulated to find the one that best fits reality. For this work, the software of finite differences in three dimensions, FLAC 3D, was employed. The results of the study confirmed that the detachment was originated as a consequence of one sliding in the layer wall, due to the large roof span present in the place of the accident, and probably triggered as a consequence of the existence of a protection pillar insufficient. The results allowed to establish some corrective measures avoiding future risks. For example, the dimensions of the protection zones that must be remained unexploited and their interaction with the crossing areas between galleries, or the use of more adequate supports for these conditions, in which the significant deformations may discourage the use of rigid supports such as shotcrete. At last, a grid of seismic control was proposed as a predictive system. Its efficiency was tested along the investigation period employing three control equipment that detected new incidents (although smaller) in other similar areas of the mine. These new incidents show that the use of explosives produces vibrations which are a new risk factor to analyse in a next future.

Keywords: Forensic analysis, hypothesis modelling, roof failure, seismic monitoring.

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Authors: Mohammed Bilal

Abstract:

The precise prediction of aerodynamic behavior is necessary for the design and optimization of airfoils for a variety of applications. Turbulence, a phenomenon of complex and irregular flow, significantly affects the aerodynamic properties of airfoils. Therefore, turbulence modeling is essential for accurately predicting the behavior of airfoils in simulations. This study investigates five commonly employed turbulence models: Spalart-Allmaras (SA) model, k-epsilon model, k-omega model, Reynolds Stress Model (RSM), and Large Eddy Simulation (LES) model. The paper includes a comparison of the models' precision, computational expense, and applicability to various flow conditions. The strengths and weaknesses of each model are highlighted, allowing researchers and engineers to make informed decisions regarding simulations of specific airfoils. Unquestionably, the continuous development of turbulence modeling will contribute to further improvements in airfoil design and optimization, which will be advantageous to numerous industries.

Keywords: Computational fluid dynamics, airfoil, turbulence, aircraft.

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Authors: Latifeh PourMohammadBagher

Abstract:

In this paper I have developed a system for evaluating the degree of fear emotion that the intelligent agent-based system may feel when it encounters to a persecuting event. In this paper I want to describe behaviors of emotional agents using human behavior in terms of the way their emotional states evolve over time. I have implemented a fuzzy inference system using Java environment. As the inputs of this system, I have considered three parameters related on human fear emotion. The system outputs can be used in agent decision making process or choosing a person for team working systems by combination the intensity of fear to other emotion intensities.

Keywords: Emotion simulation, Fear, Fuzzy intelligent agent

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Authors: Djamel Saba, Fatima Zohra Laallam, Brahim Berbaoui

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This paper presents a contribution to the design of a multi-agent for the energy management system in a hybrid energy system (SEH). The multi-agent-based energy-coordination management system (MA-ECMS) is based mainly on coordination between agents. The agents share the tasks and exchange information through communications protocols to achieve the main goal. This intelligent system can fully manage the consumption and production or simply to make proposals for action he thinks is best. The initial step is to give a presentation for the system that we want to model in order to understand all the details as much as possible. In our case, it is to implement a system for simulating a process control of energy management.

Keywords: Multi agents system, hybrid energy system, communications protocols, modelization, simulation, control process, energy management.

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Authors: Xinyan Zhang, Zhipeng Tan, Shan Fan

Abstract:

The first layer of defense against data loss is the backup data. This paper implements an agent-based network backup system used the backup, server-storage and server-backup agent these tripartite construction, and the snapshot and hierarchical index are used in the NSBS. It realizes the control command and data flow separation, balances the system load, thereby improving efficiency of the system backup and recovery. The test results show the agent-based network backup system can effectively improve the task-based concurrency, reasonably allocate network bandwidth, the system backup performance loss costs smaller and improves data recovery efficiency by 20%.

Keywords: Agent, network backup system, three architecture model, NSBS.

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Authors: Karim Hamidi Machekposhti, Hossein Sedghi, Abdolrasoul Telvari, Hossein Babazadeh

Abstract:

Floods have huge environmental and economic impact. Therefore, flood prediction is given a lot of attention due to its importance. This study analysed the annual maximum streamflow (discharge) (AMS or AMD) of Karkheh River in Karkheh River Basin for flood predicting using ARIMA model. For this purpose, we use the Box-Jenkins approach, which contains four-stage method model identification, parameter estimation, diagnostic checking and forecasting (predicting). The main tool used in ARIMA modelling was the SAS and SPSS software. Model identification was done by visual inspection on the ACF and PACF. SAS software computed the model parameters using the ML, CLS and ULS methods. The diagnostic checking tests, AIC criterion, RACF graph and RPACF graphs, were used for selected model verification. In this study, the best ARIMA models for Annual Maximum Discharge (AMD) time series was (4,1,1) with their AIC value of 88.87. The RACF and RPACF showed residuals’ independence. To forecast AMD for 10 future years, this model showed the ability of the model to predict floods of the river under study in the Karkheh River Basin. Model accuracy was checked by comparing the predicted and observation series by using coefficient of determination (R²).

Keywords: Time series modelling, stochastic processes, ARIMA model, Karkheh River.

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Authors: Joshua Prakash, Chin Jeng Feng

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The paper describes the workings for four models of CONWIP systems used till date; the basic CONWIP system, the hybrid CONWIP system, the multi-product CONWIP system, and the parallel CONWIP system. The final novel model is introduced in this paper in a general form. These models may be adopted for analysis for both simulation studies and implementation on the shop floor. For each model, input parameters of interest are highlighted and their impacts on several system performance measures are addressed.

Keywords: CONWIP, hybrid CONWIP, mixed CONWIP, multi-product CONWIP.

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Authors: H. Mahboubi, B. Moshiri, A. Khaki Seddigh

Abstract:

Recently, a great amount of interest has been shown in the field of modeling and controlling hybrid systems. One of the efficient and common methods in this area utilizes the mixed logicaldynamical (MLD) systems in the modeling. In this method, the system constraints are transformed into mixed-integer inequalities by defining some logic statements. In this paper, a system containing three tanks is modeled as a nonlinear switched system by using the MLD framework. Comparing the model size of the three-tank system with that of a two-tank system, it is deduced that the number of binary variables, the size of the system and its complexity tremendously increases with the number of tanks, which makes the control of the system more difficult. Therefore, methods should be found which result in fewer mixed-integer inequalities.

Keywords: Hybrid systems, mixed-integer inequalities, mixed logical dynamical systems, multi-tank system.

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Authors: J. Ritonja

Abstract:

The biochemical technology has been developing extremely fast since the middle of the last century. The main reason for such development represents a requirement for large production of high-quality biologically manufactured products such as pharmaceuticals, foods, and beverages. The impact of the biochemical industry on the world economy is enormous. The great importance of this industry also results in intensive development in scientific disciplines relevant to the development of biochemical technology. In addition to developments in the fields of biology and chemistry, which enable to understand complex biochemical processes, development in the field of control theory and applications is also very important. In the paper, the control for the biochemical reactor for the milk fermentation was studied. During the fermentation process, the biophysical quantities must be precisely controlled to obtain the high-quality product. To control these quantities, the bioreactor’s stirring drive and/or heating system can be used. Available commercial biochemical reactors are equipped with open loop or conventional linear closed loop control system. Due to the outstanding parameters variations and the partial nonlinearity of the biochemical process, the results obtained with these control systems are not satisfactory. To improve the fermentation process, the self-tuning adaptive control system was proposed. The use of the self-tuning adaptive control is suggested because the parameters’ variations of the studied biochemical process are very slow in most cases. To determine the linearized mathematical model of the fermentation process, the recursive least square identification method was used. Based on the obtained mathematical model the linear quadratic regulator was tuned. The parameters’ identification and the controller’s synthesis are executed on-line and adapt the controller’s parameters to the fermentation process’ dynamics during the operation. The use of the proposed combination represents the original solution for the control of the milk fermentation process. The purpose of the paper is to contribute to the progress of the control systems for the biochemical reactors. The proposed adaptive control system was tested thoroughly. From the obtained results it is obvious that the proposed adaptive control system assures much better following of the reference signal as a conventional linear control system with fixed control parameters.

Keywords: Adaptive control, biochemical reactor, linear quadratic regulator, recursive least square identification.

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Authors: Nasser Mohamed Ramli, Mohamad Syafiq Mohamad

Abstract:

Many types of controllers were applied on the continuous stirred tank reactor (CSTR) unit to control the temperature. In this research paper, Proportional-Integral-Derivative (PID) controller are compared with Fuzzy Logic controller for temperature control of CSTR. The control system for temperature non-isothermal of a CSTR will produce a stable response curve to its set point temperature. A mathematical model of a CSTR using the most general operating condition was developed through a set of differential equations into S-function using MATLAB. The reactor model and S-function are developed using m.file. After developing the S-function of CSTR model, User-Defined functions are used to link to SIMULINK file. Results that are obtained from simulation and temperature control were better when using Fuzzy logic control compared to PID control.

Keywords: CSTR, temperature, PID, fuzzy logic.

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Authors: Rahib Abiyev, Vasif H. Abiyev, C. Ardil

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In this paper the development of neural network based fuzzy inference system for electricity consumption prediction is considered. The electricity consumption depends on number of factors, such as number of customers, seasons, type-s of customers, number of plants, etc. It is nonlinear process and can be described by chaotic time-series. The structure and algorithms of neuro-fuzzy system for predicting future values of electricity consumption is described. To determine the unknown coefficients of the system, the supervised learning algorithm is used. As a result of learning, the rules of neuro-fuzzy system are formed. The developed system is applied for predicting future values of electricity consumption of Northern Cyprus. The simulation of neuro-fuzzy system has been performed.

Keywords: Fuzzy logic, neural network, neuro-fuzzy system, neuro-fuzzy prediction.

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Authors: Jing Zhang, Jie Chen

Abstract:

In this paper, we deal with the optimal I/O point location in an automated parking system. In this system, the S/R machine (storage and retrieve machine) travels independently in vertical and horizontal directions. Based on the characteristics of the parking system and the basic principle of AS/RS system (Automated Storage and Retrieval System), we obtain the continuous model in units of time. For the single command cycle using the randomized storage policy, we calculate the probability density function for the system travel time and thus we develop the travel time model. And we confirm that the travel time model shows a good performance by comparing with discrete case. Finally in this part, we establish the optimal model by minimizing the expected travel time model and it is shown that the optimal location of the I/O point is located at the middle of the left-hand above corner.

Keywords: Parking system, optimal location, response time, S/R machine.

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Authors: Essam Al-Daoud

Abstract:

A potentially serious problem with current payment systems is that their underlying hard problems from number theory may be solved by either a quantum computer or unanticipated future advances in algorithms and hardware. A new quantum payment system is proposed in this paper. The suggested system makes use of fundamental principles of quantum mechanics to ensure the unconditional security without prior arrangements between customers and vendors. More specifically, the new system uses Greenberger-Home-Zeilinger (GHZ) states and Quantum Key Distribution to authenticate the vendors and guarantee the transaction integrity.

Keywords: Bell state, GHZ state, Quantum key distribution, Quantum payment system.

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Authors: S. Mehran, S. Rouhi, F.Rouzbahani, E. Haghgoo

Abstract:

In this paper dynamics of a vapour bubble generated due to a local energy input inside a vertical rigid cylinder and in the absence of buoyancy forces is investigated. Different ratios of the diameter of the rigid cylinder to the maximum radius of the bubble are considered. The Boundary Integral Equation Method is employed for numerical simulation of the problem. Results show that during the collapse phase of the bubble inside a vertical rigid cylinder, two liquid micro jets are developed on the top and bottom sides of the vapour bubble and are directed inward. Results also show that existence of a deposit rib inside the vertical rigid cylinder slightly increases the life time of the bubble. It is found that by increasing the ratio of the cylinder diameter to the maximum radius of the bubble, the rate of the growth and collapse phases of the bubble increases and the life time of the bubble decreases.

Keywords: Vapour bubble, Vertical rigid cylinder, Boundaryelement method.

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Authors: Nurul Bahiyah Ahmad Khairudin, Habibah A Wahab

Abstract:

A new approach to predict the 3D structures of proteins by combining the knowledge-based method and Molecular Dynamics Simulation is presented on the chicken villin headpiece subdomain (HP-36). Comparative modeling is employed as the knowledge-based method to predict the core region (Ala9-Asn28) of the protein while the remaining residues are built as extended regions (Met1-Lys8; Leu29-Phe36) which then further refined using Molecular Dynamics Simulation for 120 ns. Since the core region is built based on a high sequence identity to the template (65%) resulting in RMSD of 1.39 Å from the native, it is believed that this well-developed core region can act as a 'nucleation center' for subsequent rapid downhill folding. Results also demonstrate that the formation of the non-native contact which tends to hamper folding rate can be avoided. The best 3D model that exhibits most of the native characteristics is identified using clustering method which then further ranked based on the conformational free energies. It is found that the backbone RMSD of the best model compared to the NMR-MDavg is 1.01 Å and 3.53 Å, for the core region and the complete protein, respectively. In addition to this, the conformational free energy of the best model is lower by 5.85 kcal/mol as compared to the NMR-MDavg. This structure prediction protocol is shown to be effective in predicting the 3D structure of small globular protein with a considerable accuracy in much shorter time compared to the conventional Molecular Dynamics simulation alone.

Keywords: 3D model, Chicken villin headpiece subdomain, Molecular dynamic simulation NMR-MDavg, RMSD.

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Authors: Shuenn-Yih Chang, Chiu-Li Huang

Abstract:

Three structure-dependent integration methods have been developed for solving equations of motion, which are second-order ordinary differential equations, for structural dynamics and earthquake engineering applications. Although they generally have the same numerical properties, such as explicit formulation, unconditional stability and second-order accuracy, a different performance is found in solving the free vibration response to either linear elastic or nonlinear systems with high frequency modes. The root cause of this different performance in the free vibration responses is analytically explored herein. As a result, it is verified that a weak instability is responsible for the different performance of the integration methods. In general, a weak instability will result in an inaccurate solution or even numerical instability in the free vibration responses of high frequency modes. As a result, a weak instability must be prohibited for time integration methods.

Keywords: Dynamic analysis, high frequency, integration method, overshoot, weak instability.

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