Search results for: stochastic optimal control technique

Authors: Meriem Bahij, Ahmed Nafidi, Boujemâa Achchab, Sílvio M. A. Gama, José A. O. Matos

Abstract:

Stochastic modeling concerns the use of probability to model real-world situations in which uncertainty is present. Therefore, the purpose of stochastic modeling is to estimate the probability of outcomes within a forecast, i.e. to be able to predict what conditions or decisions might happen under different situations. In the present study, we present a model of a stochastic diffusion process based on the bi-Weibull distribution function (its trend is proportional to the bi-Weibull probability density function). In general, the Weibull distribution has the ability to assume the characteristics of many different types of distributions. This has made it very popular among engineers and quality practitioners, who have considered it the most commonly used distribution for studying problems such as modeling reliability data, accelerated life testing, and maintainability modeling and analysis. In this work, we start by obtaining the probabilistic characteristics of this model, as the explicit expression of the process, its trends, and its distribution by transforming the diffusion process in a Wiener process as shown in the Ricciaardi theorem. Then, we develop the statistical inference of this model using the maximum likelihood methodology. Finally, we analyse with simulated data the computational problems associated with the parameters, an issue of great importance in its application to real data with the use of the convergence analysis methods. Overall, the use of a stochastic model reflects only a pragmatic decision on the part of the modeler. According to the data that is available and the universe of models known to the modeler, this model represents the best currently available description of the phenomenon under consideration.

Keywords: Diffusion process, discrete sampling, likelihood estimation method, simulation, stochastic diffusion equation, trends functions, bi-parameters Weibull density function.

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Authors: Ahmed Abdolkhalig

Abstract:

This paper examines many mathematical methods for molding the hourly price forward curve (HPFC); the model will be constructed by numerous regression methods, like polynomial regression, radial basic function neural networks & a furrier series. Examination the models goodness of fit will be done by means of statistical & graphical tools. The criteria for choosing the model will depend on minimize the Root Mean Squared Error (RMSE), using the correlation analysis approach for the regression analysis the optimal model will be distinct, which are robust against model misspecification. Learning & supervision technique employed to determine the form of the optimal parameters corresponding to each measure of overall loss. By using all the numerical methods that mentioned previously; the explicit expressions for the optimal model derived and the optimal designs will be implemented.

Keywords: Forward curve, furrier series, regression, radial basic function neural networks.

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Authors: Norsinnira Zainul Azlan, Hiroshi Yamaura

Abstract:

This paper presents a new adaptive impedance control strategy, based on Function Approximation Technique (FAT) to compensate for unknown non-flat environment shape or time-varying environment location. The target impedance in the force controllable direction is modified by incorporating adaptive compensators and the uncertainties are represented by FAT, allowing the update law to be derived easily. The force error feedback is utilized in the estimation and the accurate knowledge of the environment parameters are not required by the algorithm. It is shown mathematically that the stability of the controller is guaranteed based on Lyapunov theory. Simulation results presented to demonstrate the validity of the proposed controller.

Keywords: Adaptive impedance control, Function Approximation Technique (FAT), impedance control, unknown environment position.

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Authors: Mehdi Nasri, Hossein Nezamabadi-pour, Malihe Maghfoori

Abstract:

This Paper presents a particle swarm optimization (PSO) method for determining the optimal proportional-integral-derivative (PID) controller parameters, for speed control of a linear brushless DC motor. The proposed approach has superior features, including easy implementation, stable convergence characteristic and good computational efficiency. The brushless DC motor is modelled in Simulink and the PSO algorithm is implemented in MATLAB. Comparing with Genetic Algorithm (GA) and Linear quadratic regulator (LQR) method, the proposed method was more efficient in improving the step response characteristics such as, reducing the steady-states error; rise time, settling time and maximum overshoot in speed control of a linear brushless DC motor.

Keywords: Brushless DC motor, Particle swarm optimization, PID Controller, Optimal control.

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Authors: Pham Van Nha, Le Cam Binh

Abstract:

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: F. Caliskan

Abstract:

This paper presents a Neural Network (NN) identification of icing parameters in an A340 aircraft and a reconfiguration technique to keep the A/C performance close to the performance prior to icing. Five aircraft parameters are assumed to be considerably affected by icing. The off-line training for identifying the clear and iced dynamics is based on the Levenberg-Marquard Backpropagation algorithm. The icing parameters are located in the system matrix. The physical locations of the icing are assumed at the right and left wings. The reconfiguration is based on the technique known as the control mixer approach or pseudo inverse technique. This technique generates the new control input vector such that the A/C dynamics is not much affected by icing. In the simulations, the longitudinal and lateral dynamics of an Airbus A340 aircraft model are considered, and the stability derivatives affected by icing are identified. The simulation results show the successful NN identification of the icing parameters and the reconfigured flight dynamics having the similar performance before the icing. In other words, the destabilizing icing affect is compensated.

Keywords: Aircraft Icing, Stability Derivatives, Neural NetworkIdentification, Reconfiguration.

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Authors: Ginalber L. O. Serra

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This work proposes a recursive weighted ELS algorithm for system identification by applying numerically robust orthogonal Householder transformations. The properties of the proposed algorithm show it obtains acceptable results in a noisy environment: fast convergence and asymptotically unbiased estimates. Comparative analysis with others robust methods well known from literature are also presented.

Keywords: Stochastic Systems, Robust Identification, Parameter Estimation, Systems Identification.

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Authors: Chih-Hui Chiu, Chun-Hsien Lin

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In this study, a robust intelligent backstepping tracking control (RIBTC) system combined with adaptive output recurrent cerebellar model articulation control (AORCMAC) and H∞ control technique is proposed for wheeled inverted pendulums (WIPs) real-time control with exact system dynamics unknown. Moreover, a robust H∞ controller is designed to attenuate the effect of the residual approximation errors and external disturbances with desired attenuation level. The experimental results indicate that the WIPs can stand upright stably when using the proposed RIBTC.

Keywords: Wheeled inverted pendulum, backsteppingtracking control, H∞ control, adaptive output recurrentcerebellar model articulation control.

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Authors: Xin Zhao, Yin-fan Zhu, Wei-ping Wang, Qun Li

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The Influence Diagrams (IDs) is a kind of Probabilistic Belief Networks for graphic modeling. The usage of IDs can improve the communication among field experts, modelers, and decision makers, by showing the issue frame discussed from a high-level point of view. This paper enhances the Time-Sliced Influence Diagrams (TSIDs, or called Dynamic IDs) based formalism from a Discrete Event Systems Modeling and Simulation (DES M&S) perspective, for Exploring Analysis (EA) modeling. The enhancements enable a modeler to specify times occurred of endogenous events dynamically with stochastic sampling as model running and to describe the inter- influences among them with variable nodes in a dynamic situation that the existing TSIDs fails to capture. The new class of model is named Dynamic-Stochastic Influence Diagrams (DSIDs). The paper includes a description of the modeling formalism and the hiberarchy simulators implementing its simulation algorithm, and shows a case study to illustrate its enhancements.

Keywords: Time-sliced influence diagrams, discrete event systems, dynamic-stochastic influence diagrams, modeling formalism, simulation algorithm.

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Authors: H. Shayeghi, H. Hosseini, A. Shabani, M. Mahdavi

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In this paper, optimal generation expansion planning (GEP) is investigated considering purchase prices, profits of independent power producers (IPPs) and reliability criteria using a new method based on hybrid coded Genetic Algorithm (GA) and Particle Swarm Optimization (PSO). In this approach, optimal purchase price of each IPP is obtained by HCGA and reliability criteria are calculated by PSO technique. It should be noted that reliability criteria and the rate of carbon dioxide (CO2) emission have been considered as constraints of the GEP problem. Finally, the proposed method has been tested on the case study system. The results evaluation show that the proposed method can simply obtain optimal purchase prices of IPPs and is a fast method for calculation of reliability criteria in expansion planning. Also, considering the optimal purchase prices and profits of IPPs in generation expansion planning are caused that the expansion costs are decreased and the problem is solved more exactly.

Keywords: GEP Problem, IPPs, Reliability Criteria, GA, PSO.

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Authors: Norsinnira Zainul Azlan, Hiroshi Yamaura

Abstract:

This study is concerned with a new adaptive impedance control strategy to compensate for unknown time-varying environment stiffness and position. The uncertainties are expressed by Function Approximation Technique (FAT), which allows the update laws to be derived easily using Lyapunov stability theory. Computer simulation results are presented to validate the effectiveness of the proposed strategy.

Keywords: Adaptive Impedance Control, Function Approximation Technique (FAT), unknown time-varying environment position and stiffness.

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Authors: Ahmed Z. Gabr, Ahmed A. Helal, Hussein E. Said

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With the incessant increase of power systems capacity and voltage grade, the safety of grounding grid becomes more and more prominent. In this paper, the designing substation grounding grid is presented by means of genetic algorithm (GA). This approach purposes to control the grounding cost of the power system with the aid of controlling grounding rod number and conductor lengths under the same safety limitations. The proposed technique is used for the design of the substation grounding grid in Khalda Petroleum Company “El-Qasr” power plant and the design was simulated by using CYMGRD software for results verification. The result of the design is highly complying with IEEE 80-2000 standard requirements.

Keywords: Genetic algorithm, optimum grounding grid design, power system analysis, power system protection, single layer model, substation.

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Authors: S. Rozhkova, O. Rozhkova, A. Harlova, V. Lasukov

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For optimal unbiased filter as mean-square and in the case of functioning anomalous noises in the observation memory channel, we have proved insensitivity of filter to inaccurate knowledge of the anomalous noise intensity matrix and its equivalence to truncated filter plotted only by non anomalous components of an observation vector.

Keywords: Mathematical expectation, filtration, anomalous noise, memory.

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Authors: Aleksandra Aleksandrovna Filimonova, Lev Sergeevich Kazarinov, Tatyana Aleksandrovna Barbasova

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A method of effective planning and control of industrial facility energy consumption is offered. The method allows optimally arranging the management and full control of complex production facilities in accordance with the criteria of minimal technical and economic losses at the forecasting control. The method is based on the optimal construction of the power efficiency characteristics with the prescribed accuracy. The problem of optimal designing of the forecasting model is solved on the basis of three criteria: maximizing the weighted sum of the points of forecasting with the prescribed accuracy; the solving of the problem by the standard principles at the incomplete statistic data on the basis of minimization of the regularized function; minimizing the technical and economic losses due to the forecasting errors.

Keywords: Energy consumption, energy efficiency, energy management system, forecasting model, power efficiency characteristics.

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Authors: Wen-Jye Shyr, Chia-Ming Lin, Hung-Yun Feng

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The purpose of this study was to develop an energy management system for university campuses based on the Internet of Things (IoT) technique. The proposed IoT technique based on WebAccess is used via network browser Internet Explore and applies TCP/IP protocol. The case study of IoT for lighting energy usage management system was proposed. Structure of proposed IoT technique included perception layer, equipment layer, control layer, application layer and network layer.

Keywords: Energy management, IoT technique, Sensor, WebAccess

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Authors: T. Kerdchuen

Abstract:

This paper proposes the stochastic tabu search (STS) for improving the measurement scheme for power system state estimation. If the original measured scheme is not observable, the additional measurements with minimum number of measurements are added into the system by STS so that there is no critical measurement pair. The random bit flipping and bit exchanging perturbations are used for generating the neighborhood solutions in STS. The Pδ observable concept is used to determine the network observability. Test results of 10 bus, IEEE 14 and 30 bus systems are shown that STS can improve the original measured scheme to be observable without critical measurement pair. Moreover, the results of STS are superior to deterministic tabu search (DTS) in terms of the best solution hit.

Keywords: Measurement Scheme, Power System StateEstimation, Network Observability, Stochastic Tabu Search (STS).

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Authors: Zoran Nikoloski, Narsingh Deo, Ludek Kucera

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Despite the recent surge of research in control of worm propagation, currently, there is no effective defense system against such cyber attacks. We first design a distributed detection architecture called Detection via Distributed Blackholes (DDBH). Our novel detection mechanism could be implemented via virtual honeypots or honeynets. Simulation results show that a worm can be detected with virtual honeypots on only 3% of the nodes. Moreover, the worm is detected when less than 1.5% of the nodes are infected. We then develop two control strategies: (1) optimal dynamic trafficblocking, for which we determine the condition that guarantees minimum number of removed nodes when the worm is contained and (2) predictive dynamic traffic-blocking–a realistic deployment of the optimal strategy on scale-free graphs. The predictive dynamic traffic-blocking, coupled with the DDBH, ensures that more than 40% of the network is unaffected by the propagation at the time when the worm is contained.

Keywords: Network worms, distributed detection, optimaltraffic-blocking, individual-based simulation.

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Authors: Kevin Spencer G. Anglim, Zhenyu Zhang, Qingbin Gao

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Reusable launch vehicles (RLVs) present a more environmentally-friendly approach to accessing space when compared to traditional launch vehicles that are discarded after each flight. This paper studies the recyclable nature of RLVs by presenting a solution method for determining minimum-fuel optimal trajectories using principles from optimal control theory and particle swarm optimization (PSO). This problem is formulated as a minimum-landing error powered descent problem where it is desired to move the RLV from a fixed set of initial conditions to three different sets of terminal conditions. However, unlike other powered descent studies, this paper considers the highly nonlinear effects caused by atmospheric drag, which are often ignored for studies on the Moon or on Mars. Rather than optimizing the controls directly, the throttle control is assumed to be bang-off-bang with a predetermined thrust direction for each phase of flight. The PSO method is verified in a one-dimensional comparison study, and it is then applied to the two-dimensional cases, the results of which are illustrated.

Keywords: Minimum-fuel optimal trajectory, particle swarm optimization, reusable rocket, SpaceX.

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Authors: M. F. Omar, R. A. Salam, R. Abdullah, N. A. Rashid

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Proteins or genes that have similar sequences are likely to perform the same function. One of the most widely used techniques for sequence comparison is sequence alignment. Sequence alignment allows mismatches and insertion/deletion, which represents biological mutations. Sequence alignment is usually performed only on two sequences. Multiple sequence alignment, is a natural extension of two-sequence alignment. In multiple sequence alignment, the emphasis is to find optimal alignment for a group of sequences. Several applicable techniques were observed in this research, from traditional method such as dynamic programming to the extend of widely used stochastic optimization method such as Genetic Algorithms (GAs) and Simulated Annealing. A framework with combination of Genetic Algorithm and Simulated Annealing is presented to solve Multiple Sequence Alignment problem. The Genetic Algorithm phase will try to find new region of solution while Simulated Annealing can be considered as an alignment improver for any near optimal solution produced by GAs.

Keywords: Simulated annealing, genetic algorithm, sequence alignment, multiple sequence alignment.

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Authors: Anatoli Torokhti, Stanley Miklavcic

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Suppose KY and KX are large sets of observed and reference signals, respectively, each containing N signals. Is it possible to construct a filter F : KY → KX that requires a priori information only on few signals, p  N, from KX but performs better than the known filters based on a priori information on every reference signal from KX? It is shown that the positive answer is achievable under quite unrestrictive assumptions. The device behind the proposed method is based on a special extension of the piecewise linear interpolation technique to the case of random signal sets. The proposed technique provides a single filter to process any signal from the arbitrarily large signal set. The filter is determined in terms of pseudo-inverse matrices so that it always exists.

Keywords: Wiener filter, filtering of stochastic signals.

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Authors: Hassan Manouzi, Taous-Meriem Laleg-Kirati

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In this paper we study mathematically the eigenvalue problem for stochastic elliptic partial differential equation of Wick type. Using the Wick-product and the Wiener-Itô chaos expansion, the stochastic eigenvalue problem is reformulated as a system of an eigenvalue problem for a deterministic partial differential equation and elliptic partial differential equations by using the Fredholm alternative. To reduce the computational complexity of this system, we shall use a decomposition method using the Wiener-Itô chaos expansion. Once the approximation of the solution is performed using the finite element method for example, the statistics of the numerical solution can be easily evaluated.

Keywords: Eigenvalue problem, Wick product, SPDEs, finite element, Wiener-Itô chaos expansion.

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Authors: Anshu Manik, William G. Buttlar, Kasthurirangan Gopalakrishnan

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Over the years, there is a growing trend towards quality-based specifications in highway construction. In many Quality Control/Quality Assurance (QC/QA) specifications, the contractor is primarily responsible for quality control of the process, whereas the highway agency is responsible for testing the acceptance of the product. A cooperative investigation was conducted in Illinois over several years to develop a prototype End-Result Specification (ERS) for asphalt pavement construction. The final characteristics of the product are stipulated in the ERS and the contractor is given considerable freedom in achieving those characteristics. The risk for the contractor or agency depends on how the acceptance limits and processes are specified. Stochastic simulation models are very useful in estimating and analyzing payment risk in ERS systems and these form an integral part of the Illinois-s prototype ERS system. This paper describes the development of an innovative methodology to estimate the variability components in in-situ density, air voids and asphalt content data from ERS projects. The information gained from this would be crucial in simulating these ERS projects for estimation and analysis of payment risks associated with asphalt pavement construction. However, these methods require at least two parties to conduct tests on all the split samples obtained according to the sampling scheme prescribed in present ERS implemented in Illinois.

Keywords: Asphalt Pavement, Risk Analysis, StochasticSimulation, QC/QA.

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Authors: N. Ouldcherchali, M. S. Boucherit, L. Barazane, A. Morsli

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In this study, we proposed two techniques to track the maximum power point (MPPT) of a photovoltaic system. The first is an intelligent control technique, and the second is robust used for variable structure system. In fact the characteristics I-V and P–V of the photovoltaic generator depends on the solar irradiance and temperature. These climate changes cause the fluctuation of maximum power point; a maximum power point tracking technique (MPPT) is required to maximize the output power. For this we have adopted a control by fuzzy logic (FLC) famous for its stability and robustness. And a Siding Mode Control (SMC) widely used for variable structure system. The system comprises a photovoltaic panel (PV), a DC-DC converter, which is considered as an adaptation stage between the PV and the load. The modelling and simulation of the system is developed using MATLAB/Simulink. SMC technique provides a good tracking speed in fast changing irradiation and when the irradiation changes slowly or it is constant the panel power of FLC technique presents a much smoother signal with less fluctuations.

Keywords: Fuzzy logic controller, maximum power point, photovoltaic system, tracker, sliding mode controller.

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Authors: Violeta Damjanovic-Behrendt

Abstract:

This paper presents an approach for optimal cyber security decisions to protect instances of a federated Internet of Things (IoT) platform in the cloud. The presented solution implements the repeated Stackelberg Security Game (SSG) and a model called Stochastic Human behaviour model with AttRactiveness and Probability weighting (SHARP). SHARP employs the Subjective Utility Quantal Response (SUQR) for formulating a subjective utility function, which is based on the evaluations of alternative solutions during decision-making. We augment the repeated SSG (including SHARP and SUQR) with a reinforced learning algorithm called Naïve Q-Learning. Naïve Q-Learning belongs to the category of active and model-free Machine Learning (ML) techniques in which the agent (either the defender or the attacker) attempts to find an optimal security solution. In this way, we combine GT and ML algorithms for discovering optimal cyber security policies. The proposed security optimization components will be validated in a collaborative cloud platform that is based on the Industrial Internet Reference Architecture (IIRA) and its recently published security model.

Keywords: Security, internet of things, cloud computing, Stackelberg security game, machine learning, Naïve Q-learning.

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Authors: R. Khaniki, M.B. Menhaj, H. Eliasi

Abstract:

This paper describes the application of a model predictive controller to the problem of batch reactor temperature control. Although a great deal of work has been done to improve reactor throughput using batch sequence control, the control of the actual reactor temperature remains a difficult problem for many operators of these processes. Temperature control is important as many chemical reactions are sensitive to temperature for formation of desired products. This controller consist of two part (1) a nonlinear control method GLC (Global Linearizing Control) to create a linear model of system and (2) a Model predictive controller used to obtain optimal input control sequence. The temperature of reactor is tuned to track a predetermined temperature trajectory that applied to the batch reactor. To do so two input signals, electrical powers and the flow of coolant in the coil are used. Simulation results show that the proposed controller has a remarkable performance for tracking reference trajectory while at the same time it is robust against noise imposed to system output.

Keywords: Generalized Predictive Control (GPC), TemperatureControl, Global Linearizing Control (GLC), Batch Reactor.

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Authors: R. Khaniki, M.B. Menhaj, H. Eliasi

Abstract:

This paper describes the application of a model predictive controller to the problem of batch reactor temperature control. Although a great deal of work has been done to improve reactor throughput using batch sequence control, the control of the actual reactor temperature remains a difficult problem for many operators of these processes. Temperature control is important as many chemical reactions are sensitive to temperature for formation of desired products. This controller consist of two part (1) a nonlinear control method GLC (Global Linearizing Control) to create a linear model of system and (2) a Model predictive controller used to obtain optimal input control sequence. The temperature of reactor is tuned to track a predetermined temperature trajectory that applied to the batch reactor. To do so two input signals, electrical powers and the flow of coolant in the coil are used. Simulation results show that the proposed controller has a remarkable performance for tracking reference trajectory while at the same time it is robust against noise imposed to system output.

Keywords: Generalized Predictive Control (GPC), TemperatureControl, Global Linearizing Control (GLC), Batch Reactor.

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Authors: N. Phumchusri, K. Roekdethawesab, M. Lohatepanont

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Overbooking is an approach of selling more goods or services than available capacities because sellers anticipate that some buyers will not show-up or may cancel their bookings. At present, many airlines deploy overbooking strategy in order to deal with the uncertainty of their customers. Particularly, some airlines sell more cargo capacity than what they have available to freight forwarders with beliefs that some of them will cancel later. In this paper, we propose methods to find the optimal overbooking level of volume and weight for air cargo in order to minimize the total cost, containing cost of spoilage and cost of offloaded. Cancellations of volume and weight are jointly random variables with a known joint distribution. Heuristic approaches applying the idea of weight and volume independency is considered to find an appropriate answer to the full problem. Computational experiments are used to explore the performance of approaches presented in this paper, as compared to a naïve method under different scenarios.

Keywords: Air cargo overbooking, offloaded capacity, optimal overbooking level, revenue management, spoilage capacity.

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Authors: M. Saravanan, J. Raja Murugadoss, V. Jayanthi

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Optimal design of structure has a main role in reduction of material usage which leads to deduction in the final cost of construction projects. Evolutionary approaches are found to be more successful techniques for solving size and shape structural optimization problem since it uses a stochastic random search instead of a gradient search. By reviewing the recent literature works the problem found was the optimization of weight. A new meta-heuristic algorithm called as Cuckoo Search (CS) Algorithm has used for the optimization of the total weight of the truss structures. This paper has used set of 10 bars and 25 bars trusses for the testing purpose. The main objective of this work is to reduce the number of iterations, weight and the total time consumption. In order to demonstrate the effectiveness of the present method, minimum weight design of truss structures is performed and the results of the CS are compared with other algorithms.

Keywords: Cuckoo search algorithm, levy’s flight, meta-heuristic, optimal weight.

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Authors: Syeda Maria Ali Shah, Asif Mansoor, Talat Sharafat Rehmani, Safia Mirza

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The stock market of any country acts as a predictor of the economy. The spread of the COVID-19 pandemic has severely impacted the global financial markets. Besides, it has also critically affected the economy of Pakistan. In this study, we consider the role of the Karachi Stock Exchange (KSE) with regard to the Pakistan Stock Exchange and quantify the impact on macroeconomic variables in presence of COVID-19. The suitable macroeconomic variables are used to quantify the impact of COVID-19 by developing the stochastic model. The sufficiency of the computed model is attained by means of available techniques in the literature. The estimated equations are used to forecast the impact of pandemic on macroeconomic variables. The constructed model can help the policymakers take counteractive measures for restricting the influence of viruses on the Karachi Stock Market.

Keywords: COVID-19, Karachi Stock Market, macroeconomic variables, stochastic model, forecasting.

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Authors: Paola Lecca, Lorenzo Dematte, Corrado Priami

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The present models and simulation algorithms of intracellular stochastic kinetics are usually based on the premise that diffusion is so fast that the concentrations of all the involved species are homogeneous in space. However, recents experimental measurements of intracellular diffusion constants indicate that the assumption of a homogeneous well-stirred cytosol is not necessarily valid even for small prokaryotic cells. In this work a mathematical treatment of diffusion that can be incorporated in a stochastic algorithm simulating the dynamics of a reaction-diffusion system is presented. The movement of a molecule A from a region i to a region j of the space is represented as a first order reaction Ai k- ! Aj , where the rate constant k depends on the diffusion coefficient. The diffusion coefficients are modeled as function of the local concentration of the solutes, their intrinsic viscosities, their frictional coefficients and the temperature of the system. The stochastic time evolution of the system is given by the occurrence of diffusion events and chemical reaction events. At each time step an event (reaction or diffusion) is selected from a probability distribution of waiting times determined by the intrinsic reaction kinetics and diffusion dynamics. To demonstrate the method the simulation results of the reaction-diffusion system of chaperoneassisted protein folding in cytoplasm are shown.

Keywords: Reaction-diffusion systems, diffusion coefficient, stochastic simulation algorithm.

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