Search results for: Immersed Boundary Method

Authors: Xuewen Yu, Danhui Dan

Abstract:

The identification of impact loads and some hard-to-obtain system parameters is crucial for analysis, validation, and evaluation activities in the engineering field. This paper proposes a method based on 1D-CNN to identify impact loads and partial system parameters from the measured responses. To this end, forward computations are conducted to provide datasets consisting of triples (parameter θ, input u, output y). Two neural networks are then trained: one to learn the mapping from output y to input u and another to learn the mapping from input and output (u, y) to parameter θ. Subsequently, by feeding the measured output response into the trained neural networks, the input impact load and system parameter can be calculated, respectively. The method is tested on two simulated examples and shows sound accuracy in estimating the impact load (waveform and location) and system parameter.

Keywords: Convolutional neural network, impact load identification, system parameter identification, inverse problem.

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Authors: W. Srisang, K. Jaroensutasinee, M. Jaroensutasinee

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This study examined a habitat-suitability assessment method namely the Ecological Niche Factor Analysis (ENFA). A virtual species was created and then dispatched in a geographic information system model of a real landscape in three historic scenarios: (1) spreading, (2) equilibrium, and (3) overabundance. In each scenario, the virtual species was sampled and these simulated data sets were used as inputs for the ENFA to reconstruct the habitat suitability model. The 'equilibrium' scenario gives the highest quantity and quality among three scenarios. ENFA was sensitive to the distribution scenarios but not sensitive to sample sizes. The use of a virtual species proved to be a very efficient method, allowing one to fully control the quality of the input data as well as to accurately evaluate the predictive power of the analyses.

Keywords: Habitat-Suitability Models, Ecological niche factoranalysis, Climatic factors, Geographic information system.

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Authors: Soon-Tai Park, Jong-Whoi Shin, Bog-Ki Min, Ik-Sub Lee, Gang-Shin Lee, Jae-Il Lee

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As the information age matures, major social infrastructures such as communication, finance, military and energy, have become ever more dependent on information communication systems. And since these infrastructures are connected to the Internet, electronic intrusions such as hacking and viruses have become a new security threat. Especially, disturbance or neutralization of a major social infrastructure can result in extensive material damage and social disorder. To address this issue, many nations around the world are researching and developing various techniques and information security policies as a government-wide effort to protect their infrastructures from newly emerging threats. This paper proposes an evaluation method for information security levels of CIIP (Critical Information Infrastructure Protection), which can enhance the security level of critical information infrastructure by checking the current security status and establish security measures accordingly to protect infrastructures effectively.

Keywords: Information Security Evaluation Methodology, Critical Information Infrastructure Protection.

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Authors: Abdulrahman S. Alturki, John S. Loomis

Abstract:

This paper discusses a corner detection algorithm for camera calibration. Calibration is a necessary step in many computer vision and image processing applications. Robust corner detection for an image of a checkerboard is required to determine intrinsic and extrinsic parameters. In this paper, an algorithm for fully automatic and robust X-corner detection is presented. Checkerboard corner points are automatically found in each image without user interaction or any prior information regarding the number of rows or columns. The approach represents each X-corner with a quadratic fitting function. Using the fact that the X-corners are saddle points, the coefficients in the fitting function are used to identify each corner location. The automation of this process greatly simplifies calibration. Our method is robust against noise and different camera orientations. Experimental analysis shows the accuracy of our method using actual images acquired at different camera locations and orientations.

Keywords: Camera Calibration, Corner Detector, Saddle Points, X-Corners.

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Authors: R. K. Apalowo, D. Chronopoulos

Abstract:

A Finite Element (FE) based scheme is presented for quantifying guided wave interaction with Localised Nonlinear Structural Damage (LNSD) within structures of arbitrary layering and geometric complexity. The through-thickness mode-shape of the structure is obtained through a wave and finite element method. This is applied in a time domain FE simulation in order to generate time harmonic excitation for a specific wave mode. Interaction of the wave with LNSD within the system is computed through an element activation and deactivation iteration. The scheme is validated against experimental measurements and a WFE-FE methodology for calculating wave interaction with damage. Case studies for guided wave interaction with crack and delamination are presented to verify the robustness of the proposed method in classifying and identifying damage.

Keywords: Layered Structures, nonlinear ultrasound, wave interaction with nonlinear damage, wave finite element, finite element.

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Authors: Chien-Chih Chen, Ya-Hsin Hsueh, Zong-Cian He

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With getting older in the whole population, the prevalence of stroke and its residual disability is getting higher and higher recently in Taiwan. The functional electrical stimulation cycling system (FESCS) is useful for hemiplegic patients. Because that the muscle of stroke patients is under hybrid activation. The raw electromyography (EMG) represents the residual muscle force of stroke subject whereas the peak-to-peak of stimulus EMG indicates the force enhancement benefiting from ES. It seems that EMG signals could be used for a parameter of feedback control mechanism. So, we design the feedback control protocol of FESCS, it includes physiological signal recorder, FPGA biomedical module, DAC and electrical stimulation circuit. Using the intensity of real-time EMG signal obtained from patients, as a feedback control method for the output voltage of FES-cycling system.

Keywords: Functional Electrical Stimulation cycling system EMG, control protocol.

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Authors: Darren Zou

Abstract:

Forecasting the stock market is a very challenging task. Various economic indicators such as GDP, exchange rates, interest rates, and unemployment have a substantial impact on the stock market. Time series models are the traditional methods used to predict stock market changes. In this paper, a machine learning method, Bayesian Additive Regression Tree (BART) is used in predicting stock market indexes based on multiple economic indicators. BART can be used to model heterogeneous treatment effects, and thereby works well when models are misspecified. It also has the capability to handle non-linear main effects and multi-way interactions without much input from financial analysts. In this research, BART is proposed to provide a reliable prediction on day-to-day stock market activities. By comparing the analysis results from BART and with time series method, BART can perform well and has better prediction capability than the traditional methods.

Keywords: Bayesian, Forecast, Stock, BART.

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Authors: C. M. A. Robles G., R. A. Hernandez-Becerril

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We board the problem of creating a seismic alert system, based upon artificial neural networks, trained by using the well-known back-propagation and genetic algorithms, in order to emit the alarm for the population located into a specific city, about an eminent earthquake greater than 4.5 Richter degrees, and avoiding disasters and human loses. In lieu of using the propagation wave, we employed the magnitude of the earthquake, to establish a correlation between the recorded magnitudes from a controlled area and the city, where we want to emit the alarm. To measure the accuracy of the posed method, we use a database provided by CIRES, which contains the records of 2500 quakes incoming from the State of Guerrero and Mexico City. Particularly, we performed the proposed method to generate an issue warning in Mexico City, employing the magnitudes recorded in the State of Guerrero.

Keywords: Seismic Alert System, Artificial Neural Networks, Genetic Algorithms.

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Authors: Mat Syai'in, Adi Soeprijanto

Abstract:

An Optimal Power Flow based on Improved Particle Swarm Optimization (OPF-IPSO) with Generator Capability Curve Constraint is used by NN-OPF as a reference to get pattern of generator scheduling. There are three stages in Designing NN-OPF. The first stage is design of OPF-IPSO with generator capability curve constraint. The second stage is clustering load to specific range and calculating its index. The third stage is training NN-OPF using constructive back propagation method. In training process total load and load index used as input, and pattern of generator scheduling used as output. Data used in this paper is power system of Java-Bali. Software used in this simulation is MATLAB.

Keywords: Optimal Power Flow, Generator Capability Curve, Improved Particle Swarm Optimization, Neural Network

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Authors: Basak Oguz Yolcular

Abstract:

A large amount of valuable information is available in plain text clinical reports. New techniques and technologies are applied to extract information from these reports. In this study, we developed a domain based software system to transform 600 Otorhinolaryngology discharge notes to a structured form for extracting clinical data from the discharge notes. In order to decrease the system process time discharge notes were transformed into a data table after preprocessing. Several word lists were constituted to identify common section in the discharge notes, including patient history, age, problems, and diagnosis etc. N-gram method was used for discovering terms co-Occurrences within each section. Using this method a dataset of concept candidates has been generated for the validation step, and then Predictive Apriori algorithm for Association Rule Mining (ARM) was applied to validate candidate concepts.

Keywords: association rule mining, otorhinolaryngology, predictive apriori, text mining

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Authors: A. H. Elkholy, A. H. Falah

Abstract:

A new approach has been developed to estimate the load share and distribution of worm gear drives, and to calculate the instantaneous tooth meshing stiffness. In the approach, the worm gear drive was modelled as a series of spur gear slices, and each slice was analyzed separately using the well-established formulae of spur gear loading and stresses. By combining the results obtained for all slices, the entire envolute worm gear set loading and stressing was obtained. The geometric modelling method presented allows tooth elastic deformation and tooth root stresses of worm gear drives under different load conditions to be investigated. Based on the slicing method introduced in this study, the instantaneous meshing stiffness and load share are obtained. In comparison with existing methods, this approach has both good analysis accuracy and less computing time.

Keywords: Gear, load/stress distribution, worm, wheel, tooth stiffness, contact line.

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Authors: Rabah Haoui

Abstract:

This work presents a numerical simulation of the interaction of an incident shock wave propagates from the left to the right with a cone placed in a tube at shock. The Mathematical model is based on a non stationary, viscous and axisymmetric flow. The Discretization of the Navier-stokes equations is carried out by the finite volume method in the integral form along with the Flux Vector Splitting method of Van Leer. Here, adequate combination of time stepping parameter, CFL coefficient and mesh size level is selected to ensure numerical convergence. The numerical simulation considers a shock tube filled with air. The incident shock wave propagates to the right with a determined Mach number and crosses the cone by leaving behind it a stationary detached shock wave in front of the nose cone. This type of interaction is observed according to the time of flow.

Keywords: Supersonic flow, viscous flow, finite volume, cone body

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Authors: Sahar Dehyouri, Seyed Jamal Farajollah Hosseini

Abstract:

Perspective of food security in 21 century showed shortage of food that production is faced to vital problem. Food security strategy is applied longtime method to assess required food. Meanwhile, nanotechnology revolution changes the world face. Nanotechnology is adequate method utilize of its characteristics to decrease environmental problems and possible further access to food for small farmers. This article will show impact of production and adoption of nanocrops on food security. Population is researchers of agricultural research center of Esfahan province. The results of study show that there was a relationship between uses, conversion, distribution, and production of nanocrops, operative human resources, operative circumstance, and constrains of usage of nanocrops and food security. Multivariate regression analysis by enter model shows that operative circumstance, use, production and constrains of usage of nanocrops had positive impact on food security and they determine in four steps 20 percent of it.

Keywords: adoption, food safety, food security, nanocrops

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Authors: Mir Shahriar Emami, Mohammad Reza Meybodi

Abstract:

Prime Factorization based on Quantum approach in two phases has been performed. The first phase has been achieved at Quantum computer and the second phase has been achieved at the classic computer (Post Processing). At the second phase the goal is to estimate the period r of equation xrN ≡ 1 and to find the prime factors of the composite integer N in classic computer. In this paper we present a method based on Randomized Approach for estimation the period r with a satisfactory probability and the composite integer N will be factorized therefore with the Randomized Approach even the gesture of the period is not exactly the real period at least we can find one of the prime factors of composite N. Finally we present some important points for designing an Emulator for Quantum Computer Simulation.

Keywords: Quantum Prime Factorization, RandomizedAlgorithms, Quantum Computer Simulation, Quantum Computation.

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Authors: Yi Liao, Wencheng Yang, Gangyi Jiang

Abstract:

According to investigating impact of complexity of stereoscopic frame pairs on stereoscopic video coding and transmission, a new rate control algorithm is presented. The proposed rate control algorithm is performed on three levels: stereoscopic group of pictures (SGOP) level, stereoscopic frame (SFrame) level and frame level. A temporal-spatial frame complexity model is firstly established, in the bits allocation stage, the frame complexity, position significance and reference property between the left and right frames are taken into account. Meanwhile, the target buffer is set according to the frame complexity. Experimental results show that the proposed method can efficiently control the bitrates, and it outperforms the fixed quantization parameter method from the rate distortion perspective, and average PSNR gain between rate-distortion curves (BDPSNR) is 0.21dB.

Keywords: Stereoscopic video coding, rate control, stereoscopic group of pictures, complexity of stereoscopic frame pairs.

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Authors: Mojtaba Aghamiri Esfahani, Mohammad Karkon, Seyed Majid Hosseini Nezhad, Reza Hosseini-Ara

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In this study, the effect of uncertainty in elastic modulus of a plate on free vibration response is investigated. For this purpose, the elastic modulus of the plate is modeled as stochastic variable with normal distribution. Moreover, the distance autocorrelation function is used for stochastic field. Then, by applying the finite element method and Monte Carlo simulation, stochastic finite element relations are extracted. Finally, with a numerical test, the effect of uncertainty in the elastic modulus on free vibration response of a plate is studied. The results show that the effect of uncertainty in elastic modulus of the plate cannot play an important role on the free vibration response.

Keywords: Stochastic finite elements, plate bending, free vibration, Monte Carlo, Neumann expansion method.

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Authors: S. Rao Rayapudi

Abstract:

Economic Load Dispatch (ELD) is a method of determining the most efficient, low-cost and reliable operation of a power system by dispatching available electricity generation resources to supply load on the system. The primary objective of economic dispatch is to minimize total cost of generation while honoring operational constraints of available generation resources. In this paper an intelligent water drop (IWD) algorithm has been proposed to solve ELD problem with an objective of minimizing the total cost of generation. Intelligent water drop algorithm is a swarm-based natureinspired optimization algorithm, which has been inspired from natural rivers. A natural river often finds good paths among lots of possible paths in its ways from source to destination and finally find almost optimal path to their destination. These ideas are embedded into the proposed algorithm for solving economic load dispatch problem. The main advantage of the proposed technique is easy is implement and capable of finding feasible near global optimal solution with less computational effort. In order to illustrate the effectiveness of the proposed method, it has been tested on 6-unit and 20-unit test systems with incremental fuel cost functions taking into account the valve point-point loading effects. Numerical results shows that the proposed method has good convergence property and better in quality of solution than other algorithms reported in recent literature.

Keywords: Economic load dispatch, Transmission loss, Optimization, Valve point loading, Intelligent Water Drop Algorithm.

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Authors: Azizollah Khormali, Seyyed Shahab Tabatabaee Moradi, Dmitry Petrakov

Abstract:

One of the most important parameters in petroleum reservoirs is the pressure distribution along the reservoir, as the pressure varies with the time and location. A popular method to determine the pressure distribution in a reservoir in the unsteady state regime of flow is applying Darcy’s equation and solving this equation numerically. The numerical simulation of reservoirs is based on these numerical solutions of different partial differential equations (PDEs) representing the multiphase flow of fluids. Pressure profile has obtained in a one dimensional system solving Darcy’s equation explicitly. Changes of pressure profile in three situations are investigated in this work. These situations include section length changes, step time changes and time approach to infinity. The effects of these changes in pressure profile are shown and discussed in the paper.

Keywords: Explicit solution, Numerical simulation, Petroleum reservoir, Pressure distribution.

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Authors: W. T. Hsu, H. L. Tsai

Abstract:

The rapid aging of the population is a common trend in the world. However, the progress of modern medical technology has increased the average life expectancy. The global population structure has changed dramatically, and the elderly population has risen rapidly. In the face of rapid population growth, it must be noted issues of the aging population must face up to, which are the physiological, psychological, and social problems associated with aging. This study aims to investigate how insurance agents are actively dealing with an aging society, their own aging anxiety, and their exercise habits. Purposive sampling was the sampling method of this study, a total of 204 respondents were surveyed and 204 valid surveys were returned. The returned valid ratio was 100%. Statistical method included descriptive statistics, t-test, and one-way ANOVA. The results of the study found that the insurance agent’s age, seniority, exercise habits to aging anxiety are significantly different.

Keywords: Insurance agent, aging anxiety, exercise habits, elderly.

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Authors: Soo-young Ye, Jun-mo Park, Jae-hyung Kim, Jae-hee Jung, Ah-young Jeon, In-cheol Kim, Jung-man Son, Ki-gon Nam, Seong-wan Baik, Jung-hoon Ro, Gye-rok Jeon

Abstract:

The linear SEF (Spectral Edge Frequency) parameter and spectrum analysis method can not reflect the non-linear of EEG. This method can not contribute to acquire real time analysis and obtain a high confidence in the clinic due to low discrimination. To solve the problems, the development of a new index is carried out using the bispectrum analyzing the EEG(electroencephalogram) including the non-linear characteristic. After analyzing the bispectrum of the 2 dimension, the most significant power spectrum density peaks appeared abundantly at the specific area in awakening and anesthesia state. These points are utilized to create the new index since many peaks appeared at the specific area in the frequency coordinate. The measured range of an index was 0-100. An index is 20-50 at an anesthesia, while the index is 90-60 at the awake. New index could afford to effectively discriminate the awake and anesthesia state.

Keywords: Bispectrum, anesthesia depth, EEG, SEF.

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Authors: Mostafa.A. Fellani, Dawo.E. Abaid

Abstract:

This paper presents a controller design technique for Synchronous Reluctance Motor to improve its dynamic performance with fast response and high accuracy. The sliding mode control is the most attractive and suitable method to use for this purpose, since it is simple in design and for its insensitivity to parameter variations or external disturbances. When this method implemented it yields fast dynamic response without overshoot and a zero steady-state error. The current loop control with decentralized sliding mode is presented in this paper. The mathematical model for the synchronous machine, the inverter and the controller is developed. The stability of the sliding mode controller is analyzed. Simulation of synchronous reluctance motor and the controller with PWM-inverter has been curried out, using the SIMULINK software package of MATLAB. Simulation results are presented to show the effectiveness of the approach.

Keywords: Dynamic Simulation, MATLAB, PWM-inverter, Reluctance Machine, Sliding-mode.

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Authors: Kong Fah Tee, Lutfor Rahman Khan, Hongshuang Li

Abstract:

An advanced Monte Carlo simulation method, called Subset Simulation (SS) for the time-dependent reliability prediction for underground pipelines has been presented in this paper. The SS can provide better resolution for low failure probability level with efficient investigating of rare failure events which are commonly encountered in pipeline engineering applications. In SS method, random samples leading to progressive failure are generated efficiently and used for computing probabilistic performance by statistical variables. SS gains its efficiency as small probability event as a product of a sequence of intermediate events with larger conditional probabilities. The efficiency of SS has been demonstrated by numerical studies and attention in this work is devoted to scrutinise the robustness of the SS application in pipe reliability assessment. It is hoped that the development work can promote the use of SS tools for uncertainty propagation in the decision-making process of underground pipelines network reliability prediction.

Keywords: Underground pipelines, Probability of failure, Reliability and Subset Simulation.

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Authors: Malinwo Estone Ayikpa

Abstract:

With the rapid increase of grid-connected PV systems over the last decades, genuine challenges have arisen for engineers and professionals of energy field in the planning and operation of existing distribution networks with the integration of new generation sources. However, the conventional distribution network, in its design was not expected to receive other generation outside the main power supply. The tools generally used to analyze the networks become inefficient and cannot take into account all the constraints related to the operation of grid-connected PV systems. Some of these constraints are voltage control difficulty, reverse power flow, and especially voltage unbalance which could be due to the poor distribution of single-phase PV systems in the network. In order to analyze the impact of the connection of small and large number of PV systems to the distribution networks, this paper presents an efficient optimization tool that minimizes voltage unbalance in three-phase distribution networks with active and reactive power injections from the allocation of single-phase and three-phase PV plants. Reactive power can be generated or absorbed using the available capacity and the adjustable power factor of the inverter. Good reduction of voltage unbalance can be achieved by reactive power control of the PV systems. The presented tool is based on the three-phase current injection method and the PV systems are modeled via an equivalent circuit. The primal-dual interior point method is used to obtain the optimal operating points for the systems.

Keywords: Photovoltaic generation, primal-dual interior point method, three-phase optimal power flow, unbalanced system.

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Authors: M. Rezki, A. Belaidi

Abstract:

This paper deals with a method of learning to solve a real problem in biomedical engineering from a technical study of muscle fatigue. Electromyography (EMG) is a technique for evaluating and recording the electrical activity produced by skeletal muscles (viewpoint: anatomical and physiological). EMG is used as a diagnostics tool for identifying neuromuscular diseases, assessing low-back pain and muscle fatigue in general. In order to study the EMG signal for detecting fatigue in a muscle, we have taken a real problem which touches the tramway conductor the handle bar. For the study, we have used a typical autonomous platform in order to get signals at real time. In our case study, we were confronted with complex problem to do our experiments in a tram. This type of problem is recurring among students. To teach our students the method to solve this kind of problem, we built a similar system. Through this study, we realized a lot of objectives such as making the equipment for simulation, the study of detection of muscle fatigue and especially how to manage a study of biomedical looking.

Keywords: EMG, health platform, conductor’s tram, muscle fatigue.

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Authors: Karuna Tuchinda, Sasithon Bland

Abstract:

This work investigates the wear of a steam turbine blade coated with titanium nitride (TiN), and compares to the wear of uncoated blades. The coating is deposited on by physical vapor deposition (PVD) method. The working conditions of the blade were simulated and surface temperature and pressure values as well as flow velocity and flow direction were obtained. This data was used in the finite element wear model developed here in order to predict the wear of the blade. The wear mechanisms considered are erosive wear due to particle impingement and fluid jet, and fatigue wear due to repeated impingement of particles and fluid jet. Results show that the life of the TiN-coated blade is approximately 1.76 times longer than the life of the uncoated one.

Keywords: Physical vapour deposition, steam turbine blade, titanium-based coating, wear prediction.

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Authors: Manal Mhada, BrahimEzzahiri, Ouafae Benlhabib

Abstract:

Seventy-nine accessions, including two local wild species (Chenopodium album and C. murale) and several cultivated quinoa lines developed through recurrent selection in Morocco were screened for their resistance against Peronospora farinose, the causal agent of downy mildew disease. The method of artificial inoculation on detached healthy leaves taken from the middle stage of the plant was used. Screened accessions showed different levels of quantitative resistance to downy mildew as they were scored through the calculation of their area under disease progress curve and their two resistance components, the incubation period and the latent period. Significant differences were found between accessions regarding the three criteria (Incubation Period, Latent Period and Area Under Diseases Progress Curve). Accessions M2a and S938/1 were ranked resistant as they showed the longest Incubation Period (7 days) and Latent Period (12 days) and the lowest area under diseases progress curve (4). Therefore, M24 is the most susceptible accession as it has presented the highest area under diseases progress curve (34.5) and the shortest Incubation Period (1 day) and Latent Period (3 days). In parallel to this evaluation approach, the accession resistance was confirmed under the field conditions through natural infection by using the tree-leaf method. The high correlation found between detached leaf inoculation method and field screening under natural infection allows us to use this laboratory technique with sureness in further selection works.

Keywords: Detached leaf inoculation, Downy mildew, Field screening, Quinoa.

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Authors: Meredith Stevenson, John E. Porter

Abstract:

Since the pioneering work of Zadeh, fuzzy set theory has been applied to a myriad of areas. Song and Chissom introduced the concept of fuzzy time series and applied some methods to the enrollments of the University of Alabama. In recent years, a number of techniques have been proposed for forecasting based on fuzzy set theory methods. These methods have either used enrollment numbers or differences of enrollments as the universe of discourse. We propose using the year to year percentage change as the universe of discourse. In this communication, the approach of Jilani, Burney, and Ardil is modified by using the year to year percentage change as the universe of discourse. We use enrollment figures for the University of Alabama to illustrate our proposed method. The proposed method results in better forecasting accuracy than existing models.

Keywords: Fuzzy forecasting, fuzzy time series, fuzzified enrollments, time-invariant model

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Authors: Quoc-Nam Tran

Abstract:

The theory of Groebner Bases, which has recently been honored with the ACM Paris Kanellakis Theory and Practice Award, has become a crucial building block to computer algebra, and is widely used in science, engineering, and computer science. It is wellknown that Groebner bases computation is EXP-SPACE in a general polynomial ring setting. However, for many important applications in computer science such as satisfiability and automated verification of hardware and software, computations are performed in a Boolean ring. In this paper, we give an algorithm to show that Groebner bases computation is PSPACE in Boolean rings. We also show that with this discovery, the Groebner bases method can theoretically be as efficient as other methods for automated verification of hardware and software. Additionally, many useful and interesting properties of Groebner bases including the ability to efficiently convert the bases for different orders of variables making Groebner bases a promising method in automated verification.

Keywords: Algorithm, Complexity, Groebner basis, Applications of Computer Science.

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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: M. Pasbani Khiavi, A. R. M. Gharabaghi, K. Abedi

Abstract:

The mechanical behavior of porous media is governed by the interaction between its solid skeleton and the fluid existing inside its pores. The interaction occurs through the interface of gains and fluid. The traditional analysis methods of porous media, based on the effective stress and Darcy's law, are unable to account for these interactions. For an accurate analysis, the porous media is represented in a fluid-filled porous solid on the basis of the Biot theory of wave propagation in poroelastic media. In Biot formulation, the equations of motion of the soil mixture are coupled with the global mass balance equations to describe the realistic behavior of porous media. Because of irregular geometry, the domain is generally treated as an assemblage of fmite elements. In this investigation, the numerical formulation for the field equations governing the dynamic response of fluid-saturated porous media is analyzed and employed for the study of transient wave motion. A finite element model is developed and implemented into a computer code called DYNAPM for dynamic analysis of porous media. The weighted residual method with 8-node elements is used for developing of a finite element model and the analysis is carried out in the time domain considering the dynamic excitation and gravity loading. Newmark time integration scheme is developed to solve the time-discretized equations which are an unconditionally stable implicit method Finally, some numerical examples are presented to show the accuracy and capability of developed model for a wide variety of behaviors of porous media.

Keywords: Dynamic analysis, Interaction, Porous media, time domain

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