Search results for: Homotopy Perturbation Method
18869 An Analytical Study on the Vibration Reduction Method of Railway Station Using TPU
Authors: Jinho Hur, Minjung Shin, Heekyu Kim
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In many places, new railway constructions in the city are being used to build a viaduct station to take advantage of the space below the line, for difficulty of securing railway site and disconnections of areas. The space under the viaduct has limited to use by noise and vibration. In order to use it for various purposes, reducing noise and vibration is required. The vibration reduction method for new structures is recently developed enough to use as accommodation, but the reduction method for existing structures is still far-off. In this study, it suggests vibration reduction method by filling vibration reduction material to column members which is path of structure-bone-noise from trains run. Because most of railroad stations are reinforced concrete structures. It compares vibration reduction of station applied the method and original station by FEM analysis. As a result, reduction of vibration acceleration level in bandwidth 15~30Hz can be reduced. Therefore, using this method for viaduct railroad station, vibration of station is expected to be reduced.Keywords: structure borne noise, TPU, viaduct rail station, vibration reduction method
Procedia PDF Downloads 54418868 Application of Two Stages Adaptive Neuro-Fuzzy Inference System to Improve Dissolved Gas Analysis Interpretation Techniques
Authors: Kharisma Utomo Mulyodinoto, Suwarno, A. Abu-Siada
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Dissolved Gas Analysis is one of impressive technique to detect and predict internal fault of transformers by using gas generated by transformer oil sample. A number of methods are used to interpret the dissolved gas from transformer oil sample: Doernenberg Ratio Method, IEC (International Electrotechnical Commission) Ratio Method, and Duval Triangle Method. While the assessment of dissolved gas within transformer oil samples has been standardized over the past two decades, analysis of the results is not always straight forward as it depends on personnel expertise more than mathematical formulas. To get over this limitation, this paper is aimed at improving the interpretation of Doernenberg Ratio Method, IEC Ratio Method, and Duval Triangle Method using Two Stages Adaptive Neuro-Fuzzy Inference System (ANFIS). Dissolved gas analysis data from 520 faulty transformers was analyzed to establish the proposed ANFIS model. Results show that the developed ANFIS model is accurate and can standardize the dissolved gas interpretation process with accuracy higher than 90%.Keywords: ANFIS, dissolved gas analysis, Doernenberg ratio method, Duval triangular method, IEC ratio method, transformer
Procedia PDF Downloads 15018867 An Improved Tie Force Method for Progressive Collapse Resistance Design of Precast Concrete Cross Wall Structures
Authors: M. Tohidi, J. Yang, C. Baniotopoulos
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Progressive collapse of buildings typically occurs when abnormal loading conditions cause local damages, which leads to a chain reaction of failure and ultimately catastrophic collapse. The tie force (TF) method is one of the main design approaches for progressive collapse. As the TF method is a simplified method, further investigations on the reliability of the method is necessary. This study aims to develop an improved TF method to design the cross wall structures for progressive collapse. To this end, the pullout behavior of strands in grout was firstly analyzed; and then, by considering the tie force-slip relationship in the friction stage together with the catenary action mechanism, a comprehensive analytical method was developed. The reliability of this approach is verified by the experimental results of concrete block pullout tests and full scale floor-to-floor joints tests undertaken by Portland Cement Association (PCA). Discrepancies in the tie force between the analytical results and codified specifications have suggested the deficiency of TF method, hence an improved model based on the analytical results has been proposed to address this concern.Keywords: cross wall, progressive collapse, ties force method, catenary, analytical
Procedia PDF Downloads 46918866 The Improved Element Free Galerkin Method for 2D Heat Transfer Problems
Authors: Imen Debbabi, Hédi BelHadjSalah
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The Improved Element Free Galerkin (IEFG) method is presented to treat the steady states and the transient heat transfer problems. As a result of a combination between the Improved Moving Least Square (IMLS) approximation and the Element Free Galerkin (EFG) method, the IEFG's shape functions don't have the Kronecker delta property and the penalty method is used to impose the Dirichlet boundary conditions. In this paper, two heat transfer problems, transient and steady states, are studied to improve the efficiency of this meshfree method for 2D heat transfer problems. The performance of the IEFG method is shown using the comparison between numerical and analytic results.Keywords: meshfree methods, the Improved Moving Least Square approximation (IMLS), the Improved Element Free Galerkin method (IEFG), heat transfer problems
Procedia PDF Downloads 39418865 Adomian’s Decomposition Method to Functionally Graded Thermoelastic Materials with Power Law
Authors: Hamdy M. Youssef, Eman A. Al-Lehaibi
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This paper presents an iteration method for the numerical solutions of a one-dimensional problem of generalized thermoelasticity with one relaxation time under given initial and boundary conditions. The thermoelastic material with variable properties as a power functional graded has been considered. Adomian’s decomposition techniques have been applied to the governing equations. The numerical results have been calculated by using the iterations method with a certain algorithm. The numerical results have been represented in figures, and the figures affirm that Adomian’s decomposition method is a successful method for modeling thermoelastic problems. Moreover, the empirical parameter of the functional graded, and the lattice design parameter have significant effects on the temperature increment, the strain, the stress, the displacement.Keywords: Adomian, decomposition method, generalized thermoelasticity, algorithm
Procedia PDF Downloads 14318864 The Development of a New Block Method for Solving Stiff ODEs
Authors: Khairil I. Othman, Mahfuzah Mahayaddin, Zarina Bibi Ibrahim
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We develop and demonstrate a computationally efficient numerical technique to solve first order stiff differential equations. This technique is based on block method whereby three approximate points are calculated. The Cholistani of varied step sizes are presented in divided difference form. Stability regions of the formulae are briefly discussed in this paper. Numerical results show that this block method perform very well compared to existing methods.Keywords: block method, divided difference, stiff, computational
Procedia PDF Downloads 43018863 Analysis of the Aquifer Vulnerability of a Miopliocene Arid Area Using Drastic and SI Models
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Many methods in the groundwater vulnerability have been developed in the world (methods like PRAST, DRIST, APRON/ARAA, PRASTCHIM, GOD). In this study, our choice dealt with two recent complementary methods using category mapping of index with weighting criteria (Point County Systems Model MSCP) namely the standard DRASTIC method and SI (Susceptibility Index). At present, these two methods are the most used for the mapping of the intrinsic vulnerability of groundwater. Two classes of groundwater vulnerability in the Biskra sandy aquifer were identified by the DRASTIC method (average and high) and the SI method (very high and high). Integrated analysis has revealed that the high class is predominant for the DRASTIC method whereas for that of SI the preponderance is for the very high class. Furthermore, we notice that the method SI estimates better the vulnerability for the pollution in nitrates, with a rate of 85 % between the concentrations in nitrates of groundwater and the various established classes of vulnerability, against 75 % for the DRASTIC method. By including the land use parameter, the SI method produced more realistic results.Keywords: DRASTIC, SI, GIS, Biskra sandy aquifer, Algeria
Procedia PDF Downloads 48818862 Chaotic Sequence Noise Reduction and Chaotic Recognition Rate Improvement Based on Improved Local Geometric Projection
Authors: Rubin Dan, Xingcai Wang, Ziyang Chen
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A chaotic time series noise reduction method based on the fusion of the local projection method, wavelet transform, and particle swarm algorithm (referred to as the LW-PSO method) is proposed to address the problem of false recognition due to noise in the recognition process of chaotic time series containing noise. The method first uses phase space reconstruction to recover the original dynamical system characteristics and removes the noise subspace by selecting the neighborhood radius; then it uses wavelet transform to remove D1-D3 high-frequency components to maximize the retention of signal information while least-squares optimization is performed by the particle swarm algorithm. The Lorenz system containing 30% Gaussian white noise is simulated and verified, and the phase space, SNR value, RMSE value, and K value of the 0-1 test method before and after noise reduction of the Schreiber method, local projection method, wavelet transform method, and LW-PSO method are compared and analyzed, which proves that the LW-PSO method has a better noise reduction effect compared with the other three common methods. The method is also applied to the classical system to evaluate the noise reduction effect of the four methods and the original system identification effect, which further verifies the superiority of the LW-PSO method. Finally, it is applied to the Chengdu rainfall chaotic sequence for research, and the results prove that the LW-PSO method can effectively reduce the noise and improve the chaos recognition rate.Keywords: Schreiber noise reduction, wavelet transform, particle swarm optimization, 0-1 test method, chaotic sequence denoising
Procedia PDF Downloads 20018861 Numerical Solution of Integral Equations by Using Discrete GHM Multiwavelet
Authors: Archit Yajnik, Rustam Ali
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In this paper, numerical method based on discrete GHM multiwavelets is presented for solving the Fredholm integral equations of second kind. There is hardly any article available in the literature in which the integral equations are numerically solved using discrete GHM multiwavelet. A number of examples are demonstrated to justify the applicability of the method. In GHM multiwavelets, the values of scaling and wavelet functions are calculated only at t = 0, 0.5 and 1. The numerical solution obtained by the present approach is compared with the traditional Quadrature method. It is observed that the present approach is more accurate and computationally efficient as compared to quadrature method.Keywords: GHM multiwavelet, fredholm integral equations, quadrature method, function approximation
Procedia PDF Downloads 46218860 Generation of Numerical Data for the Facilitation of the Personalized Hyperthermic Treatment of Cancer with An Interstital Antenna Array Using the Method of Symmetrical Components
Authors: Prodromos E. Atlamazoglou
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The method of moments combined with the method of symmetrical components is used for the analysis of interstitial hyperthermia applicators. The basis and testing functions are both piecewise sinusoids, qualifying our technique as a Galerkin one. The dielectric coatings are modeled by equivalent volume polarization currents, which are simply related to the conduction current distribution, avoiding in that way the introduction of additional unknowns or numerical integrations. The results of our method for a four dipole circular array, are in agreement with those already published in literature for a same hyperthermia configuration. Apart from being accurate, our approach is more general, more computationally efficient and takes into account the coupling between the antennas.Keywords: hyperthermia, integral equations, insulated antennas, method of symmetrical components
Procedia PDF Downloads 25918859 On a Transient Magnetohydrodynamics Heat Transfer Within Radiative Porous Channel Due to Convective Boundary Condition
Authors: Bashiru Abdullahi, Isah Bala Yabo, Ibrahim Yakubu Seini
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In this paper, the steady/transient MHD heat transfer within radiative porous channel due to convective boundary conditions is considered. The solution of the steady-state and that of the transient version were conveyed by Perturbation and Finite difference methods respectively. The heat transfer mechanism of the present work ascertains the influence of Biot number〖(B〗_i1), magnetizing parameter (M), radiation parameter(R), temperature difference, suction/injection(S) Grashof number (Gr) and time (t) on velocity (u), temperature(θ), skin friction(τ), and Nusselt number (Nu). The results established were discussed with the help of a line graph. It was found that the velocity, temperature, and skin friction decay with increasing suction/injection and magnetizing parameters while the Nusselt number upsurges with suction/injection at y = 0 and falls at y =1. The steady-state solution was in perfect agreement with the transient version for a significant value of time t. It is interesting to report that the Biot number has a cogent influence consequently, as its values upsurge the result of the present work slant the extended literature.Keywords: heat transfer, thermal radiation, porous channel, MHD, transient, convective boundary condition
Procedia PDF Downloads 12118858 A New Family of Globally Convergent Conjugate Gradient Methods
Authors: B. Sellami, Y. Laskri, M. Belloufi
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Conjugate gradient methods are an important class of methods for unconstrained optimization, especially for large-scale problems. Recently, they have been much studied. In this paper, a new family of conjugate gradient method is proposed for unconstrained optimization. This method includes the already existing two practical nonlinear conjugate gradient methods, which produces a descent search direction at every iteration and converges globally provided that the line search satisfies the Wolfe conditions. The numerical experiments are done to test the efficiency of the new method, which implies the new method is promising. In addition the methods related to this family are uniformly discussed.Keywords: conjugate gradient method, global convergence, line search, unconstrained optimization
Procedia PDF Downloads 41018857 A Comparison Study of Different Methods Used in the Detection of Giardia lamblia on Fecal Specimen of Children
Authors: Muhammad Farooq Baig
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Objective: The purpose of this study was to compare results obtained using a single fecal specimen for O&P examination, direct immunofluorescence assay (DFA), and two conventional staining methods. Design: Hundred and fifty children fecal specimens were collected and examined by each method. The O&P and the DFA were used as the reference method. Setting: The study was performed at the laboratory in the Basic Medical Science Institute JPMC Karachi. Patients or Other Participants: The fecal specimens were collected from children with a suspected Giardia lamblia infection. Main Outcome Measures: The amount of agreement and disagreement between methods.1) Presence of giardiasis in our population. 2) The sensitivity and specificity of each method. Results: There was 45(30%) positive 105 (70%) negative on DFA, 41 (27.4%) positive 109 (72.6%) negative on iodine and 34 (22.6%) positive 116(77.4%) on saline method. The sensitivity and specificity of DFA in comparision to iodine were 92.2%, 92.7% respectively. The sensitivity and specificity of DFA in comparisoin to saline method were 91.2%, 87.9% respectively. The sensitivity of iodine method and saline method in compariosn to DFA were 82.2%, 68.8% respectively. There is mark diffrence in sensitivity of DFA to conventional method. Conclusion: The study supported findings of other investigators who concluded that DFA method have the greater sensitivity. The immunologic methods were more efficient and quicker than the conventional O&P method.Keywords: direct immunofluorescence assay (DFA), ova and parasite (O&P), Giardia lamblia, children, medical science
Procedia PDF Downloads 42518856 A Novel Eccentric Lapping Method with Two Rotatable Lapping Plates for Finishing Cemented Carbide Balls
Authors: C. C. Lv, Y. L. Sun, D. W. Zuo
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Cemented carbide balls are usually implemented in industry under the environment of high speed, high temperature, corrosiveness and strong collisions. However, its application is limited due to high fabrication cost, processing efficiency and quality. A novel eccentric lapping method with two rotatable lapping plates was proposed in this paper. A mathematical model was constructed to analyze the influence of each design parameter on this lapping method. To validate this new lapping method, an orthogonal experiment was conducted with cemented carbide balls (YG6). The simulation model was verified and the optimal lapping parameters were derived. The results show that the surface roundness of the balls reaches to 0.65um from 2um in 1 hour using this lapping method. So, using this novel lapping method, it can effectively improve the machining precision and efficiency of cemented carbide balls.Keywords: cemented carbide balls, eccentric lapping, high precision, lapping tracks, V-groove
Procedia PDF Downloads 39518855 A Variant of Newton's Method with Free Second-Order Derivative
Authors: Young Hee Geum
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In this paper, we present the iterative method and determine the control parameters to converge cubically for solving nonlinear equations. In addition, we derive the asymptotic error constant.Keywords: asymptotic error constant, iterative method, multiple root, root-finding, order of convergent
Procedia PDF Downloads 29418854 The Comparison and Optimization of the Analytic Method for Canthaxanthin, Food Colorants
Authors: Hee-Jae Suh, Kyung-Su Kim, Min-Ji Kim, Yeon-Seong Jeong, Ok-Hwan Lee, Jae-Wook Shin, Hyang-Sook Chun, Chan Lee
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Canthaxanthin is keto-carotenoid produced from beta-carotene and it has been approved to be used in many countries as a food coloring agent. Canthaxanthin has been analyzed using High Performance Liquid Chromatography (HPLC) system with various ways of pretreatment methods. Four official methods for verification of canthaxanthin at FSA (UK), AOAC (US), EFSA (EU) and MHLW (Japan) were compared to improve its analytical and the pretreatment method. The Linearity, the limit of detection (LOD), the limit of quantification (LOQ), the accuracy, the precision and the recovery ratio were determined from each method with modification in pretreatment method. All HPLC methods exhibited correlation coefficients of calibration curves for canthaxanthin as 0.9999. The analysis methods from FSA, AOAC, and MLHW showed the LOD of 0.395 ppm, 0.105 ppm, and 0.084 ppm, and the LOQ of 1.196 ppm, 0.318 ppm, 0.254 ppm, respectively. Among tested methods, HPLC method of MHLW with modification in pretreatments was finally selected for the analysis of canthaxanthin in lab, because it exhibited the resolution factor of 4.0 and the selectivity of 1.30. This analysis method showed a correlation coefficients value of 0.9999 and the lowest LOD and LOQ. Furthermore, the precision ratio was lower than 1 and the accuracy was almost 100%. The method presented the recovery ratio of 90-110% with modification in pretreatment method. The cross-validation of coefficient variation was 5 or less among tested three institutions in Korea.Keywords: analytic method, canthaxanthin, food colorants, pretreatment method
Procedia PDF Downloads 68318853 Apoptosis Activity of Persea declinata (Bl.) Kosterm Bark Methanolic Crude Extract
Authors: P. Narrima, C. Y. Looi, M. A. Mohd, H. M. Ali
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Persea declinata (Bl.) Kosterm is a member of the Lauraceae family, widely distributed in Southeast Asia. It is from the same genus with avocado (Persea americana Mill), which is widely consumed as food and for medicinal purposes. In the present study, we examined the anticancer properties of Persea declinata (Bl.) Kosterm bark methanolic crude extract (PDM). PDM exhibited a potent antiproliferative effect in MCF-7 human breast cancer cells, with an IC50 value of 16.68 µg/mL after 48h of treatment. We observed that PDM caused cell cycle arrest and subsequent apoptosis in MCF-7 cells, as exhibited by increased population at G0/G1 phase, higher lactate dehydrogenase (LDH) release, and DNA fragmentation. Mechanistic studies showed that PDM caused significant elevation in ROS production, leading to perturbation of mitochondrial membrane potential, cell permeability, and activation of caspases-3/7. On the other hand, real-time PCR and Western blot analysis showed that PDM treatment increased the expression of the proapoptotic molecule, Bax, but decreased the expression of prosurvival proteins, Bcl-2 and Bcl-xL, in a dose-dependent manner. These findings imply that PDM could inhibit proliferation in MCF-7 cells via cell cycle arrest and apoptosis induction, indicating its potential as a therapeutic agent worthy of further development.Keywords: antiproliferative, apoptosis, MCF-7 human breast cancer, Persea declinata
Procedia PDF Downloads 24318852 Evaluation of a Risk Assessment Method for Fiber Emissions from Sprayed Asbestos-Containing Materials
Authors: Yukinori Fuse, Masato Kawaguchi
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A quantitative risk assessment method was developed for fiber emissions from sprayed asbestos-containing materials (ACMs). In Japan, instead of being quantitative, these risk assessments have relied on the subjective judgment of skilled engineers, which may vary from one person to another. Therefore, this closed sampling method aims at avoiding any potential variability between assessments. This method was used to assess emissions from ACM sprayed in eleven buildings and the obtained results were compared with the subjective judgments of a skilled engineer. An approximate correlation tendency was found between both approaches. In spite of existing uncertainties, the closed sampling method is useful for public health protection. We firmly believe that this method may find application in the management and renovation decisions of buildings using friable and sprayed ACM.Keywords: asbestos, renovation, risk assessment, maintenance
Procedia PDF Downloads 37918851 Modification of Newton Method in Two Points Block Differentiation Formula
Authors: Khairil Iskandar Othman, Nadhirah Kamal, Zarina Bibi Ibrahim
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Block methods for solving stiff systems of ordinary differential equations (ODEs) are based on backward differential formulas (BDF) with PE(CE)2 and Newton method. In this paper, we introduce Modified Newton as a new strategy to get more efficient result. The derivation of BBDF using modified block Newton method is presented. This new block method with predictor-corrector gives more accurate result when compared to the existing BBDF.Keywords: modified Newton, stiff, BBDF, Jacobian matrix
Procedia PDF Downloads 38018850 Numerical Wave Solutions for Nonlinear Coupled Equations Using Sinc-Collocation Method
Authors: Kamel Al-Khaled
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In this paper, numerical solutions for the nonlinear coupled Korteweg-de Vries, (abbreviated as KdV) equations are calculated by Sinc-collocation method. This approach is based on a global collocation method using Sinc basis functions. First, discretizing time derivative of the KdV equations by a classic finite difference formula, while the space derivatives are approximated by a $\theta-$weighted scheme. Sinc functions are used to solve these two equations. Soliton solutions are constructed to show the nature of the solution. The numerical results are shown to demonstrate the efficiency of the newly proposed method.Keywords: Nonlinear coupled KdV equations, Soliton solutions, Sinc-collocation method, Sinc functions
Procedia PDF Downloads 52518849 Study of the Stability of Underground Mines by Numerical Method: The Mine Chaabet El Hamra, Algeria
Authors: Nakache Radouane, M. Boukelloul, M. Fredj
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Method room and pillar sizes are key factors for safe mining and their recovery in open-stop mining. This method is advantageous due to its simplicity and requirement of little information to be used. It is probably the most representative method among the total load approach methods although it also remains a safe design method. Using a finite element software (PLAXIS 3D), analyses were carried out with an elasto-plastic model and comparisons were made with methods based on the total load approach. The results were presented as the optimization for improving the ore recovery rate while maintaining a safe working environment.Keywords: room and pillar, mining, total load approach, elasto-plastic
Procedia PDF Downloads 33018848 Method Development and Validation for Quantification of Active Content and Impurities of Clodinafop Propargyl and Its Enantiomeric Separation by High-Performance Liquid Chromatography
Authors: Kamlesh Vishwakarma, Bipul Behari Saha, Sunilkumar Sing, Abhishek Mishra, Sreenivas Rao
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A rapid, sensitive and inexpensive method has been developed for complete analysis of Clodinafop Propargyl. Clodinafop Propargyl enantiomers were separated on chiral column, Chiral Pak AS-H (250 mm. 4.6mm x 5µm) with mobile phase n-hexane: IPA (96:4) at flow rate 1.5 ml/min. The effluent was monitored by UV detector at 230 nm. Clodinafop Propagyl content and impurity quantification was done with reverse phase HPLC. The present study describes a HPLC method using simple mobile phase for the quantification of Clodinafop Propargyl and its impurities. The method was validated and found to be accurate, precise, convenient and effective. Moreover, the lower solvent consumption along with short analytical run time led to a cost effective analytical method.Keywords: Clodinafop Propargyl, method, validation, HPLC-UV
Procedia PDF Downloads 37118847 Static Light Scattering Method for the Analysis of Raw Cow's Milk
Authors: V. Villa-Cruz, H. Pérez-Ladron de Guevara, J. E. Diaz-Díaz
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Static Light Scattering (SLS) was used as a method to analyse cow's milk raw, coming from the town of Lagos de Moreno, Jalisco, Mexico. This method is based on the analysis of the dispersion of light laser produced by a set of particles in solution. Based on the above, raw milk, which contains particles of fat globules, with a diameter of 2000 nm and particles of micelles of protein with 300 nm in diameter were analyzed. For this, dilutions of commercial milk were made (1.0%, 2.0% and 3.3%) to obtain a pattern of laser light scattering and also made measurements of raw cow's milk. Readings were taken in a sweep initial angle 10° to 170°, results were analyzed with the program OriginPro 7. The SLS method gives us an estimate of the percentage of fat content in milk samples. It can be concluded that the SLS method, is a quick method of analysis to detect adulteration in raw cow's milk.Keywords: light scattering, milk analysis, adulteration in milk, micelles, OriginPro
Procedia PDF Downloads 37518846 Software Engineering Inspired Cost Estimation for Process Modelling
Authors: Felix Baumann, Aleksandar Milutinovic, Dieter Roller
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Up to this point business process management projects in general and business process modelling projects in particular could not rely on a practical and scientifically validated method to estimate cost and effort. Especially the model development phase is not covered by a cost estimation method or model. Further phases of business process modelling starting with implementation are covered by initial solutions which are discussed in the literature. This article proposes a method of filling this gap by deriving a cost estimation method from available methods in similar domains namely software development or software engineering. Software development is regarded as closely similar to process modelling as we show. After the proposition of this method different ideas for further analysis and validation of the method are proposed. We derive this method from COCOMO II and Function Point which are established methods of effort estimation in the domain of software development. For this we lay out similarities of the software development rocess and the process of process modelling which is a phase of the Business Process Management life-cycle.Keywords: COCOMO II, busines process modeling, cost estimation method, BPM COCOMO
Procedia PDF Downloads 44118845 Isotope Effects on Inhibitors Binding to HIV Reverse Transcriptase
Authors: Agnieszka Krzemińska, Katarzyna Świderek, Vicente Molinier, Piotr Paneth
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In order to understand in details the interactions between ligands and the enzyme isotope effects were studied between clinically used drugs that bind in the active site of Human Immunodeficiency Virus Reverse Transcriptase, HIV-1 RT, as well as triazole-based inhibitor that binds in the allosteric pocket of this enzyme. The magnitudes and origins of the resulting binding isotope effects were analyzed. Subsequently, binding isotope effect of the same triazole-based inhibitor bound in the active site were analyzed and compared. Together, these results show differences in binding origins in two sites of the enzyme and allow to analyze binding mode and place of newly synthesized inhibitors. Typical protocol is described below on the example of triazole ligand in the allosteric pocket. Triazole was docked into allosteric cavity of HIV-1 RT with Glide using extra-precision mode as implemented in Schroedinger software. The structure of HIV-1 RT was obtained from Protein Data Bank as structure of PDB ID 2RKI. The pKa for titratable amino acids was calculated using PROPKA software, and in order to neutralize the system 15 Cl- were added using tLEaP package implemented in AMBERTools ver.1.5. Also N-terminals and C-terminals were build using tLEaP. The system was placed in 144x160x144Å3 orthorhombic box of water molecules using NAMD program. Missing parameters for triazole were obtained at the AM1 level using Antechamber software implemented in AMBERTools. The energy minimizations were carried out by means of a conjugate gradient algorithm using NAMD. Then system was heated from 0 to 300 K with temperature increment 0.001 K. Subsequently 2 ns Langevin−Verlet (NVT) MM MD simulation with AMBER force field implemented in NAMD was carried out. Periodic Boundary Conditions and cut-offs for the nonbonding interactions, range radius from 14.5 to 16 Å, are used. After 2 ns relaxation 200 ps of QM/MM MD at 300 K were simulated. The triazole was treated quantum mechanically at the AM1 level, protein was described using AMBER and water molecules were described using TIP3P, as implemented in fDynamo library. Molecules 20 Å apart from the triazole were kept frozen, with cut-offs established on range radius from 14.5 to 16 Å. In order to describe interactions between triazole and RT free energy of binding using Free Energy Perturbation method was done. The change in frequencies from ligand in solution to ligand bounded in enzyme was used to calculate binding isotope effects.Keywords: binding isotope effects, molecular dynamics, HIV, reverse transcriptase
Procedia PDF Downloads 43218844 Selection the Most Suitable Method for DNA Extraction from Muscle of Iran's Canned Tuna by Comparison of Different DNA Extraction Methods
Authors: Marjan Heidarzadeh
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High quality and purity of DNA isolated from canned tuna is essential for species identification. In this study, the efficiency of five different methods for DNA extraction was compared. Method of national standard in Iran, the CTAB precipitation method, Wizard DNA Clean Up system, Nucleospin and GenomicPrep were employed. DNA was extracted from two different canned tuna in brine and oil of the same tuna species. Three samples of each type of product were analyzed with the different methods. The quantity and quality of DNA extracted was evaluated using the 260 nm absorbance and ratio A260/A280 by spectrophotometer picodrop. Results showed that the DNA extraction from canned tuna preserved in different liquid media could be optimized by employing a specific DNA extraction method in each case. Best results were obtained with CTAB method for canned tuna in oil and with Wizard method for canned tuna in brine.Keywords: canned tuna PCR, DNA, DNA extraction methods, species identification
Procedia PDF Downloads 65818843 An Optimized Method for Calculating the Linear and Nonlinear Response of SDOF System Subjected to an Arbitrary Base Excitation
Authors: Hossein Kabir, Mojtaba Sadeghi
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Finding the linear and nonlinear responses of a typical single-degree-of-freedom system (SDOF) is always being regarded as a time-consuming process. This study attempts to provide modifications in the renowned Newmark method in order to make it more time efficient than it used to be and make it more accurate by modifying the system in its own non-linear state. The efficacy of the presented method is demonstrated by assigning three base excitations such as Tabas 1978, El Centro 1940, and MEXICO CITY/SCT 1985 earthquakes to a SDOF system, that is, SDOF, to compute the strength reduction factor, yield pseudo acceleration, and ductility factor.Keywords: single-degree-of-freedom system (SDOF), linear acceleration method, nonlinear excited system, equivalent displacement method, equivalent energy method
Procedia PDF Downloads 32018842 A Semi-Implicit Phase Field Model for Droplet Evolution
Authors: M. H. Kazemi, D. Salac
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A semi-implicit phase field method for droplet evolution is proposed. Using the phase field Cahn-Hilliard equation, we are able to track the interface in multiphase flow. The idea of a semi-implicit finite difference scheme is reviewed and employed to solve two nonlinear equations, including the Navier-Stokes and the Cahn-Hilliard equations. The use of a semi-implicit method allows us to have larger time steps compared to explicit schemes. The governing equations are coupled and then solved by a GMRES solver (generalized minimal residual method) using modified Gram-Schmidt orthogonalization. To show the validity of the method, we apply the method to the simulation of a rising droplet, a leaky dielectric drop and the coalescence of drops. The numerical solutions to the phase field model match well with existing solutions over a defined range of variables.Keywords: coalescence, leaky dielectric, numerical method, phase field, rising droplet, semi-implicit method
Procedia PDF Downloads 48418841 Teacher’s Perception of Dalcroze Method Course as Teacher’s Enhancement Course: A Case Study in Hong Kong
Authors: Ka Lei Au
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The Dalcroze method has been emerging in music classrooms, and music teachers are encouraged to integrate music and movement in their teaching. Music programs in colleges in Hong Kong have been introducing method courses such as Orff and Dalcroze method in music teaching as teacher’s education program. Since the targeted students of the course are music teachers who are making the decision of what approach to use in their classroom, their perception is significantly valued to identify how this approach is applicable in their teaching in regards to the teaching and learning culture and environment. This qualitative study aims to explore how the Dalcroze method as a teacher’s education course is perceived by music teachers from three aspects: 1) application in music teaching, 2) self-enhancement, 3) expectation. Through the lens of music teachers, data were collected from 30 music teachers who are taking the Dalcroze method course in music teaching in Hong Kong by the survey. The findings reveal the value and their intention of the Dalcroze method in Hong Kong. It also provides a significant reference for better development of such courses in the future in adaption to the culture, teaching and learning environment and teacher’s, student’s and parent’s perception of this approach.Keywords: Dalcroze method, music teaching, perception, self-enhancement, teacher’s education
Procedia PDF Downloads 40518840 Computation of Stress Intensity Factor Using Extended Finite Element Method
Authors: Mahmoudi Noureddine, Bouregba Rachid
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In this paper the stress intensity factors of a slant-cracked plate of AISI 304 stainless steel, have been calculated using extended finite element method and finite element method (FEM) in ABAQUS software, the results were compared with theoretical values.Keywords: stress intensity factors, extended finite element method, stainless steel, abaqus
Procedia PDF Downloads 619