Search results for: molecular dynamics method

Authors: Agnieszka Danek, Rafał Pokrzywa

Abstract:

Approximate tandem repeats in a genomic sequence are two or more contiguous, similar copies of a pattern of nucleotides. They are used in DNA mapping, studying molecular evolution mechanisms, forensic analysis and research in diagnosis of inherited diseases. All their functions are still investigated and not well defined, but increasing biological databases together with tools for identification of these repeats may lead to discovery of their specific role or correlation with particular features. This paper presents a new approach for finding approximate tandem repeats in a given sequence, where the similarity between consecutive repeats is measured using the Hamming distance. It is an enhancement of a method for finding exact tandem repeats in DNA sequences based on the Burrows- Wheeler transform.

Keywords: approximate tandem repeats, Burrows-Wheeler transform, Hamming distance, suffix array

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Authors: Moghadazadeh Zahra, Towfighi Jafar, Mofarahi Masoud

Abstract:

This article is presented an experimental and modeling study of a four-bed pressure swing adsorption process using zeolite13X to provide oxygen-enriched air. The binary mixture N2/O2 (79/21 vol %) was used as a feed stream. The effects of purge/feed ratio (P/F), adsorption pressure, cyclic time and product flow rate on product purity and recovery under nonisothermal condition were studied. The adsorption dynamics of process were determined using a mathematical model incorporated mass and energy balances. A Mathlab code using finite difference method was developed to solve the set of coupled differential-algebraic equations, and the simulation results are agreed well with experimental results.

Keywords: Pressure swing adsorption (PSA), Oxygen, Zeolite 13X.

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Authors: E. Popov, N. Yorino, Y. Zoka, Y. Sasaki, H. Sugihara

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This paper discusses the performance of critical trajectory method (CTrj) for power system transient stability analysis under various loading settings and heavy fault condition. The method obtains Controlling Unstable Equilibrium Point (CUEP) which is essential for estimation of power system stability margins. The CUEP is computed by applying the CTrjto the boundary controlling unstable equilibrium point (BCU) method. The Proposed method computes a trajectory on the stability boundary that starts from the exit point and reaches CUEP under certain assumptions. The robustness and effectiveness of the method are demonstrated via six power system models and five loading conditions. As benchmark is used conventional simulation method whereas the performance is compared with and BCU Shadowing method.

Keywords: Power system, Transient stability, Critical trajectory method, Energy function method.

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Authors: Min Sun, Zhenyu Liu

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In this paper, a new descent-projection method with a new search direction for monotone structured variational inequalities is proposed. The method is simple, which needs only projections and some function evaluations, so its computational load is very tiny. Under mild conditions on the problem-s data, the method is proved to converges globally. Some preliminary computational results are also reported to illustrate the efficiency of the method.

Keywords: variational inequalities, monotone function, global convergence.

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Authors: Mohammed Bilal

Abstract:

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

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

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Authors: Ernesto A. Lagarda-Leyva, Manuel A. Valenzuela L., José G. Oshima C., Arnulfo A. Naranjo-Flores

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From August to December of 2016, a diagnostic and strategic planning study was carried out on the supply chain of the company Agropecuaria GABO S.A. de C.V. The final product of the study was the development of the strategic plan and a project portfolio to meet the demands of the three links in the supply chain of the Roma tomato exported annually to the United States of America. In this project, the strategic objective of ensuring the proper handling of the product was selected and one of the goals associated with this was the employment of quantitative methods to support decision making. Considering the antecedents, the objective of this case study was to develop a model to analyze the behavioral dynamics in the distribution chain, from the logistics of storage and shipment of Roma tomato in 81-case pallets (11.5 kg per case), to the two pre-cooling rooms and eventual loading onto transports, seeking to reduce the bottleneck and the associated costs by means of a dynamic interface. The methodology used was that of system dynamics, considering four phases that were adapted to the purpose of the study: 1) the conceptualization phase; 2) the formulation phase; 3) the evaluation phase; and 4) the communication phase. The main practical conclusions lead to the possibility of reducing both the bottlenecks in the cooling rooms and the costs by simulating scenarios and modifying certain policies. Furthermore, the creation of the dynamic interface between the model and the stakeholders was achieved by generating interaction with buttons and simple instructions that allow making modifications and observing diverse behaviors.

Keywords: Agrilogistics, distribution, scenarios, system dynamics.

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Authors: Abolfazl Hosseinkhani, Sepehr Sanaye

Abstract:

Different approaches have been used to predict the performance of the vertical axis wind turbines (VAWT), such as experimental, computational fluid dynamics (CFD), and analytical methods. Analytical methods, such as momentum models that use streamtubes, have low computational cost and sufficient accuracy. The double multiple streamtube (DMST) is one of the most commonly used of momentum models, which divide the rotor plane of VAWT into upwind and downwind. In fact, results from the DMST method have shown some discrepancy compared with experiment results; that is because the Darrieus turbine is a complex and aerodynamically unsteady configuration. In this study, analytical-experimental-based corrections, including dynamic stall, streamtube expansion, and finite blade length correction are used to improve the DMST method. Results indicated that using these corrections for a SANDIA 17-m VAWT will lead to improving the results of DMST.

Keywords: Vertical axis wind turbine, analytical, double multiple streamtube, streamtube expansion model, dynamic stall model, finite blade length correction.

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Authors: J.S.C. Prentice

Abstract:

The RK5GL3 method is a numerical method for solving initial value problems in ordinary differential equations, and is based on a combination of a fifth-order Runge-Kutta method and 3-point Gauss-Legendre quadrature. In this paper we describe the propagation of local errors in this method, and show that the global order of RK5GL3 is expected to be six, one better than the underlying Runge- Kutta method.

Keywords: RK5GL3, RKrGLm, Runge-Kutta, Gauss-Legendre, initial value problem, order, local error, global error.

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Authors: F. Sokhanvar, A. B. Khoshnevis

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In the present work steady inviscid hypersonic flows are calculated by approximate Method. Maslens' inverse method is the chosen approximate method. For the inverse problem, parabolic shock shape is chosen for the two-dimensional flow, and the body shape and flow field are calculated using Maslen's method. For the axisymmetric inverse problem paraboloidal shock is chosen and the surface distribution of pressure is obtained.

Keywords: Hypersonic flow, Inverse problem method

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Authors: Shang-Ping Lin, Shi-Hwa Lo, Ho-Li Yang

Abstract:

Company mergers and acquisitions reached their peak in the twenty-first century. Mergers and acquisitions have become one of the competitive strategies for external growth. In general, it is believed that mergers and acquisitions can create synergies. However, they require complete information technology system and service integration, especially in the banking industry. Much of the research has focused on performance evaluation, shareholder equity allocation, or even the increase of company market value after the merger and acquisition, whereas few scholars have focused on information system integration post merger and acquisition. This study indicates the role of information systems after a merger and acquisition, explaining the benefits of information system integration using a merger and acquisition case in the banking industry as an example. In addition, we discuss factors that affect the performance of information system integration, and utilize system dynamics to interpret the relationship among factors that affect information system integration performance in the banking industry after a merger and acquisition.

Keywords: Merger and Acquisition, Information SystemIntegration, System Dynamics

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Authors: S. Jain, Y. Deshpande

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The fluid mechanics principle is used extensively in designing axial flow fans and their associated equipment. This paper presents a computational fluid dynamics (CFD) modeling of air flow distribution from a radiator axial flow fan used in an acid pump truck Tier4 (APT T4) Repower. This axial flow fan augments the transfer of heat from the engine mounted on the APT T4. CFD analysis was performed for an area weighted average static pressure difference at the inlet and outlet of the fan. Pressure contours, velocity vectors, and path lines were plotted for detailing the flow characteristics for different orientations of the fan blade. The results were then compared and verified against known theoretical observations and actual experimental data. This study shows that a CFD simulation can be very useful for predicting and understanding the flow distribution from a radiator fan for further research work.

Keywords: Computational fluid dynamics (CFD), acid pump truck (APT) Tier4 Repower, axial flow fan, area weighted average static pressure difference, and contour plots.

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Authors: V. Geza, J. Vencels, G. Zageris, S. Pavlovs

Abstract:

One of the most perspective methods to produce SoG-Si is refinement via metallurgical route. The most critical part of this route is refinement from boron and phosphorus. Therefore, a new approach could address this problem. We propose an approach of creating surface waves on silicon melt’s surface in order to enlarge its area and accelerate removal of boron via chemical reactions and evaporation of phosphorus. A two dimensional numerical model is created which includes coupling of electromagnetic and fluid dynamic simulations with free surface dynamics. First results show behaviour similar to experimental results from literature.

Keywords: Numerical modelling, silicon refinement, surface waves, VOF method.

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Authors: Guangbin Wang, Liangliang Li, Fuping Tan

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In this paper, we give the generalized alternating twostage method in which the inner iterations are accomplished by a generalized alternating method. And we present convergence results of the method for solving nonsingular linear systems when the coefficient matrix of the linear system is a monotone matrix or an H-matrix.

Keywords: Generalized alternating two-stage method, linear system, convergence.

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Authors: Morteza Abbaszadeh, Parvin Nikpoorparizi, Mina Shahrooz

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For the first time since 1940 and presentation of theodorson-s theory, distribution of thrust, torque and efficiency along the blade of a counter rotating propeller axial fan was studied with a novel method in this research. A constant chord, constant pitch symmetric fan was investigated with Reynolds Stress Turbulence method in this project and H.E.S. method was utilized to obtain distribution profiles from C.F.D. tests outcome. C.F.D. test results were validated by estimation from Playlic-s analytical method. Final results proved ability of H.E.S. method to obtain distribution profiles from C.F.D test results and demonstrated interesting facts about effects of solidity and differences between distributions in front and rear section.

Keywords: C.F.D Test, Counter Rotating Propeller, H.E.S. Method, R.S.M. Method

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Authors: A. A. James, A. O. Adesanya, M. R. Odekunle, D. G. Yakubu

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This paper examines the development of one step, five hybrid point method for the solution of first order initial value problems. We adopted the method of collocation and interpolation of power series approximate solution to generate a continuous linear multistep method. The continuous linear multistep method was evaluated at selected grid points to give the discrete linear multistep method. The method was implemented using a constant order predictor of order seven over an overlapping interval. The basic properties of the derived corrector was investigated and found to be zero stable, consistent and convergent. The region of absolute stability was also investigated. The method was tested on some numerical experiments and found to compete favorably with the existing methods.

Keywords: Interpolation, Approximate Solution, Collocation, Differential system, Half step, Converges, Block method, Efficiency.

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Authors: Ben Richard Hughes, Ng Ping Sze Cherisa, Osman Beg

Abstract:

Various solar energy technologies exist and they have different application techniques in the generation of electrical power. The widespread use of photovoltaic (PV) modules in such technologies has been limited by relatively high costs and low efficiencies. The efficiency of PV panels decreases as the operating temperatures increase. This is due to the affect of solar intensity and ambient temperature. In this work, Computational Fluid Dynamics (CFD) was used to model the heat transfer from a standard PV panel and thus determine the rate of dissipation of heat. To accurately model the specific climatic conditions of the United Arab Emirates (UAE), a case study of a new build green building in Dubai was used. A finned heat pipe arrangement is proposed and analyzed to determine the improved heat dissipation and thus improved performance efficiency of the PV panel. A prototype of the arrangement is built for experimental testing to validate the CFD modeling and proof of concept.

Keywords: Computational Fluid Dynamics, Improving Efficiency, Photovoltaic (PV) Panels, Heat-pipe

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Authors: Mohammad Taghi Darvishi, Maliheh Najafi, Mohammad Najafi

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In this paper, using (G/G )-expansion method and modified F-expansion method, we give some explicit formulas of exact traveling wave solutions for the (3+1)-dimensional breaking soliton equation. A modified F-expansion method is proposed by taking full advantages of F-expansion method and Riccati equation in seeking exact solutions of the equation.

Keywords: Exact solution, The (3+1)-dimensional breaking soliton equation, ( G G )-expansion method, Riccati equation, Modified Fexpansion method.

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Authors: M. Omer Faruk, A. M. A. M. Zonaed Siddiki, M. Fazal Karim, Md. Masuduzzaman, S. Chowdhury, Md. Shafiqul Islam, M. Alamgir Hossain

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The dog tapeworms Echinococcus granulosus develop hydatid cysts in various organs in human and domestic animals worldwide including Bangladesh. The aim of this study was to identify and characterize the genotype of E. granulosus isolated from cattle using 12S rRNA and Cytochrome oxidase 1 (COX 1) genes. A total of 43 hydatid cyst samples were collected from 390 examined cattle samples derived from slaughterhouses. Among them, three cysts were fertile. Genomic DNA was extracted from germinal membrane and/or protoscoleces followed by PCR amplification of mitochondrial 12S rRNA and Cytochrome oxidase 1 gene fragments. The sequence data revealed existence of G1 (64.28%) and possible G3 (21.43%) genotypes for the first time in Bangladesh. The study indicates that common sheep strain G1 is the dominant subtype of E. granulosus in Chittagong region of Bangladesh. This will increase our understanding of the epidemiology of hydatidosis in the southern part of the country and will be useful to plan suitable control measures in the long run.

Keywords: Echinococcus granulosus, molecular characterization, cattle, Bangladesh.

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Authors: Danupun Visuwan, Pongchanun Luangpaiboon

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This paper presents the determination of the proper quality costs parameters which provide the optimum return. The system dynamics simulation was applied. The simulation model was constructed by the real data from a case of the electronic devices manufacturer in Thailand. The Steepest Descent algorithm was employed to optimise. The experimental results show that the company should spend on prevention and appraisal activities for 850 and 10 Baht/day respectively. It provides minimum cumulative total quality cost, which is 258,000 Baht in twelve months. The effect of the step size in the stage of improving the variables to the optimum was also investigated. It can be stated that the smaller step size provided a better result with more experimental runs. However, the different yield in this case is not significant in practice. Therefore, the greater step size is recommended because the region of optima could be reached more easily and rapidly.

Keywords: Quality costs, Steepest Descent Algorithm, StepSize, System Dynamics Simulation

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Authors: Hassan Saberi-Nik, Mahin Golchaman

Abstract:

This paper applies the homotopy analysis method method to a nonlinear differential-difference equation arising in nanotechnology. Continuum hypothesis on nanoscales is invalid, and a differential-difference model is considered as an alternative approach to describing discontinued problems. Comparison of the approximate solution with the exact one reveals that the method is very effective.

Keywords: Homotopy analysis method, differential-difference, nanotechnology.

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Authors: Lei Wang, Sizong Guo

Abstract:

In this paper, we study the numerical method for solving second-order fuzzy differential equations using Adomian method under strongly generalized differentiability. And, we present an example with initial condition having four different solutions to illustrate the efficiency of the proposed method under strongly generalized differentiability.

Keywords: Fuzzy-valued function, fuzzy initial value problem, strongly generalized differentiability, adomian decomposition method.

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Authors: Yiqin Lin, Liang Bao

Abstract:

This paper is devoted to the numerical solution of large-scale linear ill-posed systems. A multilevel regularization method is proposed. This method is based on a synthesis of the Arnoldi-Tikhonov regularization technique and the multilevel technique. We show that if the Arnoldi-Tikhonov method is a regularization method, then the multilevel method is also a regularization one. Numerical experiments presented in this paper illustrate the effectiveness of the proposed method.

Keywords: Discrete ill-posed problem, Tikhonov regularization, discrepancy principle, Arnoldi process, multilevel method.

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Authors: Wenjun Zhang, Yunqing Du, Ming L. Wang

Abstract:

Noninvasive diagnostics of diseases via breath analysis has attracted considerable scientific and clinical interest for many years and become more and more promising with the rapid advancements in nanotechnology and biotechnology. The volatile organic compounds (VOCs) in exhaled breath, which are mainly blood borne, particularly provide highly valuable information about individuals’ physiological and pathophysiological conditions. Additionally, breath analysis is noninvasive, real-time, painless, and agreeable to patients. We have developed a wireless sensor array based on single-stranded DNA (ssDNA)-functionalized single-walled carbon nanotubes (SWNT) for the detection of a number of physiological indicators in breath. Seven DNA sequences were used to functionalize SWNT sensors to detect trace amount of methanol, benzene, dimethyl sulfide, hydrogen sulfide, acetone, and ethanol, which are indicators of heavy smoking, excessive drinking, and diseases such as lung cancer, breast cancer, and diabetes. Our test results indicated that DNA functionalized SWNT sensors exhibit great selectivity, sensitivity, and repeatability; and different molecules can be distinguished through pattern recognition enabled by this sensor array. Furthermore, the experimental sensing results are consistent with the Molecular Dynamics simulated ssDNAmolecular target interaction rankings. Thus, the DNA-SWNT sensor array has great potential to be applied in chemical or biomolecular detection for the noninvasive diagnostics of diseases and personal health monitoring.

Keywords: Breath analysis, DNA-SWNT sensor array, diagnosis, noninvasive.

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Authors: T. J. Jamaleddine

Abstract:

Purge columns or degasser vessels are widely used in the polyolefin process for removing trapped hydrocarbons and in-excess catalyst residues from the polymer particles. A uniform distribution of purged gases coupled with a plug-flow characteristic inside the column system is desirable to obtain optimum desorption characteristics of trapped hydrocarbon and catalyst residues. Computational Fluid Dynamics (CFD) approach is a promising tool for design optimization of these vessels. The success of this approach is profoundly dependent on the solution strategy and the choice of geometrical layout at the vessel outlet. Filling the column with solids and initially solving for the solids flow minimized numerical diffusion substantially. Adopting a cylindrical configuration at the vessel outlet resulted in less numerical instability and resembled the hydrodynamics flow of solids in the hopper segment reasonably well.

Keywords: CFD, gas-solids flow, gas purging, species transport, purge column, degasser vessel.

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Authors: K. M. Tan, A. Anvar, T.F. Lu

Abstract:

A sophisticated simulator provides a cost-effective measure to carry out preliminary mission testing and diagnostic while reducing potential failures for real life at sea trials. The presented simulation framework covers three key areas: AUV modeling, sensor modeling, and environment modeling. AUV modeling mainly covers the area of AUV dynamics. Sensor modeling deals with physics and mathematical models that govern each sensor installed onto the AUV. Environment model incorporates the hydrostatic, hydrodynamics, and ocean currents that will affect the AUV in a real-time mission. Based on this designed simulation framework, custom scenarios provided by the user can be modeled and its corresponding behaviors can be observed. This paper focuses on the accuracy of the simulated data from AUV model and environmental model derived from a developed AUV test-bed which was jointly upgraded by DSTO and the University of Adelaide. The main contribution of this paper is to experimentally verify the accuracy of the proposed simulation framework.

Keywords: Autonomous Underwater Vehicle (AUV), simulator, framework, robotics, maritime robot, modeling.

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Authors: Min Sun, Jing Liu

Abstract:

In this paper, we focus on the alternating direction method, which is one of the most effective methods for solving structured variational inequalities(VI). In fact, we propose a proximal parallel alternating direction method which only needs to solve two strongly monotone sub-VI problems at each iteration. Convergence of the new method is proved under mild assumptions. We also present some preliminary numerical results, which indicate that the new method is quite efficient.

Keywords: structured variational inequalities, proximal point method, global convergence

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Authors: Kero T., Söderberg R., Andersson M., Lindkvist L.

Abstract:

The introduction of mass-customization has enabled new ways to treat patients within medicine. However, the introduction of industrialized treatments has also meant new obstacles. The purpose of this study was to introduce and theoretically test a method for improving dental crown fit. The optimization method allocates support points in order to check the final variation for dental crowns. Three different types of geometries were tested and compared. The three geometries were also divided into three sub-geometries: Current method, Optimized method and Feasible method. The Optimized method, using the whole surface for support points, provided the best results. The results support the objective of the study. It also seems that the support optimization method can dramatically improve the robustness of dental crown treatments.

Keywords: Bio-medicine, Dentistry, Mass-customization, Optimization and Robust design.

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Authors: Saeideh Hesam, Alireza Nazemi, Ahmad Haghbin

Abstract:

This paper presents the approximate analytical solution of a Zakharov-Kuznetsov ZK(m, n, k) equation with the help of the differential transform method (DTM). The DTM method is a powerful and efficient technique for finding solutions of nonlinear equations without the need of a linearization process. In this approach the solution is found in the form of a rapidly convergent series with easily computed components. The two special cases, ZK(2,2,2) and ZK(3,3,3), are chosen to illustrate the concrete scheme of the DTM method in ZK(m, n, k) equations. The results demonstrate reliability and efficiency of the proposed method.

Keywords: Zakharov-Kuznetsov equation, differential transform method, closed form solution.

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Authors: Ala'eddin A. Saif , Z. A. Z. Jamal, Z. Sauli, P. Poopalan

Abstract:

The ferroelectric behavior of barium strontium titanate (BST) in thin film form has been investigated in order to study the possibility of using BST for ferroelectric gate-field effect transistor (FeFET) for memory devices application. BST thin films have been fabricated as Al/BST/Pt/SiO2/Si-gate configuration. The variation of the dielectric constant (ε) and tan δ with frequency have been studied to ensure the dielectric quality of the material. The results show that at low frequencies, ε increases as the Ba content increases, whereas at high frequencies, it shows the opposite variation, which is attributed to the dipole dynamics. tan δ shows low values with a peak at the mid-frequency range. The ferroelectric behavior of the Al/BST/Pt/SiO2/Si has been investigated using C-V characteristics. The results show that the strength of the ferroelectric hysteresis loop increases as the Ba content increases; this is attributed to the grain size and dipole dynamics effect.

Keywords: BST thin film, Electrical properties, Ferroelectrichysteresis, Ferroelectric FET.

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Authors: Sarun Phibanchon

Abstract:

The solitary wave solution of the quadratic nonlinear Schrdinger equation is determined by the iterative method called Petviashvili method. This solution is also used for the initial condition for the time evolution to study the stability analysis. The spectral method is applied for the time evolution.

Keywords: soliton, iterative method, spectral method, plasma

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