Search results for: Ab initio molecular dynamics simulations

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

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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: Z. Popova, L. S. Pereira, М. Ivanova, P. Alexandrova, K. Doneva, V. Alexandrov, M. Kercheva

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This study assesses the vulnerability of Bulgarian agriculture to drought using the WINISAREG model and seasonal standard precipitation index SPI(2) for the period 1951-2004. This model was previously validated for maize on soils of different water holding capacity (TAW) in various locations. Simulations are performed for Plovdiv, Stara Zagora and Sofia. Results relative to Plovdiv show that in soils of large TAW (180 mm m-1) net irrigation requirements (NIRs) range 0-40 mm in wet years and 350-380 mm in dry years. In soils of small TAW (116 mm m-1), NIRs reach 440 mm in the very dry year. NIRs in Sofia are about 80 mm smaller. Rainfed maize is associated with great yield variability (29%91%) were found for seasonal agricultural drought relating the SPI (2) for “July-Aug" with the simulated RYD of rainfed maize while in Stara Zagora and Sofia the relationships are less accurate (R2>71%). When rainfed maize is grown on soils of large TAW economical losses are produced when high peak season SPI (2) < -0.50 in Plovdiv/Stara Zagora and SPI (2) < -0.90 in Sofia. The corresponding NIR thresholds were identified.

Keywords: Drought vulnerability, ISAREG simulation model, South Bulgaria, SPI-index

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Authors: Sandu L., Topală F., Porojan S.

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Cast metal inlays can be used on molars requiring a class II restoration instead amalgam and offer a durable alternative. Because it is known that class II inlays may increase the susceptibility to fracture, it is important to ensure optimal performance in selection of the adequate preparation design to reduce stresses in teeth structures and also in the restorations. The aim of the study was to investigate the influence of preparation design on stress distribution in molars with different class II preparations and in cast metal inlays. The first step of the study was to achieve 3D models in order to analyze teeth and cast metal class II inlays. The geometry of the intact tooth was obtained by 3D scanning using a manufactured device. With a NURBS modeling program the preparations and the appropriately inlays were designed. 3D models of first upper molars of the same shape and size were created. Inlay cavities designs were created using literature data. The geometrical model was exported and the mesh structure of the solid 3D model was created for structural simulations. Stresses were located around the occlusal contact areas. For the studied cases, the stress values were not significant influenced by the taper of the preparation. it was demonstrated stresses are higher in the cast metal restorations and therefore the strength of the teeth is not affected.

Keywords: cast metal inlays, class II restoration, molars, 3D models, structural simulations.

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

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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: Wenjun Zhang, Yunqing Du, Ming L. Wang

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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: Irakli V. Gugushvili, Nickolay M. Evstigneev

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Numerical integration of initial boundary problem for advection equation in 3 ℜ is considered. The method used is  conditionally stable semi-Lagrangian advection scheme with high order interpolation on unstructured mesh. In order to increase time step integration the BFECC method with limiter TVD correction is used. The method is adopted on parallel graphic processor unit environment using NVIDIA CUDA and applied in Navier-Stokes solver. It is shown that the calculation on NVIDIA GeForce 8800  GPU is 184 times faster than on one processor AMDX2 4800+ CPU. The method is extended to the incompressible fluid dynamics solver. Flow over a Cylinder for 3D case is compared to the experimental data.

Keywords: Advection equations, CUDA technology, Flow overthe 3D Cylinder, Incompressible Pressure Projection Solver, Parallel computation.

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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: E. Abedi, A. Ahmadi Nadooshan, S. Salehi

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Modeling and vibration of a flexible link manipulator with tow flexible links and rigid joints are investigated which can include an arbitrary number of flexible links. Hamilton principle and finite element approach is proposed to model the dynamics of flexible manipulators. The links are assumed to be deflection due to bending. The association between elastic displacements of links is investigated, took into account the coupling effects of elastic motion and rigid motion. Flexible links are treated as Euler-Bernoulli beams and the shear deformation is thus abandoned. The dynamic behavior due to flexibility of links is well demonstrated through numerical simulation. The rigid-body motion and elastic deformations are separated by linearizing the equations of motion around the rigid body reference path. Simulation results are shown on for both position and force trajectory tracking tasks in the presence of varying parameters and unknown dynamics remarkably well. The proposed method can be used in both dynamic simulation and controller design.

Keywords: Flexible manipulator, flexible link, dynamicmodeling, end point.

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Authors: T. J. Jamaleddine

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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

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

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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: Akhilesh Khapre, Basudeb Munshi

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A computational fluid dynamics simulation is done for non-Newtonian fluid in a baffled stirred tank. The CMC solution is taken as non-Newtonian shear thinning fluid for simulation. The Reynolds Average Navier Stocks equation with steady state multi reference frame approach is used to simulate flow in the stirred tank. The turbulent flow field is modelled using realizable k-ε turbulence model. The simulated velocity profiles of Rushton turbine is validated with literature data. Then, the simulated flow field of CD-6 impeller is compared with the Rushton turbine. The flow field generated by CD-6 impeller is less in magnitude than the Rushton turbine. The impeller global parameter, power number and flow number, and entropy generation due to viscous dissipation rate is also reported.

Keywords: Computational fluid dynamics, non-Newtonian, Rushton turbine, CD-6 impeller, power number, flow number, viscous dissipation rate.

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Authors: Mohamed Hafez, Georg Hausner

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The full length mitochondrial small subunit ribosomal (mt-rns) gene has been characterized for Ophiostoma novo-ulmi subspecies americana. The gene was also characterized for Ophiostoma ulmi and a group II intron was noted in the mt-rns gene of O. ulmi. The insertion in the mt-rns gene is at position S952 and it is a group IIB1 intron that encodes a double motif LAGLIDADG homing endonuclease from an open reading frame located within a loop of domain III. Secondary structure models for the mt-rns RNA of O. novo-ulmi subsp. americana and O. ulmi were generated to place the intron within the context of the ribosomal RNA. The in vivo splicing of the O.ul-mS952 group II intron was confirmed with reverse transcription-PCR. A survey of 182 strains of Dutch Elm Diseases causing agents showed that the mS952 intron was absent in what is considered to be the more aggressive species O. novo-ulmi but present in strains of the less aggressive O. ulmi. This observation suggests that the O.ul-mS952 intron can be used as a PCR-based molecular marker to discriminate between O. ulmi and O. novo-ulmi subsp. americana.

Keywords: Dutch Elm Disease, group II introns, mtDNA, species identification

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Authors: Etsuo Morishita

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In this paper, we show shallow water in a tin box as an analogous simulation tool for high-speed aerodynamics education and research. It is customary that we use a water tank to create shallow water flow. While a flow in a water tank is not necessarily uniform and is sometimes wavy, we can visualize a clear supercritical flow even when we move a body manually in stationary water in a simple shallow tin box. We can visualize a blunt shock wave around a moving circular cylinder together with a shock pattern around a diamond airfoil. Another interesting analogous experiment is a hydrodynamic shock tube with water and tea. We observe the contact surface clearly due to color difference of the two liquids those are invisible in the real gas dynamics experiment. We first revisit the similarities between high-speed aerodynamics and shallow water hydraulics. Several educational and research experiments are then introduced for engineering students. Shallow water experiments in a tin box simulate properly the high-speed flows.

Keywords: Aerodynamics compressible flow, gas dynamics, hydraulics, shock wave.

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Authors: Dany Ng Cheong Vee, Preethee Nunkoo Gonpot, Noor-Ul-Hacq Sookia

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In this paper, we consider the application of Extreme Value Theory as a risk measurement tool. The Value at Risk, for a set of indices, from six Stock Exchanges of Frontier markets is calculated using the Peaks over Threshold method and the performance of the model index-wise is evaluated using coverage tests and loss functions. Our results show that “fattailedness” alone of the data is not enough to justify the use of EVT as a VaR approach. The structure of the returns dynamics is also a determining factor. This approach works fine in markets which have had extremes occurring in the past thus making the model capable of coping with extremes coming up (Colombo, Tunisia and Zagreb Stock Exchanges). On the other hand, we find that indices with lower past than present volatility fail to adequately deal with future extremes (Mauritius and Kazakhstan). We also conclude that using EVT alone produces quite static VaR figures not reflecting the actual dynamics of the data.

Keywords: Extreme Value theory, Financial Crisis 2008, Frontier Markets, Value at Risk.

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Authors: Hamad N. Altalyan, Brian G. Jones, John Bradd

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A comprehensive study was conducted to examine the removal of inorganic contaminants that exist in surface and groundwater in the Illawarra and Sydney regions. The ability of multi-walled carbon nanotubes (MWCNT), as a generation of membrane technology, was examined using a dead-end filtration cell setup. A set of ten compounds were examined in this study that represent the significant inorganic cations and anions commonly found in contaminated surface and groundwater. The performance of MWCNT buckypaper membranes in excluding anions was found to be better than that of its cation exclusion. This phenomenon can be attributed to the Donnan exclusion mechanism (charge repulsion mechanism). Furthermore, the results revealed that phosphate recorded the highest exclusion value reaching 69.2%, whereas the lowest rejection value was for potassium where no removal occurred (0%). The reason for this is that the molecular weight of phosphate (95.0 g/mol) is greater than the molecular weight of potassium (39.10 g/mol).

Keywords: Nanotechnology, buckypaper, carbon nanotube, CNT, multi-walled carbon nanotube, MWCNT, Botany Bay, Russell Vale.

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Authors: B. Aydinli, A. Caglar

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Renewable energy sources have gained ultimate urgency due to the need of the preservation of the environment for a sustainable development. Pyrolysis is an ultimate promising process in the recycling and acquisition of precious chemicals from wastes. Here, the co-pyrolysis of hazelnut shell with ultra-high molecular weight polyethylene was carried out catalytically and noncatalytically at 500 and 650 ºC. Potassium dichromate was added in certain amounts to act as a catalyst. The liquid, solid and gas products quantities were determined by gravimetry. As a main result, remarkable increases in gasification were observed by using this catalyst for pure components and their blends especially at 650 ºC. The increase in gas product quantity was compensated mainly with the decreases in the solid products and additionally in some cases liquid products quantities. These observations may stem from mainly the activation of carbon-carbon bonds rather than carbon-hydrogen bonds via potassium dichromate. Also, the catalytic effect of potassium dichromate on HS: PEO and HS: UHMWPE co-pyrolysis was compared.

Keywords: Hazelnut shell, Polyethylene oxide, Potassium Dichromate, Pyrolysis, UHMWPE

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Authors: Divya Rajavathsavai, Akhilesh Khapre, Basudeb Munshi

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The computational fluid dynamics (CFD) study of stirred tank with the air-water interface are carried out in the presence of different types of the impeller and with or without baffles. A multiple reference frame (MRF) approach with the volume of fluid (VOF) method is used to capture the air-water interface. The RANS (Reynolds Averaged Navier-Stokes) equations with k-ε turbulence model are solved to predict the flow behavior of water and air phase which are treated as a different phases. The predicted results have shown that the VOF method is able to capture the interface in the unbaffled tank. While, the VOF method is showing an unfeasible results in the baffled tank with high rotational impeller speed. For continuous stirred tank, the air-water interface is disturbed by the inflow and the level of water is also increased with time.

Keywords: Computational Fluid Dynamics, stirred tank, airwater interface, multiple reference frame, volume of fluid, Reynolds Averaged Navier-Stokes equations.

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Authors: Farhad Asadi, Hossein Sadati

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In fields such as neuroscience and especially in cognition modeling of mental processes, uncertainty processing in temporal zone of signal is vital. In this paper, Bayesian online inferences in estimation of change-points location in signal are constructed. This method separated the observed signal into independent series and studies the change and variation of the regime of data locally with related statistical characteristics. We give conditions on simulations of the method when the data characteristics of signals vary, and provide empirical evidence to show the performance of method. It is verified that correlation between series around the change point location and its characteristics such as Signal to Noise Ratios and mean value of signal has important factor on fluctuating in finding proper location of change point. And one of the main contributions of this study is related to representing of these influences of signal statistical characteristics for finding abrupt variation in signal. There are two different structures for simulations which in first case one abrupt change in temporal section of signal is considered with variable position and secondly multiple variations are considered. Finally, influence of statistical characteristic for changing the location of change point is explained in details in simulation results with different artificial signals.

Keywords: Time series, fluctuation in statistical characteristics, optimal learning.

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Authors: F. Sangiorgio, J. Silfwerbrand, G. Mancini

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Geometric and mechanical properties all influence the resistance of RC structures and may, in certain combination of property values, increase the risk of a brittle failure of the whole system. This paper presents a statistical and probabilistic investigation on the resistance of RC beams designed according to Eurocodes 2 and 8, and subjected to multiple failure modes, under both the natural variation of material properties and the uncertainty associated with cross-section and transverse reinforcement geometry. A full probabilistic model based on JCSS Probabilistic Model Code is derived. Different beams are studied through material nonlinear analysis via Monte Carlo simulations. The resistance model is consistent with Eurocode 2. Both a multivariate statistical evaluation and the data clustering analysis of outcomes are then performed. Results show that the ultimate load behaviour of RC beams subjected to flexural and shear failure modes seems to be mainly influenced by the combination of the mechanical properties of both longitudinal reinforcement and stirrups, and the tensile strength of concrete, of which the latter appears to affect the overall response of the system in a nonlinear way. The model uncertainty of the resistance model used in the analysis plays undoubtedly an important role in interpreting results.

Keywords: Modelling, Monte Carlo Simulations, Probabilistic Models, Data Clustering, Reinforced Concrete Members, Structural Design.

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Authors: Soyoon Bak, Sunyoung Bu, Philsu Kim

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In this paper, a backward semi-Lagrangian scheme combined with the second-order backward difference formula is designed to calculate the numerical solutions of nonlinear advection-diffusion equations. The primary aims of this paper are to remove any iteration process and to get an efficient algorithm with the convergence order of accuracy 2 in time. In order to achieve these objects, we use the second-order central finite difference and the B-spline approximations of degree 2 and 3 in order to approximate the diffusion term and the spatial discretization, respectively. For the temporal discretization, the second order backward difference formula is applied. To calculate the numerical solution of the starting point of the characteristic curves, we use the error correction methodology developed by the authors recently. The proposed algorithm turns out to be completely iteration free, which resolves the main weakness of the conventional backward semi-Lagrangian method. Also, the adaptability of the proposed method is indicated by numerical simulations for Burgers’ equations. Throughout these numerical simulations, it is shown that the numerical results is in good agreement with the analytic solution and the present scheme offer better accuracy in comparison with other existing numerical schemes.

Keywords: Semi-Lagrangian method, Iteration free method, Nonlinear advection-diffusion equation.

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Authors: Keny Ordaz-Hernandez, Xavier Fischer, Fouad Bennis

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This article illustrates a model selection management approach for virtual prototypes in interactive simulations. In those numerical simulations, the virtual prototype and its environment are modelled as a multiagent system, where every entity (prototype,human, etc.) is modelled as an agent. In particular, virtual prototyp ingagents that provide mathematical models of mechanical behaviour inform of computational methods are considered. This work argues that selection of an appropriate model in a changing environment,supported by models? characteristics, can be managed by the deter-mination a priori of specific exploitation and performance measures of virtual prototype models. As different models exist to represent a single phenomenon, it is not always possible to select the best one under all possible circumstances of the environment. Instead the most appropriate shall be selecting according to the use case. The proposed approach consists in identifying relevant metrics or indicators for each group of models (e.g. entity models, global model), formulate their qualification, analyse the performance, and apply the qualification criteria. Then, a model can be selected based on the performance prediction obtained from its qualification. The authors hope that this approach will not only help to inform engineers and researchers about another approach for selecting virtual prototype models, but also assist virtual prototype engineers in the systematic or automatic model selection.

Keywords: Virtual prototype models, domain, qualification criterion, model qualification, model assessment, environmental modelling.

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Authors: Dhananjay C. Joshi, Jung-Hsin Lin

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Protein-protein interactions (PPI) play a crucial role in many biological processes such as cell signalling, transcription, translation, replication, signal transduction, and drug targeting, etc. Structural information about protein-protein interaction is essential for understanding the molecular mechanisms of these processes. Structures of protein-protein complexes are still difficult to obtain by biophysical methods such as NMR and X-ray crystallography, and therefore protein-protein docking computation is considered an important approach for understanding protein-protein interactions. However, reliable prediction of the protein-protein complexes is still under way. In the past decades, several grid-based docking algorithms based on the Katchalski-Katzir scoring scheme were developed, e.g., FTDock, ZDOCK, HADDOCK, RosettaDock, HEX, etc. However, the success rate of protein-protein docking prediction is still far from ideal. In this work, we first propose a more practical measure for evaluating the success of protein-protein docking predictions,the rate of first success (RFS), which is similar to the concept of mean first passage time (MFPT). Accordingly, we have assessed the ZDOCK bound and unbound benchmarks 2.0 and 3.0. We also createda new benchmark set for protein-protein docking predictions, in which the complexes have experimentally determined binding affinity data. We performed free energy calculation based on the solution of non-linear Poisson-Boltzmann equation (nlPBE) to improve the binding mode prediction. We used the well-studied thebarnase-barstarsystem to validate the parameters for free energy calculations. Besides,thenlPBE-based free energy calculations were conducted for the badly predicted cases by ZDOCK and ZRANK. We found that direct molecular mechanics energetics cannot be used to discriminate the native binding pose from the decoys.Our results indicate that nlPBE-based calculations appeared to be one of the promising approaches for improving the success rate of binding pose predictions.

Keywords: protein-protein docking, protein-protein interaction, molecular mechanics energetics, Poisson-Boltzmann calculations

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Authors: Bao Jinsong, Hu Xiaofeng, Wang Wei, Yu Dili, Jin Ye

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The paper researched and presented a virtual simulation system based on a full-digital lunar terrain, integrated with kinematics and dynamics module as well as autonomous navigation simulation module. The system simulation models are established. Enabling technologies such as digital lunar surface module, kinematics and dynamics simulation, Autonomous navigation are investigated. A prototype system for lunar rover locomotion simulation is developed based on these technologies. Autonomous navigation is a key echnology in lunar rover system, but rarely involved in virtual simulation system. An autonomous navigation simulation module have been integrated in this prototype system, which was proved by the simulation results that the synthetic simulation and visualizing analysis system are established in the system, and the system can provide efficient support for research on the autonomous navigation of lunar rover.

Keywords: Lunar rover, virtual simulation, autonomous navigation, full-digital lunar terrain

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Authors: Rajendraprasad Narne, P. C. Panda

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In this article, coordinated tuning of power system stabilizer (PSS) with static var compensator (SVC) and thyristor controlled series capacitor (TCSC) in multi-machine power system is proposed. The design of proposed coordinated damping controller is formulated as an optimization problem and the controller gains are optimized instantaneously using advanced adaptive particle swarm optimization (AAPSO). The objective function is framed with the inter-area speed deviations of the generators and it is minimized using AAPSO to improve the dynamic stability of power system under severe disturbance. The proposed coordinated controller performance is evaluated under a wide range of system operating conditions with three-phase fault disturbance. Using time domain simulations the damping characteristics of proposed controller is compared with individually tuned PSS, SVC and TCSC controllers. Finally, the real-time simulations are carried out in Opal-RT hardware simulator to synchronize the proposed controller performance in the real world.

Keywords: Advanced adaptive particle swarm optimization, Coordinated design, Power system stabilizer, Real-time implementation, static var compensator, Thyristor controlled series capacitor.

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Authors: Hosein Falahaty, Hitoshi Gotoh, Abbas Khayyer

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Performance of a Hamiltonian based particle method in simulation of nonlinear structural dynamics is subjected to investigation in terms of stability and accuracy. The governing equation of motion is derived based on Hamilton's principle of least action, while the deformation gradient is obtained according to Weighted Least Square method. The hyper-elasticity models of Saint Venant-Kirchhoff and a compressible version similar to Mooney- Rivlin are engaged for the calculation of second Piola-Kirchhoff stress tensor, respectively. Stability along with accuracy of numerical model is verified by reproducing critical stress fields in static and dynamic responses. As the results, although performance of Hamiltonian based model is evaluated as being acceptable in dealing with intense extensional stress fields, however kinds of instabilities reveal in the case of violent collision which can be most likely attributed to zero energy singular modes.

Keywords: Hamilton's principle of least action, particle based method, hyper-elasticity, analysis of stability.

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Authors: Taiki Baba, Tomoaki Hashimoto

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The random dither quantization method enables us to achieve much better performance than the simple uniform quantization method for the design of quantized control systems. Motivated by this fact, the stochastic model predictive control method in which a performance index is minimized subject to probabilistic constraints imposed on the state variables of systems has been proposed for linear feedback control systems with random dither quantization. In other words, a method for solving optimal control problems subject to probabilistic state constraints for linear discrete-time control systems with random dither quantization has been already established. To our best knowledge, however, the feasibility of such a kind of optimal control problems has not yet been studied. Our objective in this paper is to investigate the feasibility of stochastic model predictive control problems for linear discrete-time control systems with random dither quantization. To this end, we provide the results of numerical simulations that verify the feasibility of stochastic model predictive control problems for linear discrete-time control systems with random dither quantization.

Keywords: Model predictive control, stochastic systems, probabilistic constraints, random dither quantization.

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Authors: Mehrdad N. Khajavi , Golamhassan Paygane, Ali Hakima

Abstract:

Vehicle which are turning or maneuvering at high speeds are susceptible to sliding and subsequently deviate from desired path. In this paper the dynamics governing the Yaw/Roll behavior of a vehicle has been simulated. Two different simulations have been used one for the real vehicle, for which a fuzzy controller is designed to increase its directional stability property. The other simulation is for a hypothetical vehicle with much higher tire cornering stiffness which is capable of developing the required lateral forces at the tire-ground patch contact to attain the desired lateral acceleration for the vehicle to follow the desired path without slippage. This simulation model is our reference model. The logic for keeping the vehicle on the desired track in the cornering or maneuvering state is to have some braking forces on the inner or outer tires based on the direction of vehicle deviation from the desired path. The inputs to our vehicle simulation model is steer angle δ and vehicle velocity V , and the outputs can be any kinematical parameters like yaw rate, yaw acceleration, side slip angle, rate of side slip angle and so on. The proposed fuzzy controller is a feed forward controller. This controller has two inputs which are steer angle δ and vehicle velocity V, and the output of the controller is the correcting moment M, which guides the vehicle back to the desired track. To develop the membership functions for the controller inputs and output and the fuzzy rules, the vehicle simulation has been run for 1000 times and the correcting moment have been determined by trial and error. Results of the vehicle simulation with fuzzy controller are very promising and show the vehicle performance is enhanced greatly over the vehicle without the controller. In fact the vehicle performance with the controller is very near the performance of the reference ideal model.

Keywords: Vehicle, Directional Stability, Fuzzy Logic Controller, ANFIS..

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Authors: Khemanand Moheeput, Smita S. D. Goorah, Satish K. Ramchurn

Abstract:

We report a computational study of the spreading dynamics of a viral infection in a complex (scale-free) network. The final epidemic size distribution (FESD) was found to be unimodal or bimodal depending on the value of the basic reproductive number R0 . The FESDs occurred on time-scales long enough for intermediate-time epidemic size distributions (IESDs) to be important for control measures. The usefulness of R0 for deciding on the timeliness and intensity of control measures was found to be limited by the multimodal nature of the IESDs and by its inability to inform on the speed at which the infection spreads through the population. A reduction of the transmission probability at the hubs of the scale-free network decreased the occurrence of the larger-sized epidemic events of the multimodal distributions. For effective epidemic control, an early reduction in transmission at the index cell and its neighbors was essential.

Keywords: Basic reproductive number, epidemic control, scalefree network, viral infection.

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