Search results for: molecular modeling

Authors: J. Davoodi, F. Katouzi

Abstract:

The aim of this research was to calculate the thermal properties of Au3Ni Nanowire. The molecular dynamics (MD) simulation technique was used to obtain the effect of radius size on the energy, the melting temperature and the latent heat of fusion at the isobaric-isothermal (NPT) ensemble. The Quantum Sutton-Chen (Q-SC) many body interatomic potentials energy have been used for Gold (Au) and Nickel (Ni) elements and a mixing rule has been devised to obtain the parameters of these potentials for nanowire stats. Our MD simulation results show the melting temperature and latent heat of fusion increase upon increasing diameter of nanowire. Moreover, the cohesive energy decreased with increasing diameter of nanowire.

Keywords: Au3Ni Nanowire, Thermal properties, Molecular dynamics simulation

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Authors: Kamel Hashem, David Mioduser

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This paper describes part of a project about Learningby- Modeling (LbM). Studying complex systems is increasingly important in teaching and learning many science domains. Many features of complex systems make it difficult for students to develop deep understanding. Previous research indicates that involvement with modeling scientific phenomena and complex systems can play a powerful role in science learning. Some researchers argue with this view indicating that models and modeling do not contribute to understanding complexity concepts, since these increases the cognitive load on students. This study will investigate the effect of different modes of involvement in exploring scientific phenomena using computer simulation tools, on students- mental model from the perspective of structure, behavior and function. Quantitative and qualitative methods are used to report about 121 freshmen students that engaged in participatory simulations about complex phenomena, showing emergent, self-organized and decentralized patterns. Results show that LbM plays a major role in students' concept formation about complexity concepts.

Keywords: Complexity, Educational technology, Learning by modeling, Mental models

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Authors: V. Vargas-Alejo, L. E. Montero-Moguel

Abstract:

Understanding the concept of function has been important in mathematics education for many years. In this study, the models built by a group of five business administration and accounting undergraduate students when carrying out a population growth activity are analyzed. The theoretical framework is the Models and Modeling Perspective. The results show how the students included tables, graphics, and algebraic representations in their models. Using technology was useful to interpret, describe, and predict the situation. The first model, the students built to describe the situation, was linear. After that, they modified and refined their ways of thinking; finally, they created exponential growth. Modeling the activity was useful to deep on mathematical concepts such as covariation, rate of change, and exponential function also to differentiate between linear and exponential growth.

Keywords: Covariation reasoning, exponential function, modeling, representations.

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Authors: H. Zabiri, N. Mazuki

Abstract:

Several valve stiction models have been proposed in the literature to help understand and study the behavior of sticky valves. In this paper, an alternative black-box modeling approach based on Neural Network (NN) is presented. It is shown that with proper network type and optimum model structures, the performance of the developed NN stiction model is comparable to other established method. The resulting NN model is also tested for its robustness against the uncertainty in the stiction parameter values. Predictive mode operation also shows excellent performance of the proposed model for multi-steps ahead prediction.

Keywords: Control valve stiction, neural network, modeling.

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Authors: Swapnoneel Roy, Minhazur Rahman, Ashok Kumar Thakur

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Bioinformatics and computational biology involve the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually on the molecular level. Research in computational biology often overlaps with systems biology. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and proteinprotein interactions, and the modeling of evolution. Various global rearrangements of permutations, such as reversals and transpositions,have recently become of interest because of their applications in computational molecular biology. A reversal is an operation that reverses the order of a substring of a permutation. A transposition is an operation that swaps two adjacent substrings of a permutation. The problem of determining the smallest number of reversals required to transform a given permutation into the identity permutation is called sorting by reversals. Similar problems can be defined for transpositions and other global rearrangements. In this work we perform a study about some genome rearrangement primitives. We show how a genome is modelled by a permutation, introduce some of the existing primitives and the lower and upper bounds on them. We then provide a comparison of the introduced primitives.

Keywords: Sorting Primitives, Genome Rearrangements, Transpositions, Block Interchanges, Strip Exchanges.

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Authors: Eda Gök

Abstract:

Peridynamics is a new modeling concept of non-local interactions for solid structures. The formulations of Peridynamic (PD) theory are based on integral equations rather than differential equations. Through, undefined equations of associated problems are avoided. PD theory might be defined as continuum version of molecular dynamics. The medium is usually modeled with mass particles bonded together. Particles interact with each other directly across finite distances through central forces named as bonds. The main assumption of this theory is that the body is composed of material points which interact with other material points within a finite distance. Although, PD theory developed for discontinuities, it gives good results for structures which have no discontinuities. In this paper, displacement control of the isotropic plate under the effect of tensile and bending loading has been investigated by means of PD theory. A MATLAB code is generated to create PD bonds and corresponding surface correction factors. Using generated MATLAB code the geometry of the specimen is generated, and the code is implemented in Finite Element Software. The results obtained from non-local continuum theory are compared with the Finite Element Analysis results and analytical solution. The results show good agreement.

Keywords: Flexural loading, non-local continuum mechanics, Peridynamic theory, solid structures, tensile loading.

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Authors: Michael R. Johnson, Ian P. McCarthy

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There is a growing body of evidence to support the proposition of product take back for remanufacturing particularly within the context of Extended Producer Responsibility (EPR). Remanufacturing however presents challenges unlike that of traditional manufacturing environments due to its high levels of uncertainty which may further distract organizations from considering its potential benefits. This paper presents a novel modeling approach for evaluating the uncertainty of part failures within the remanufacturing process and its impact on economic and environmental performance measures. This paper presents both the theoretical modeling approach and an example of its use in application.

Keywords: Remanufacturing, Demanufacturing, Extended Producer Responsibility, Sustainability, Uncertainty.

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Authors: Chen Wang, Amir Anvar

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This paper describes the modeling and simulation of an underwater robot glider used in the shallow-water environment. We followed the Equations of motion derived by [2] and simplified dynamic Equations of motion of an underwater glider according to our underwater glider. A simulation code is built and operated in the MATLAB Simulink environment so that we can make improvements to our testing glider design. It may be also used to validate a robot glider design.

Keywords: AUV, underwater glider, robot, modeling, simulation.

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Authors: David G. Maxínez, A. Ferreyra Ramírez, Ismael Echenique Álvarez, Francisco Javier Sánchez Rangel, Guillermo Castillo Tapia, Petra Baldivia Noyola, María Antonieta García Galván

Abstract:

The project describes the modeling of various architectures mechatronics specifically morphologies of robots in an educational environment. Each structure developed by students of pre-school, primary and secondary was created using the concept of reverse engineering in a constructivist environment, to later be integrated in educational software that promotes the teaching of educational Robotics in a virtual and economic environment.

Keywords: Modeling, constructivist, engineering, reverse, robotics education, virtual, morphology.

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Authors: R. O. Ocaya, J. J. Terblans

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The laws of Newtonian mechanics allow ab-initio molecular dynamics to model and simulate particle trajectories in material science by defining a differentiable potential function. This paper discusses some considerations for the coding of ab-initio programs for simulation on a standalone computer and illustrates the approach by C language codes in the context of embedded metallic atoms in the face-centred cubic structure. The algorithms use velocity-time integration to determine particle parameter evolution for up to several thousands of particles in a thermodynamical ensemble. Such functions are reusable and can be placed in a redistributable header library file. While there are both commercial and free packages available, their heuristic nature prevents dissection. In addition, developing own codes has the obvious advantage of teaching techniques applicable to new problems.

Keywords: C-language, molecular dynamics, simulation, embedded atom method.

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Authors: Yasuyuki Konishi, Masayoshi Kobayashi

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Six parameters, the effective diffusivity (De), activation energy of De, pre-exponential factor of De, amount (ASOW) of self-organized water species, and amplitude (α) of the forced oscillation of the molecular mobility (1/tC) derived from the forced cyclic temperature change operation, were characterized by using six typical foods, squid, sardines, scallops, salmon, beef, and pork, as a function of the correlation time (tC) of the water molecule-s proton retained in the foods. Each of the six parameters was clearly divided into the water species A1 and A2 at a specified value of tC =10-8s (=CtC), indicating an anomalous change in the physicochemical nature of the water species at the CtC. The forced oscillation of 1/tC clearly demonstrated a characteristic mode depending on the food shown as a three dimensional map associated with 1/tC, the amount of self-organized water, and tC.

Keywords: molecular mobility, self-organization, hysteresis, water species A1 and A2, forced cyclic temperature change operation (FCTCO)

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Authors: Reza Ziaie Moayed, Ehsan Azini

Abstract:

Jet grouting (JG) is one of the methods of improving and increasing the strength and bearing of soil in which the high pressure water or grout is injected through the nozzles into the soil. During this process, a part of the soil and grout particles comes out of the drill borehole, and the other part is mixed up with the grout in place, as a result of this process, a mass of modified soil is created. The purpose of this method is to change the soil into a mixture of soil and cement, commonly known as "soil-cement". In this paper, first, the principles of high pressure injection and then the effective parameters in the JG method are described. Then, the tests on the samples taken from the columns formed from the excavation around the soil-cement columns, as well as the static loading test on the created column, are discussed. In the other part of this paper, the soil behavior models for numerical modeling in PLAXIS software are mentioned. The purpose of this paper is to evaluate the results of numerical modeling based on in-situ static loading tests. The results indicate an acceptable agreement between the results of the tests mentioned and the modeling results. Also, modeling with this software as an appropriate option for technical feasibility can be used to soil improvement using JG.

Keywords: Jet grouting column, Soil improvement, Numerical modeling, In-situ loading test.

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Authors: Wei Dong, Guo-Ying Gu, Xiangyang Zhu, Han Ding

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This paper presents preliminary results on modeling and control of a quadrotor UAV. With aerodynamic concepts, a mathematical model is firstly proposed to describe the dynamics of the quadrotor UAV. Parameters of this model are identified by experiments with Matlab Identify Toolbox. A group of PID controllers are then designed based on the developed model. To verify the developed model and controllers, simulations and experiments for altitude control, position control and trajectory tracking are carried out. The results show that the quadrotor UAV well follows the referenced commands, which clearly demonstrates the effectiveness of the proposed approach.

Keywords: Quadrotor UAV, Modeling, Control, Aerodynamics, System Identification.

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Authors: Spyridon Nikolaidis

Abstract:

A modeling approach for CMOS gates is presented based on the use of the equivalent inverter. A new model for the inverter has been developed using a simplified transistor current model which incorporates the nanoscale effects for the planar technology. Parametric expressions for the output voltage are provided as well as the values of the output and supply current to be compatible with the CCS technology. The model is parametric according the input signal slew, output load, transistor widths, supply voltage, temperature and process. The transistor widths of the equivalent inverter are determined by HSPICE simulations and parametric expressions are developed for that using a fitting procedure. Results for the NAND gate shows that the proposed approach offers sufficient accuracy with an average error in propagation delay about 5%.

Keywords: CMOS gate modeling, Inverter modeling, transistor current model, timing model.

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Authors: Emma K. Sales, Nilda G. Butardo

Abstract:

The project was undertaken to determine the effects of modified tissue culture protocols e.g. age of culture and hormone levels (2,4-D) in generating somaclonal variation. Moreover, the utility of molecular markers (SSR and MSAP) in sorting off types/somaclones were investigated.

Results show that somaclonal variation is in effect due to prolonged subculture and high 2,4-D concentration. The resultant variation was observed to be due to high level of methylation events specifically cytosine methylation either at the internal or external cytosine and was identified by methylation sensitive amplification polymorphism (MSAP).Simple sequence repeats (SSR) on the other hand, was able to associate a marker to a trait of interest.

These therefore, show that molecular markers can be an important tool in sorting out variation/mutants at an early stage.

Keywords: Methylation, MSAP, somaclones, SSR, subculture, 2, 4-D.

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Authors: Xiaoou Li, Wen Yu

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Crude oil blending is an important unit operation in petroleum refining industry. A good model for the blending system is beneficial for supervision operation, prediction of the export petroleum quality and realizing model-based optimal control. Since the blending cannot follow the ideal mixing rule in practice, we propose a static neural network to approximate the blending properties. By the dead-zone approach, we propose a new robust learning algorithm and give theoretical analysis. Real data of crude oil blending is applied to illustrate the neuro modeling approach.

Keywords: Neural networks, modeling, stability, crude oil.

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Authors: Rony Reátegui, Cesar Chácara, Benjamin Castañeda, Rafael Aguilar

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Nowadays, Heritage Building Information Modeling (HBIM) is considered an efficient tool to represent and manage information of Cultural Heritage (CH). The basis of this tool relies on a 3D model generally obtained from a Cloud-to-BIM procedure. There are different methods to create an HBIM model that goes from manual modeling based on the point cloud to the automatic detection of shapes and the creation of objects. The selection of these methods depends on the desired Level of Development (LOD), Level of Information (LOI), Grade of Generation (GOG) as well as on the availability of commercial software. This paper presents the 3D modeling of a stone masonry chapel using Recap Pro, Revit and Dynamo interface following a three-step methodology. The first step consists of the manual modeling of simple structural (e.g., regular walls, columns, floors, wall openings, etc.) and architectural (e.g., cornices, moldings and other minor details) elements using the point cloud as reference. Then, Dynamo is used for generative modeling of complex structural elements such as vaults, infills and domes. Finally, semantic information (e.g., materials, typology, state of conservation, etc.) and pathologies are added within the HBIM model as text parameters and generic models’ families respectively. The application of this methodology allows the documentation of CH following a relatively simple to apply process that ensures adequate LOD, LOI and GOG levels. In addition, the easy implementation of the method as well as the fact of using only one BIM software with its respective plugin for the scan-to-BIM modeling process means that this methodology can be adopted by a larger number of users with intermediate knowledge and limited resources, since the BIM software used has a free student license.

Keywords: Cloud-to-BIM, cultural heritage, generative modeling, HBIM, parametric modeling, Revit.

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Authors: Volodymyr Chegel

Abstract:

The computer modeling is carried out for parameter of sensitivity of optoelectronic chemical and biosensors, using phenomena of surface plasmon resonance (SPR). The physical model of SPR-sensor-s is described with (or without) of modifications of sensitive gold film surface by a dielectric layer. The variants of increasing of sensitivity for SPR-biosensors, constructed on the principle gold – dielectric – biomolecular layer are considered. Two methods of mathematical treatment of SPR-curve are compared – traditional, with estimation of sensor-s response as shift of the SPRcurve minimum and proposed, for system with dielectric layer, using calculating of the derivative in the point of SPR-curve half-width.

Keywords: Surface Plasmon Resonance, modeling, sensitivity, biosensor

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Authors: Junyou Shi, Weiwei Cui

Abstract:

Testability modeling is a commonly used method in testability design and analysis of system. A dependency matrix will be obtained from testability modeling, and we will give a quantitative evaluation about fault detection and isolation. Based on the dependency matrix, we can obtain the diagnosis tree. The tree provides the procedures of the fault detection and isolation. But the dependency matrix usually includes built-in test (BIT) and manual test in fact. BIT runs the test automatically and is not limited by the procedures. The method above cannot give a more efficient diagnosis and use the advantages of the BIT. A Comprehensive method of fault detection and isolation is proposed. This method combines the advantages of the BIT and Manual test by splitting the matrix. The result of the case study shows that the method is effective.

Keywords: BIT, fault detection, fault isolation, testability modeling.

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Authors: M. Rahimnejad, B. Vahidi, B. Ebrahimi Hoseinzadeh, F. Yazdian, P. Motamed Fath, R. Jamjah

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In this study, we developed and simulated nano-drug delivery systems efficacy in compare to free drug prescription. Computational models can be utilized to accelerate experimental steps and control the experiments high cost. Molecular dynamics simulation (MDS), in particular NAMD was utilized to better understand the anti-cancer drug interaction with cell membrane model. Paclitaxel (PTX) and dipalmitoylphosphatidylcholine (DPPC) were selected for the drug molecule and as a natural phospholipid nanocarrier, respectively. This work focused on two important interaction parameters between molecules in terms of center of mass (COM) and van der Waals interaction energy. Furthermore, we compared the simulation results of the PTX interaction with the cell membrane and the interaction of DPPC as a nanocarrier loaded by the drug with the cell membrane. The molecular dynamic analysis resulted in low energy between the nanocarrier and the cell membrane as well as significant decrease of COM amount in the nanocarrier and the cell membrane system during the interaction. Thus, the drug vehicle showed notably better interaction with the cell membrane in compared to free drug interaction with the cell membrane.

Keywords: Anti-cancer drug, center of Mass, interaction energy, molecular dynamics simulation, nanocarrier.

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Authors: Nina Suszczanska, Przemyslaw Szmal, Slawomir Kulikow

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In the paper a method of modeling text for Polish is discussed. The method is aimed at transforming continuous input text into a text consisting of sentences in so called canonical form, whose characteristic is, among others, a complete structure as well as no anaphora or ellipses. The transformation is lossless as to the content of text being transformed. The modeling method has been worked out for the needs of the Thetos system, which translates Polish written texts into the Polish sign language. We believe that the method can be also used in various applications that deal with the natural language, e.g. in a text summary generator for Polish.

Keywords: anaphora, machine translation, NLP, sign language, text syntax.

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Authors: M. Sadeghi, A.H. Jafari, S.M.P. Firoozabadi

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Deep Brain Stimulation or DBS is the second solution for Parkinson's Disease. Its three parameters are: frequency, pulse width and voltage. They must be optimized to achieve successful treatment. Nowadays it is done clinically by neurologists and there is not certain numerical method to detect them. The aim of this research is to introduce simulation and modeling of Parkinson's Disease treatment as a computational procedure to select optimum voltage. We recorded finger tremor signals of some Parkinsonian patients under DBS treatment at constant frequency and pulse width but variable voltages; then, we adapted a new model to fit these data. The optimum voltages obtained by data fitting results were the same as neurologists- commented voltages, which means modeling can be used as an engineering method to select optimum stimulation voltages.

Keywords: modeling, Deep Brain Stimulation, Parkinson'sdisease, tremor.

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Authors: Worachat Wannawong, Usa W. HumphriesPrungchan Wongwises, Suphat Vongvisessomjai

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The mathematical modeling of storm surge in sea and coastal regions such as the South China Sea (SCS) and the Gulf of Thailand (GoT) are important to study the typhoon characteristics. The storm surge causes an inundation at a lateral boundary exhibiting in the coastal zones particularly in the GoT and some part of the SCS. The model simulations in the three dimensional primitive equations with a high resolution model are important to protect local properties and human life from the typhoon surges. In the present study, the mathematical modeling is used to simulate the typhoon–induced surges in three case studies of Typhoon Linda 1997. The results of model simulations at the tide gauge stations can describe the characteristics of storm surges at the coastal zones.

Keywords: lateral boundary, mathematical modeling, numericalsimulations, three dimensional primitive equations, storm surge.

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Authors: Mihai Caramihai, Irina Severin, Ana Aurelia Chirvase, Adrian Onu, Cristina Tanase, Camelia Ungureanu

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An immunomodulator bioproduct is prepared in a batch bioprocess with a modified bacterium Pseudomonas aeruginosa. The bioprocess is performed in 100 L Bioengineering bioreactor with 42 L cultivation medium made of peptone, meat extract and sodium chloride. The optimal bioprocess parameters were determined: temperature – 37 0C, agitation speed - 300 rpm, aeration rate – 40 L/min, pressure – 0.5 bar, Dow Corning Antifoam M-max. 4 % of the medium volume, duration - 6 hours. This kind of bioprocesses are appreciated as difficult to control because their dynamic behavior is highly nonlinear and time varying. The aim of the paper is to present (by comparison) different models based on experimental data. The analysis criteria were modeling error and convergence rate. The estimated values and the modeling analysis were done by using the Table Curve 2D. The preliminary conclusions indicate Andrews-s model with a maximum specific growth rate of the bacterium in the range of 0.8 h-1.

Keywords: bioprocess modeling, Pseudomonas aeruginosa, kinetic models,

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Authors: Amel Grissa-Touzi, Minyar Sassi

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Conception is the primordial part in the realization of a computer system. Several tools have been used to help inventors to describe their software. These tools knew a big success in the relational databases domain since they permit to generate SQL script modeling the database from an Entity/Association model. However, with the evolution of the computer domain, the relational databases proved their limits and object-relational model became used more and more. Tools of present conception don't support all new concepts introduced by this model and the syntax of the SQL3 language. We propose in this paper a tool of help to the conception and implementation of object-relational databases called «NAVIGTOOLS" that allows the user to generate script modeling its database in SQL3 language. This tool bases itself on the Entity/Association and navigational model for modeling the object-relational databases.

Keywords: Abstract Data Table, Navigational model, Objectrelational databases, References.

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Authors: Anwar H. Jarndal, Ahmed S. Elwakil

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In this paper, a fraction-order model for pad parasitic effect of GaN HEMT on Si substrate is developed and validated. Open de-embedding structure is used to characterize and de-embed substrate loading parasitic effects. Unbiased device measurements are implemented to extract parasitic inductances and resistances. The model shows very good simulation for S-parameter measurements under different bias conditions. It has been found that this approach can improve the simulation of intrinsic part of the transistor, which is very important for small- and large-signal modeling process.

Keywords: Fractional-order modeling, GaN HEMT, Si-substrate, open de-embedding structure.

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Authors: M. Nabeel Rashin, J. Hemalatha

Abstract:

Novel Coconut oil nanofluids of various concentrations have been prepared through ultrasonically assisted sol-gel method. The structural and morphological properties of the copper oxide nanoparticle have been analyzed with respectively and it revealed the monoclinic end-centered structure of crystallite and shuttle like flake morphology of agglomerates. Ultrasonic studies have been made for the nanofluids at different temperatures. The molecular interactions responsible for the changes in acoustical parameter with respect to concentration and temperature are discussed.

Keywords: Cutting Fluid, Molecular Interaction, Nanofluids, Ultrasonic

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Authors: Ahmed Arara

Abstract:

Information sharing and exchange, rather than information processing, is what characterizes information technology in the 21st century. Ontologies, as shared common understanding, gain increasing attention, as they appear as the most promising solution to enable information sharing both at a semantic level and in a machine-processable way. Domain Ontology-based modeling has been exploited to provide shareability and information exchange among diversified, heterogeneous applications of enterprises. Contextual ontologies are “an explicit specification of contextual conceptualization". That is: ontology is characterized by concepts that have multiple representations and they may exist in several contexts. Hence, contextual ontologies are a set of concepts and relationships, which are seen from different perspectives. Contextualization is to allow for ontologies to be partitioned according to their contexts. The need for contextual ontologies in enterprise modeling has become crucial due to the nature of today's competitive market. Information resources in enterprise is distributed and diversified and is in need to be shared and communicated locally through the intranet and globally though the internet. This paper discusses the roles that ontologies play in an enterprise modeling, and how ontologies assist in building a conceptual model in order to provide communicative and interoperable information systems. The issue of enterprise modeling based on contextual domain ontology is also investigated, and a framework is proposed for an enterprise model that consists of various applications.

Keywords: Contextual ontologies, Enterprise model, domainontology.

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Authors: Huiming Peng, Jianguo Wen, Hongwei Li, Jeff Chang, Xiaobo Zhou

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NFκB activation plays a crucial role in anti-apoptotic responses in response to the apoptotic signaling during tumor necrosis factor (TNFa) stimulation in Multiple Myeloma (MM). Although several drugs have been found effective for the treatment of MM by mainly inhibiting NFκB pathway, there are no any quantitative or qualitative results of comparison assessment on inhibition effect between different single drugs or drug combinations. Computational modeling is becoming increasingly indispensable for applied biological research mainly because it can provide strong quantitative predicting power. In this study, a novel computational pathway modeling approach is employed to comparably assess the inhibition effects of specific single drugs and drug combinations on the NFκB pathway in MM, especially the prediction of synergistic drug combinations.

Keywords: Computational modeling, drug combination, inhibition effect, multiple myeloma, NFkB pathway.

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Authors: H. Mahboubi, B. Moshiri, A. Khaki Seddigh

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In the past decade, because of wide applications of hybrid systems, many researchers have considered modeling and control of these systems. Since switching systems constitute an important class of hybrid systems, in this paper a method for optimal control of linear switching systems is described. The method is also applied on the two-tank system which is a much appropriate system to analyze different modeling and control techniques of hybrid systems. Simulation results show that, in this method, the goals of control and also problem constraints can be satisfied by an appropriate selection of cost function.

Keywords: Hybrid systems, optimal control, switched systems, two-tank system

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