Search results for: fluid-Structure interaction modeling

Authors: M. Salih Taci, N. Tayebi, I. Bozkır

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This paper investigates the operation of a sinusoidal supplied autotransformer on the different states of magnetic polarity of primary and secondary terminals for four different step-up and step-down analytical conditions. In this paper, a new analytical modeling and equations for dot-marked and polarity-based step-up and step-down autotransformer are presented. These models are validated by the simulation of current and voltage waveforms for each state. PSpice environment was used for simulation.

Keywords: autotransformer modeling, autotransformer simulation, step-up autotransformer, step-down autotransformer, polarity

Procedia PDF Downloads 289

Authors: Radnoosh Mirzajani, Ebrahim Mirzajani, Heshmatollah Ebrahimi-Najafabadi

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Introduction: Hydrogen peroxide can be produced over the interaction of sodium dodecyl sulfate (SDS) with hemoglobin which would facilitate the oxidation process of hemoglobin. The presence of ascorbic acid (AA) can hinder the extreme oxidation of oxyhemoglobin. Methods: Hemoglobin was purified from blood samples according to the method of Williams. UV-V is spectra of Hb solutions mixed with different concentrations of SDS and AA were recorded. Chemical components, concentration, and spectral profiles were estimated using MCR-ALS techniques. Results: The intensity of soret band of OxyHb decreased due to the interaction of Hb with SDS. Furthermore, changes were also observed for peaks at 575 and 540. Subspace plots confirm the presence of OxyHb, MetHb, and Hemichrom in each mixture. The resolved concentration profiles using MCR-ALS reveal that the mole fraction of OxyHb increased upon the presence of AA up to a concentration level of 3 mM. The higher concentration of AA shows a reverse effect. AA demonstrated a dual effect on the interaction of hemoglobin with SDS. AA disturbs the interaction of SDS and hemoglobin and exhibits an antioxidative effect. However, it caused a tiny decrease in the mole fraction of OxyHb. Conclusions: H2O2 produces upon the interaction of OxyHb with SDS. Oxidation of OxyHb facilitates due to overproduction of H2O2. Ascorbic acid interacts with H2O2 to form dehydroascorbic acid. Furthermore, the available free SDS was reduced because the Gibbs free energy for micelle production of SDS became more negative in the presence of AA.

Keywords: hemoglobin, ascorbic acid, sodium dodecyl sulfate, multivariate curve resolution, antioxidant

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Authors: Samira Karimi-Mansoub, Rahem Abri

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Currently, users expect high quality and personalized information from search results. To satisfy user’s needs, personalized approaches to web search have been proposed. These approaches can provide the most appropriate answer for user’s needs by using user context and incorporating information about query provided by combining search technologies. To carry out personalized web search, there is a need to make different techniques on whole of user search process. There are the number of possible deployment of personalized approaches such as personalized web search, personalized recommendation, personalized summarization and filtering systems and etc. but the common feature of all approaches in various domains is that user modeling is utilized to provide personalized information from the Web. So the most important work in personalized approaches is user model mining. User modeling applications and technologies can be used in various domains depending on how the user collected information may be extracted. In addition to, the used techniques to create user model is also different in each of these applications. Since in the previous studies, there was not a complete survey in this field, our purpose is to present a survey on applications and techniques of user modeling from the viewpoint of improvement in search results by considering the existing literature and researches.

Keywords: filtering systems, personalized web search, user modeling, user search behavior

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Authors: M. Mellas, S. Baaziz, A. Mabrouki, D. Benmeddour

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The reinforcement of massifs of backfill with horizontal layers of geosynthetics is an interesting economic solution, which ensures the stability of retaining walls. The mechanical behavior of reinforced soil by geosynthetic is complex, and requires studies and research to understand the mechanisms of rupture. The behavior of reinforcements in the soil and the behavior of the main elements of the system: reinforcement-wall-soil. The present study is interested in numerical modeling of a retaining wall in soil reinforced by horizontal layers of geogrids. This modeling makes use of the software FLAC3D. This work aims to analyze the effect of the length of the geogrid "L" where the soil massif is supporting a uniformly distributed surcharge "Q", taking into account the fixing elements rather than the layers of geogrids to the wall.

Keywords: retaining wall, geogrid, reinforced soil, numerical modeling, FLAC3D

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Authors: Tsugunosuke Sakai, Haruya Tamaki, Ryuichi Yoshida, Ryohei Egusa, Etsuji Yamaguchi, Shigenori Inagaki, Fusako Kusunoki, Miki Namatame, Masanori Sugimoto, Hiroshi Mizoguchi

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We aim to develop a full-body interaction game that could let children cooperate and interact with other children in small groups. As the first step for our aim, the objective of the full-body interaction game developed in this study is to make interaction between children. The game requires two children to jump together with the same timing. We let children experience the game and answer the questionnaires. The children using several strategies to coordinate the timing of their jumps were observed. These included shouting time, watching each other, and jumping in a constant rhythm as if they were skipping rope. In this manner, we observed the children playing the game while cooperating with each other. The results of a questionnaire to evaluate the proposed interactive game indicate that the jumping game was a very enjoyable experience in which the participants could immerse themselves. Therefore, the game enabled children to experience cooperation with others by using body movements.

Keywords: children, cooperation, full-body interaction game, kinect sensor

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Authors: H. Vahdani

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By the adsorption of polar compounds and/or the deposition of organic material, the wettability of originally water-wet reservoir rock can be altered. The degree of alteration is determined by the interaction of the oil constituents, the mineral surface, and the brine chemistry. Recently improving oil recovery by tuning wettability alteration is believed as a new recovery method. Various researchers have demonstrated that low salt water injection has a significant impact on oil recovery. It has been shown, for instance, that additional oil can be produced from reservoir rock by managing the injection water. Large wettability sensitivity has been observed, indicating that the oil/water capillary pressure profiles play a major role during low saline water injection simulation. Although the exact physics on how this alteration occurs is still a research topic; however, it has been reported that some of its effect can be captured by a relative permeability shift from an oil-wet system to a water-wet system. Modeling of low salt water injection mainly is based on the theory of wettability alteration and is hence strongly dependent on the wettability of the reservoir. In this article, combination of different wettabilities has been simulated and it is observed that the highest recoveries were from the cases were the reservoir initially was water-wet, and the lowest recoveries was from the cases were the reservoir initially was considered oil-wet. However for the cases where the reservoir initially was oil-wet, the effect of low-salinity waterflooding was the largest.

Keywords: low salt water injection, wettability alteration, modelling, relative permeability

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

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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: Hadas Sopher, Davide Schaumann, Yehuda E. Kalay

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This paper addresses the shortcomings of architectural computation tools in representing human behavior in built environments, prior to construction and occupancy of those environments. Evaluating whether a design fits the needs of its future users is currently done solely post construction, or is based on the knowledge and intuition of the designer. This issue is of high importance when designing complex buildings such as hospitals, where the quality of treatment as well as patient and staff satisfaction are of major concern. Existing computational pre-occupancy human behavior evaluation methods are geared mainly to test ergonomic issues, such as wheelchair accessibility, emergency egress, etc. As such, they rely on Agent Based Modeling (ABM) techniques, which emphasize the individual user. Yet we know that most human activities are social, and involve a number of actors working together, which ABM methods cannot handle. Therefore, we present an event-based model that manages the interaction between multiple Actors, Spaces, and Activities, to describe dynamically how people use spaces. This approach requires expanding the computational representation of Actors beyond their physical description, to include psychological, social, cultural, and other parameters. The model presented in this paper includes cognitive abilities and rules that describe the response of actors to their physical and social surroundings, based on the actors’ internal status. The model has been applied in a simulation of hospital wards, and showed adaptability to a wide variety of situated behaviors and interactions.

Keywords: agent based modeling, architectural design evaluation, event modeling, human behavior simulation, spatial cognition

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Authors: Rajaa Filali, Mohamed Bouhdadi

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This paper presents an incremental formal development of the Wireless Transaction Protocol (WTP) in Event-B. WTP is part of the Wireless Application Protocol (WAP) architectures and provides a reliable request-response service. To model and verify the protocol, we use the formal technique Event-B which provides an accessible and rigorous development method. This interaction between modelling and proving reduces the complexity and helps to eliminate misunderstandings, inconsistencies, and specification gaps. As result, verification of WTP allows us to find some deficiencies in the current specification.

Keywords: event-B, wireless transaction protocol, proof obligation, refinement, Rodin, ProB

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Authors: Kakali Bhadra

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Binding of small molecules to DNA and recently to RNA, continues to attract considerable attention for developing effective therapeutic agents for control of gene expression. This work focuses towards understanding interaction of harmalol, a dihydro beta-carboline alkaloid, with different nucleic acid motifs viz. double stranded CT DNA, single stranded A-form poly(A), double-stranded A-form of poly(C)·poly(G) and clover leaf tRNAphe by different spectroscopic, calorimetric and molecular modeling techniques. Results of this study converge to suggest that (i) binding constant varied in the order of CT DNA > poly(C)·poly(G) > tRNAphe > poly(A), (ii) non-cooperative binding of harmalol to poly(C)·poly(G) and poly(A) and cooperative binding with CT DNA and tRNAphe, (iii) significant structural changes of CT DNA, poly(C)·poly(G) and tRNAphe with concomitant induction of optical activity in the bound achiral alkaloid molecules, while with poly(A) no intrinsic CD perturbation was observed, (iv) the binding was predominantly exothermic, enthalpy driven, entropy favoured with CT DNA and poly(C)·poly(G) while it was entropy driven with tRNAphe and poly(A), (v) a hydrophobic contribution and comparatively large role of non-polyelectrolytic forces to Gibbs energy changes with CT DNA, poly(C)·poly(G) and tRNAphe, and (vi) intercalated state of harmalol with CT DNA and poly(C)·poly(G) structure as revealed from molecular docking and supported by the viscometric data. Furthermore, with competition dialysis assay it was shown that harmalol prefers hetero GC sequences. All these findings unequivocally pointed out that harmalol prefers binding with ds CT DNA followed by ds poly(C)·poly(G), clover leaf tRNAphe and least with ss poly(A). The results highlight the importance of structural elements in these natural beta-carboline alkaloids in stabilizing different DNA and RNA of various motifs for developing nucleic acid based better therapeutic agents.

Keywords: calorimetry, docking, DNA/RNA-alkaloid interaction, harmalol, spectroscopy

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Authors: Patrik Johansson, Selina Mardh

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The present study proposes a usability test method, Atmosphere, to assess the fitness of components and interaction patterns of design systems. The method covers the user’s perception of the components of the system, the efficiency of the logic of the interaction patterns, perceived ease of use as well as the user’s understanding of the intended outcome of interactions. These aspects are assessed by combining measures of first impression, visual affordance and expectancy. The method was applied to a design system developed for the design of an electronic health record system. The study was conducted involving 15 healthcare personnel. It could be concluded that the Atmosphere method provides tangible data that enable human-computer interaction practitioners to analyze and categorize components and patterns based on perceived usability, success rate of identifying interactive components and success rate of understanding components and interaction patterns intended outcome.

Keywords: atomic design, atmosphere methodology, design system, expectancy testing, first impression testing, usability testing, visual affordance testing

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Authors: Abigail Rosenberg, Jennifer Duan, Michael Poteuck, Chunshui Yu

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The Barry M. Goldwater Range, West in southwestern Arizona encompasses 2,808 square kilometers of Sonoran Desert. The hyper-arid range has an annual rainfall of less than 10 cm with an average high temperature of 41 degrees Celsius in July to an average low of 4 degrees Celsius in January. The range shares approximately 60 kilometers of the international border with Mexico. A majority of the range is open for recreational use, primarily off-highway vehicles. Because of its proximity to Mexico, the range is also heavily patrolled by U.S. Customs and Border Protection seeking to intercept and apprehend inadmissible people and illicit goods. Decades of off-roading and Border Patrol activities have negatively impacted this sensitive desert ecosystem. To assist the range program managers, this study is developing a model to identify erosion prone areas and calibrate the model’s parameters using the Automated Geospatial Watershed Assessment modeling tool.

Keywords: arid lands, automated geospatial watershed assessment, erosion modeling, sedimentation modeling, watershed modeling

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Authors: Meriem Boukais, B. Dennai, A. Ould- Abbas

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The efficiency of SiGe solar cells might be improved by a wide-band-gap window layer. In this work we were simulated using the one dimensional simulation program called analysis of microelectronic and photonic structures (AMPS-1D). In the modeling, the thickness of silicon window was varied from 80 to 150 nm. The rest of layer’s thicknesses were kept constant, by varying thickness of window layer the simulated device performance was demonstrate in the form of current-voltage (I-V) characteristics and quantum efficiency (QE).

Keywords: modeling, SiGe, AMPS-1D, quantum efficiency, conversion, efficiency

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Authors: Shan-Jen Cheng, Te-Jen Chang, Kuang-Hsiung Tan, Shou-Ling Kuo

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Polymer Electrolyte Membrane Fuel Cell (PEMFC) is such a time-vary nonlinear dynamic system. The traditional linear modeling approach is hard to estimate structure correctly of PEMFC system. From this reason, this paper presents a nonlinear modeling of the PEMFC using Neural Network Auto-regressive model with eXogenous inputs (NNARX) approach. The multilayer perception (MLP) network is applied to evaluate the structure of the NNARX model of PEMFC. The validity and accuracy of NNARX model are tested by one step ahead relating output voltage to input current from measured experimental of PEMFC. The results show that the obtained nonlinear NNARX model can efficiently approximate the dynamic mode of the PEMFC and model output and system measured output consistently.

Keywords: PEMFC, neural network, nonlinear modeling, NNARX

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Authors: Spyridon Nikolaidis

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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 mode, timing model

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Authors: Reza Ziaie Moayed, Ehsan Azini

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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: Emery Coppola Jr., Marwan Sadat, Il Kim, Diane Trube, Richard Kurisko

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Contamination sites like landfills often pose significant risks to receptors like surface water bodies. Surface water bodies are often a source of recreation, including fishing and swimming, which not only enhances their value but also serves as a direct exposure pathway to humans, increasing their need for protection from water quality degradation. In this paper, a case study presents the potential effects of leachate-impacted groundwater from a large closed sanitary landfill on the surface water quality of the nearby Raritan River, situated in New Jersey. The study, performed over a two year period, included in-depth field evaluation of both the groundwater and surface water systems, and was supplemented by computer modeling. The analysis required delineation of a representative average daily groundwater discharge from the Landfill shoreline into the large, highly tidal Raritan River, with a corresponding estimate of daily mass loading of potential contaminants of concern. The average daily groundwater discharge into the river was estimated from a high-resolution water level study and a 24-hour constant-rate aquifer pumping test. The significant tidal effects induced on groundwater levels during the aquifer pumping test were filtered out using an advanced algorithm, from which aquifer parameter values were estimated using conventional curve match techniques. The estimated hydraulic conductivity values obtained from individual observation wells closely agree with tidally-derived values for the same wells. Numerous models were developed and used to simulate groundwater contaminant transport and surface water quality impacts. MODFLOW with MT3DMS was used to simulate the transport of potential contaminants of concern from the down-gradient edge of the Landfill to the Raritan River shoreline. A surface water dispersion model based upon a bathymetric and flow study of the river was used to simulate the contaminant concentrations over space within the river. The modeling results helped demonstrate that because of natural attenuation, the Landfill does not have a measurable impact on the river, which was confirmed by an extensive surface water quality study.

Keywords: groundwater flow and contaminant transport modeling, groundwater/surface water interaction, landfill leachate, surface water quality modeling

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Authors: Jamaludin Sallim, Rozlina Mohamed, Roslina Abdul Hamid

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In this paper, we proposed an Ant Colony Optimization (ACO) algorithm together with Traveling Salesman Problem (TSP) approach to investigate the clustering problem in Protein Interaction Networks (PIN). We named this combination as ACOPIN. The purpose of this work is two-fold. First, to test the efficacy of ACO in clustering PIN and second, to propose the simple generalization of the ACO algorithm that might allow its application in clustering proteins in PIN. We split this paper to three main sections. First, we describe the PIN and clustering proteins in PIN. Second, we discuss the steps involved in each phase of ACO algorithm. Finally, we present some results of the investigation with the clustering patterns.

Keywords: ant colony optimization algorithm, searching algorithm, protein functional module, protein interaction network

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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: H. Shokouhmand, M. Degheh, B. Sajadi, H. Sobhani

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The induct ultraviolet germicidal irradiation (UVGI) systems are broadly used nowadays and their utilization is widened every day. Even though these systems are not applicable individually, they are very suitable supplements for the traditional filtration systems. The amount of inactivated microorganisms is dependent on the air velocity, lamp power, fluence rate distribution, and also germicidal susceptibility of microorganisms. In this paper, these factors are investigated utilizing an air-microorganism two-phase numerical model. The eulerian-lagrangian method was used to have more detailed information on the history of each particle. The UVGI system was modeled in three steps including: 1) modeling the air flow, 2) modeling the discrete phase of particles, 3) modeling the UV intensity field, and 4) modeling the particle inactivation. The results from modeling different lamp arrangements and powers showed that the system functions better at more homogeneous irradiation distribution. Since increasing the air flow rate of the device results in increasing of particle inactivation rate, the optimal air velocity shall be adjusted in accordance with the microorganism production rate, and the air quality requirement using the curves represented in this paper.

Keywords: CFD, microorganism, two-phase flow, ultraviolet germicidal irradiation

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Authors: Mohamed M. El Gendy, Ibrahim A. El Arabi, Rafeek W. Abdel-Missih, Omar A. Kandil

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Nonlinear analysis is one of the most important design and safety tools in structural engineering. Based on the finite-element method, a geometrical and material nonlinear analysis of large span reinforced concrete arches is carried out considering soil-structure interaction. The concrete section details and reinforcement distribution are taken into account. The behavior of soil is considered via Winkler's and continuum models. A computer program (NARC II) is specially developed in order to follow the structural behavior of large span reinforced concrete arches up to failure. The results obtained by the proposed model are compared with available literature for verification. This work confirmed that the geometrical and material nonlinearities, as well as soil structure interaction, have considerable influence on the structural response of reinforced concrete arches.

Keywords: nonlinear analysis, reinforced concrete arched structure, soil-structure interaction, geotechnical engineering

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Authors: S. Srinivas, N. Ramesh Babu

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This paper presents a model to predict the depth of penetration in polycrystalline ceramic material cut by abrasive waterjet. The proposed model considered the interaction of cylindrical jet with target material in upper region and neglected the role of threshold velocity in lower region. The results predicted with the proposed model are validated with the experimental results obtained with Silicon Carbide (SiC) blocks.

Keywords: abrasive waterjet cutting, analytical modeling, ceramics, micro-cutting and inter-grannular cracking

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Authors: Shilpa Kapoor, Namrata Yaduvanshi, Pooja Pawar, Sadhna Singh

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A Three Body Interaction Potential (TBIP) model is developed to study the high pressure phase transition of SrS having NaCl (B1) structure at room temperature. This model includes the long range Columbic, three body interaction forces, short range overlap forces operative up to next nearest neighbors and zero point energy effects. We have investigated the phase transition with pressure, volume collapse and second order elastic constants and found results well suited with available experimental data.

Keywords: phase transition, second order elastic constants, three body interaction forces, volume collapses

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Authors: Asmaa Sokrat, Aykut Karaman

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Public and private spaces are major components of the morphology of the city. This research aims to study the interactions between public and private domains in terms of urban space in Casablanca. The research focuses on a general vision of a socio-spatial issue. It plans to identify the public, private, and transition (semi-public, semi-private) spaces as the constituent of the urban space. Moreover, the study investigates the link between public and private spaces with the social dimensions. Additionally, the research argues that the public space is a place of social interaction; as a reflection, this interaction is the intersection between urban space and social connectedness. Besides, social interaction can be the key to distinguishing between the public and private spheres. The methodological approach of the research is based on the literature review and field study. The article is targeting a case study on the old Medina of Casablanca, from daily use of the public and private spaces, the urban tissue, and the urban space types. In conclusion, the research exhibits that a public space could influence the privacy of the residents of a local urban area; thus, this privacy is inverted on the social interaction. This social interaction is the link between the urban space and social connectedness. Hence, this equation affects the typology of the private space.

Keywords: public sphere, private sphere, social connectedness, old Medina of Casablanca

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Authors: Shayli Varasteh Moradi, Wayne A. Johnston, Dejan Gagoski, Kirill Alexandrov

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The demand for a rapid and more efficient technique to identify protein-protein interaction particularly in the areas of therapeutics and diagnostics development is growing. The method described here is a rapid in vitro protein-protein interaction analysis approach based on AlphaLISA technology combined with Leishmania tarentolae cell-free protein production (LTE) system. Cell-free protein synthesis allows the rapid production of recombinant proteins in a multiplexed format. Among available in vitro expression systems, LTE offers several advantages over other eukaryotic cell-free systems. It is based on a fast growing fermentable organism that is inexpensive in cultivation and lysate production. High integrity of proteins produced in this system and the ability to co-express multiple proteins makes it a desirable method for screening protein interactions. Following the translation of protein pairs in LTE system, the physical interaction between proteins of interests is analysed by AlphaLISA assay. The assay is performed using unpurified in vitro translation reaction and therefore can be readily multiplexed. This approach can be used in various research applications such as epitope mapping, antigen-antibody analysis and protein interaction network mapping. The intra-viral protein interaction network of Zika virus was studied using the developed technique. The viral proteins were co-expressed pair-wise in LTE and all possible interactions among viral proteins were tested using AlphaLISA. The assay resulted to the identification of 54 intra-viral protein-protein interactions from which 19 binary interactions were found to be novel. The presented technique provides a powerful tool for rapid analysis of protein-protein interaction with high sensitivity and throughput.

Keywords: AlphaLISA technology, cell-free protein expression, epitope mapping, Leishmania tarentolae, protein-protein interaction

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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, GaNHEMT, si-substrate, open de-embedding structure

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Authors: Sourav Ray, Christoph Stein, Marcus Weber

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A new class of drug candidates, initially derived from mathematical modeling of ligand-receptor interactions, activate the μ-opioid receptor (MOR) preferentially at acidic extracellular pH-levels, as present in injured tissues. This is of commercial interest because it may preclude the adverse effects of conventional MOR agonists like fentanyl, which include but are not limited to addiction, constipation, sedation, and apnea. Animal studies indicate the importance of taking the pH value of the chemical environment of MOR into account when designing new drugs. Hydrogen bonds (HBs) play a crucial role in stabilizing protein secondary structure and molecular interaction, such as ligand-protein interaction. These bonds may depend on the pH value of the chemical environment. For the MOR, antagonist naloxone and agonist [D-Ala2,N-Me-Phe4,Gly5-ol]-enkephalin (DAMGO) form HBs with ionizable residue HIS 297 at physiological pH to modulate signaling. However, such interactions were markedly reduced at acidic pH. Although fentanyl-induced signaling is also diminished at acidic pH, HBs with HIS 297 residue are not observed at either acidic or physiological pH for this strong agonist of the MOR. Molecular dynamics (MD) simulations can provide greater insight into the interaction between the ligand of interest and the HIS 297 residue. Amino acid protonation states are adjusted to the model difference in system acidity. Unbiased and unrestrained MD simulations were performed, with the ligand in the proximity of the HIS 297 residue. Ligand-receptor complexes were embedded in 1-palmitoyl-2-oleoyl-sn glycero-3-phosphatidylcholine (POPC) bilayer to mimic the membrane environment. The occurrence of HBs between the different ligands and the HIS 297 residue of MOR at acidic and physiological pH values were tracked across the various simulation trajectories. No HB formation was observed between fentanyl and HIS 297 residue at either acidic or physiological pH. Naloxone formed some HBs with HIS 297 at pH 5, but no such HBs were noted at pH 7. Interestingly, DAMGO displayed an opposite yet more pronounced HB formation trend compared to naloxone. Whereas a marginal number of HBs could be observed at even pH 5, HBs with HIS 297 were more stable and widely present at pH 7. The HB formation plays no and marginal role in the interaction of fentanyl and naloxone, respectively, with the HIS 297 residue of MOR. However, HBs play a significant role in the DAMGO and HIS 297 interaction. Post DAMGO administration, these HBs might be crucial for the remediation of opioid tolerance and restoration of opioid sensitivity. Although experimental studies concur with our observations regarding the influence of HB formation on the fentanyl and DAMGO interaction with HIS 297, the same could not be conclusively stated for naloxone. Therefore, some other supplementary interactions might be responsible for the modulation of the MOR activity by naloxone binding at pH 7 but not at pH 5. Further elucidation of the mechanism of naloxone action on the MOR could assist in the formulation of cost-effective naloxone-based treatment of opioid overdose or opioid-induced side effects.

Keywords: effect of system acidity, hydrogen bond formation, opioid action, receptor activation

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Authors: Spoorthi Sripad

Abstract:

Remote sensing is a powerful tool for acquiring information about the Earth's surface without direct contact, relying on the interaction of electromagnetic radiation with various materials and features. This paper explores the fundamental principle of "Interaction with Earth's Surface" in remote sensing, shedding light on the intricate processes that occur when electromagnetic waves encounter different surfaces. The absorption, reflection, and transmission of radiation generate distinct spectral signatures, allowing for the identification and classification of surface materials. The paper delves into the significance of the visible, infrared, and thermal infrared regions of the electromagnetic spectrum, highlighting how their unique interactions contribute to a wealth of applications, from land cover classification to environmental monitoring. The discussion encompasses the types of sensors and platforms used to capture these interactions, including multispectral and hyperspectral imaging systems. By examining real-world applications, such as land cover classification and environmental monitoring, the paper underscores the critical role of understanding the interaction with the Earth's surface for accurate and meaningful interpretation of remote sensing data.

Keywords: remote sensing, earth's surface interaction, electromagnetic radiation, spectral signatures, land cover classification, archeology and cultural heritage preservation

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Authors: Dino Carpentras, Alejandro Dinkelberg, Michael Quayle

Abstract:

Within agent-based modeling, opinion dynamics is the field that focuses on modeling people's opinions. In this prolific field, most of the literature is dedicated to the exploration of the two 'degrees of freedom' and how they impact the model’s properties (e.g., the average final opinion, the number of final clusters, etc.). These degrees of freedom are (1) the interaction rule, which determines how agents update their own opinion, and (2) the network topology, which defines the possible interaction among agents. In this work, we show that the third degree of freedom exists. This can be used to change a model's output up to 100% of its initial value or to transform two models (both from the literature) into each other. Since opinion dynamics models are representations of the real world, it is fundamental to understand how people’s opinions can be measured. Even for abstract models (i.e., not intended for the fitting of real-world data), it is important to understand if the way of numerically representing opinions is unique; and, if this is not the case, how the model dynamics would change by using different representations. The process of measuring opinions is non-trivial as it requires transforming real-world opinion (e.g., supporting most of the liberal ideals) to a number. Such a process is usually not discussed in opinion dynamics literature, but it has been intensively studied in a subfield of psychology called psychometrics. In psychometrics, opinion scales can be converted into each other, similarly to how meters can be converted to feet. Indeed, psychometrics routinely uses both linear and non-linear transformations of opinion scales. Here, we analyze how this transformation affects opinion dynamics models. We analyze this effect by using mathematical modeling and then validating our analysis with agent-based simulations. Firstly, we study the case of perfect scales. In this way, we show that scale transformations affect the model’s dynamics up to a qualitative level. This means that if two researchers use the same opinion dynamics model and even the same dataset, they could make totally different predictions just because they followed different renormalization processes. A similar situation appears if two different scales are used to measure opinions even on the same population. This effect may be as strong as providing an uncertainty of 100% on the simulation’s output (i.e., all results are possible). Still, by using perfect scales, we show that scales transformations can be used to perfectly transform one model to another. We test this using two models from the standard literature. Finally, we test the effect of scale transformation in the case of finite precision using a 7-points Likert scale. In this way, we show how a relatively small-scale transformation introduces both changes at the qualitative level (i.e., the most shared opinion at the end of the simulation) and in the number of opinion clusters. Thus, scale transformation appears to be a third degree of freedom of opinion dynamics models. This result deeply impacts both theoretical research on models' properties and on the application of models on real-world data.

Keywords: degrees of freedom, empirical validation, opinion scale, opinion dynamics

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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: fault detection, fault isolation, testability modeling, BIT

Procedia PDF Downloads 308