Search results for: Molecular Modeling

Authors: Emmanuel Iyamuremye

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Extreme rainfall events have caused significant damage to agriculture, ecology, and infrastructure, disruption of human activities, injury, and loss of life. They also have significant social, economic, and environmental consequences because they considerably damage urban as well as rural areas. Early detection of extreme maximum rainfall helps to implement strategies and measures, before they occur, hence mitigating the consequences. Extreme value theory has been used widely in modeling extreme rainfall and in various disciplines, such as financial markets, the insurance industry, failure cases. Climatic extremes have been analyzed by using either generalized extreme value (GEV) or generalized Pareto (GP) distributions, which provides evidence of the importance of modeling extreme rainfall from different regions of the world. In this paper, we focused on Peak Over Thresholds approach, where the Poisson-generalized Pareto distribution is considered as the proper distribution for the study of the exceedances. This research also considers the use of the generalized Pareto (GP) distribution with a Poisson model for arrivals to describe peaks over a threshold. The research used statistical techniques to fit models that used to predict extreme rainfall in Kigali. The results indicate that the proposed Poisson-GP distribution provides a better fit to maximum monthly rainfall data. Further, the Poisson-GP models are able to estimate various return levels. The research also found a slow increase in return levels for maximum monthly rainfall for higher return periods, and further, the intervals are increasingly wider as the return period is increasing.

Keywords: exceedances, extreme value theory, generalized Pareto distribution, Poisson generalized Pareto distribution

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Authors: Vedat Senol, Gursoy Turan, Anders Helmersson, Vortechz Andersson

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In developing a mathematical model of a real structure, the simulation results of the model may not match the real structural response. This is a general problem that arises during dynamic motion of the structure, which may be modeled by means of parameter variations in the stiffness, damping, and mass matrices. These changes in parameters need to be estimated, and the mathematical model is updated to obtain higher control performances and robustness. In this study, a linear fractional transformation (LFT) is utilized for uncertainty modeling. Further, a general approach to the design of an H∞ control of a magneto-rheological damper (MRD) for vibration reduction in a building with mass, damping, and stiffness uncertainties is presented.

Keywords: uncertainty modeling, structural control, MR Damper, H∞, robust control

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Authors: Serge B. Provost, Yishan Zhang

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A moment-based adjustment to the saddlepoint approximation is introduced in the context of density estimation. First applied to univariate distributions, this methodology is extended to the bivariate case. It then entails estimating the density function associated with each marginal distribution by means of the saddlepoint approximation and applying a bivariate adjustment to the product of the resulting density estimates. The connection to the distribution of empirical copulas will be pointed out. As well, a novel approach is proposed for estimating the support of distribution. As these results solely rely on sample moments and empirical cumulant-generating functions, they are particularly well suited for modeling massive data sets. Several illustrative applications will be presented.

Keywords: empirical cumulant-generating function, endpoints identification, saddlepoint approximation, sample moments, density estimation

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Authors: Y. Galerkin, K. Soldatova, A. Drozdov

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The 6th version of Universal modeling method for centrifugal compressor stage calculation is described. Identification of the new mathematical model was made. As a result of identification the uniform set of empirical coefficients is received. The efficiency definition error is 0,86 % at a design point. The efficiency definition error at five flow rate points (except a point of the maximum flow rate) is 1,22 %. Several variants of the stage with 3D impellers designed by 6th version program and quasi three-dimensional calculation programs were compared by their gas dynamic performances CFD (NUMECA FINE TURBO). Performance comparison demonstrated general principles of design validity and leads to some design recommendations.

Keywords: compressor design, loss model, performance prediction, test data, model stages, flow rate coefficient, work coefficient

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Authors: Dalal Alghawas, Jetty Lee, Kaisa Poutanen, Hani El-Nezami

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Oat β-glucan a water soluble non starch linear polysaccharide has been approved as a cholesterol lowering agent by various food safety administrations and is commonly used to reduce the risk of heart disease. The molecular weight of oat β-glucan can vary depending on the extraction and fractionation methods. It is not clear whether the molecular weight has a significant impact at reducing the acceleration of atherosclerosis. The aim of this study was to investigate three different oat β-glucan fractionations on the development of atherosclerosis in vivo. With special focus on plaque stability and the intestinal barrier function. To test this, ApoE-/- female mice were fed a high fat diet supplemented with oat bran, high molecular weight (HMW) oat β-glucan fractionate and low molecular weight (LMW) oat β-glucan fractionate for 16 weeks. Atherosclerosis risk markers were measured in the plasma, heart and aortic tree. Plaque size was measured in the aortic root and aortic tree. ICAM-1, VCAM-1, E-Selectin, P-Selectin, protein levels were assessed from the aortic tree to determine plaque stability at 16 weeks. The expression of p22phox at the aortic root was evaluated to study the NADPH oxidase complex involved in nitric oxide bioavailability and vascular elasticity. The tight junction proteins E-cadherin and beta-catenin from western blot analyses were analysed as an intestinal barrier function test. Plasma LPS, intestinal D-lactate levels and hepatic FMO gene expression were carried out to confirm whether the compromised intestinal barrier lead to endotoxemia. The oat bran and HMW oat β-glucan diet groups were more effective than the LMW β-glucan diet group at reducing the plaque size and showed marked improvements in plaque stability. The intestinal barrier was compromised for all the experimental groups however the endotoxemia levels were higher in the LMW β-glucan diet group. The oat bran and HMW oat β-glucan diet groups were more effective at attenuating the development of atherosclerosis. Reasons for this could be due to the LMW oat β-glucan diet group’s low viscosity in the gut and the inability to block the reabsorption of cholesterol. Furthermore the low viscosity may allow more bacterial endotoxin translocation through the impaired intestinal barrier. In future food technologists should carefully consider how to incorporate LMW oat β-glucan as a health promoting food.

Keywords: Atherosclerosis, beta glucan, endotoxemia, intestinal barrier function

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Authors: Reem Alajmi, Hind Al Harbi, Tahany Ayaad, Zainab Al Musawi

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Hard ticks Hyalomma spp. (family: Ixodidae) are obligate ectoparasite in their all life stages on some domestic animals mainly camels and cattle. Ticks may lead to many economic and public health problems because of their blood feeding behavior. Also, they act as vectors for many bacterial, viral and protozoan agents which may cause serious diseases such as tick-born encephalitis, Rocky-mountain spotted fever, Q-fever and Lyme disease which can affect human and/or animals. In the present study, molecular identification of ticks that attack camels in Riyadh region, Saudi Arabia based on the partial sequence of mitochondrial 16s rRNA gene was applied. Also, the present study aims to detect natural infections of collected camel ticks with Rickessia spp. and Borelia spp. using PCR/hybridization of Citrate synthase encoding gene present in bacterial cells. Hard ticks infesting camels were collected from different camels located in a farm in Riyadh region, Saudi Arabia. Results of the present study showed that the collected specimens belong to two species: Hyalomma dromedari represent 99% of the identified specimens and Hyalomma marginatum which account for 1 % of identified ticks. The molecular identification was made through blasting the obtained sequence of this study with sequences already present and identified in GeneBank. All obtained sequences of H. dromedarii specimens showed 97-100% identity with the same gene sequence of the same species (Accession # L34306.1) which was used as a reference. Meanwhile, no intraspecific variations of H. marginatum mesured because only one specimen was collected. Results also had shown that the intraspecific variability between individuals of H. dromedarii obtained in 92 % of samples ranging from 0.2- 6.6%, while the remaining 7 % of the total samples of H. dromedarii showed about 10.3 % individual differences. However, the interspecific variability between H. dromedarii and H. marginatum was approximately 18.3 %. On the other hand, by using the technique of PCR/hybridization, we could detect natural infection of camel ticks with Rickettsia spp. and Borrelia spp. Results revealed the natural presence of both bacteria in collected ticks. Rickettsial spp. infection present in 29% of collected ticks, while 35% of collected specimen were infected with Borrelia spp. The valuable results obtained from the present study are a new record for the molecular identification of camel ticks in Riyadh, Saudi Arabia and their natural infection with both Rickettsia spp. and Borrelia spp. These results may help scientists to provide a good and direct control strategy of ticks in order to protect one of the most important economic animals which are camels. Also results of this project spotlight on the disease that might be transmitted by ticks to put out a direct protective plan to prevent spreading of these dangerous agents. Further molecular studies are needed to confirm the results of the present study by using other mitochondrial and nuclear genes for tick identification.

Keywords: Camel ticks, Rickessia spp. , Borelia spp. , mitochondrial 16s rRNA gene

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Authors: N. Harun, E. E. Masiren, W. H. W. Ibrahim, F. Adam

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Amine absorption process is an approach for mitigation of CO2 from flue gas that produces from power plant. This process is the most common system used in chemical and oil industries for gas purification to remove acid gases. On the challenges of this process is high energy requirement for solvent regeneration to release CO2. In the past few years, mixed alkanolamines have received increasing attention. In most cases, the mixtures contain N-methyldiethanolamine (MDEA) as the base amine with the addition of one or two more reactive amines such as PZ. The reason for the application of such blend amine is to take advantage of high reaction rate of CO2 with the activator combined with the advantages of the low heat of regeneration of MDEA. Several experimental and simulation studies have been undertaken to understand this process using blend MDEA/PZ solvent. Despite those studies, the mechanism of CO2 absorption into the aqueous MDEA is not well understood and available knowledge within the open literature is limited. The aim of this study is to investigate the intermolecular interaction of the blend MDEA/PZ using Molecular Dynamics (MD) simulation. MD simulation was run under condition 313K and 1 atm using NVE ensemble at 200ps and NVT ensemble at 1ns. The results were interpreted in term of Radial Distribution Function (RDF) analysis through two system of interest i.e binary and tertiary. The binary system will explain the interaction between amine and water molecule while tertiary system used to determine the interaction between the amine and CO2 molecule. For the binary system, it was observed that the –OH group of MDEA is more attracted to water molecule compared to –NH group of MDEA. The –OH group of MDEA can form the hydrogen bond with water that will assist the solubility of MDEA in water. The intermolecular interaction probability of –OH and –NH group of MDEA with CO2 in blended MDEA/PZ is higher than using single MDEA. This findings show that PZ molecule act as an activator to promote the intermolecular interaction between MDEA and CO2.Thus, blend of MDEA with PZ is expecting to increase the absorption rate of CO2 and reduce the heat regeneration requirement.

Keywords: amine absorption process, blend MDEA/PZ, CO2 capture, molecular dynamic simulation, radial distribution function

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Authors: Shervin Khazaeli, Shahab Haj-zamani

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Recently, advanced geotechnical engineering problems related to soil movement, particle loss, and modeling of local failure (i.e. discontinua) as well as modeling the in-contact structures (i.e. continua) are of the great interest among researchers. The aim of this research is to meet the requirements with respect to the modeling of the above-mentioned two different domains simultaneously. To this end, a coupled numerical method is introduced based on Discrete Element Method (DEM) and eXtended-Finite Element Method (X-FEM). In the coupled procedure, DEM is employed to capture the interactions and relative movements of soil particles as discontinua, while X-FEM is utilized to model in-contact structures as continua, which may consist of different types of discontinuities. For verification purposes, the new coupled approach is utilized to examine benchmark problems including different contacts between/within continua and discontinua. Results are validated by comparison with those of existing analytical and numerical solutions. This study proves that extended-finite-discrete element method can be used to robustly analyze not only contact problems, but also other types of discontinuities in continua such as (i) crack formations and propagations, (ii) voids and bimaterial interfaces, and (iii) combination of previous cases. In essence, the proposed method can be used vastly in advanced soil-structure interaction problems to investigate the micro and macro behaviour of the surrounding soil and the response of the embedded structure that contains discontinuities.

Keywords: contact problems, discrete element method, extended-finite element method, soil-structure interaction

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Authors: Kyoungjin Kim

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Nanoscale thermites such as the composite mixture of nano-sized aluminum and molybdenum trioxide powders possess several technical advantages such as much higher reaction rate and shorter ignition delay, when compared to the conventional energetic formulations made of micron-sized metal and oxidizer particles. In this study, the self-propagation of combustion wave in compacted pellets of nanoscale thermite composites is modeled and computationally investigated by utilizing the activation energy reduction of aluminum particles due to nanoscale particle sizes. The present computational model predicts the speed of combustion wave propagation which is good agreement with the corresponding experiments of thermite reaction. Also, several characteristics of thermite reaction in nanoscale composites are discussed including the ignition delay and combustion wave structures.

Keywords: nanoparticles, thermite reaction, combustion wave, numerical modeling

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Authors: Meryem Kanzari, Rabah Boukhanouf, Hatem G. Ibrahim

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Indirect Evaporative Cooling process has the advantage of supplying cool air at constant moisture content. However, such system can only supply air at temperatures above wet bulb temperature. This paper presents a mathematical model for a sub-wet bulb temperature indirect evaporative cooling arrangement that can overcome this limitation and supply cool air at temperatures approaching dew point and without increasing its moisture content. In addition, the use of porous ceramics as wet media materials offers the advantage of integration into building elements. Results of the computer show that the proposed design is capable of cooling air to temperatures lower than the ambient wet bulb temperature and achieving wet bulb effectiveness of about 1.17.

Keywords: indirect evaporative cooling, porous ceramic, sub-wet bulb temperature, mathematical modeling

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Authors: Ruchi Yadav, Shivani Pandey, Prachi Srivastava

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Microarrays provide a rich source of data on the molecular working of cells. Each microarray reports on the abundance of tens of thousands of mRNAs. Virtually every human disease is being studied using microarrays with the hope of finding the molecular mechanisms of disease. Bioinformatics analysis plays an important part of processing the information embedded in large-scale expression profiling studies and for laying the foundation for biological interpretation. A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. One of the most popular platforms for microarray analysis is Bioconductor, an open source and open development software project based on the R programming language. This paper describes specific procedures for conducting quality assessment, visualization and preprocessing of Affymetrix Gene Chip and also details the different bioconductor packages used to analyze affymetrix microarray data and describe the analysis and outcome of each plots.

Keywords: microarray analysis, R language, affymetrix visualization, bioconductor

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Authors: Abas Mohsenzadeh, Tariq Bashir, Waseen Tahir, Ulf Stigh, Mikael Skrifvars, Kim Bolton

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The area of artificial muscles has received significant attention from many research domains including soft robotics, biomechanics and smart textiles in recent years. Poly(vinylidene fluoride) (PVDF) has been used to form artificial muscles since it contracts upon heating when under load. In this study, PVDF fibers were produced by melt spinning technique at different solid state draw ratios and then actuation mechanism for PVDF tie molecules within the semicrystalline region of PVDF polymer has been investigated using molecular dynamics simulations. Tie molecules are polymer chains that link two (or more) crystalline regions in semicrystalline polymers. The changes in fiber length upon heating have been investigated using a novel simulation technique. The results show that conformational changes of the tie molecules from the longer all-trans conformation at low temperature (β structure) to the shorter conformation (α structure) at higher temperature accrue by increasing the temperature. These results may be applied to understand the actuation observed for PVDF upon heating.

Keywords: poly(vinylidene fluoride), molecular dynamics, simulation, actuators, tie molecules, semicrystalline

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Authors: Iram Batool, Aamer Saeed, Irfan Zia Qureshi, Ayesha Razzaq, Saima Kalsoom

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Heterocyclic compounds analogues and their derivatives have attracted strong interest in medicinal chemistry due to their biological and pharmacological properties. A series of new thiazolopyrimidine carboxylates were conveniently synthesized by one-pot three-component reaction of ethyl acetoacetate, 2-aminothiazole and benzaldehyde substituted with electron-donating and electron-withdrawing groups in order to find some more potent antidiabetic and antibacterial drugs. The structures of synthesized compounds were characterized by elemental analysis, IR, 1H NMR, 13C NMR spectroscopy. An in vitro antidiabetic effect was evaluated in adult male BALB/c mice and antibacterial activities were tested against Micrococcus luteus, Salmonella typhimurium, Bacillus subtilis, Bordetella bronchiseptica and Escherichia coli. Some of the tested compounds proved to possess good to excellent activities more than the reference drugs. An in silico molecular docking was also performed on synthesized compounds. The current study is expected to provide useful insights into the design of antidiabetic and antibacterial drugs and understanding the mechanism by which such drugs interact with RNA and diabetes target and exert their biochemical action.

Keywords: antidiabetic, antibacterial, MOE docking, thiazolopyrimidine

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Authors: Pei-Chen Wu

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Both preexisting cross-sectional and longitudinal studies of personality-depression relationship have suffered from one main limitation: they ignored the stability of the construct of interest (e.g., personality and depression) can be expected to influence the estimate of the association between personality and depression. To address this limitation, the Trait-State-Occasion (TSO) modeling was adopted to analyze the sources of variance of the focused constructs. A TSO modeling was operated by partitioning a state variance into time-invariant (trait) and time-variant (occasion) components. Within a TSO framework, it is possible to predict change on the part of construct that really changes (i.e., time-variant variance), when controlling the trait variances. 750 high school students were followed for 4 waves over six-month intervals. The baseline data (T1) were collected from the senior high schools (aged 14 to 15 years). Participants were given Beck Depression Inventory and Big Five Inventory at each assessment. TSO modeling revealed that 70~78% of the variance in personality (five constructs) was stable over follow-up period; however, 57~61% of the variance in depression was stable. For personality construct, there were 7.6% to 8.4% of the total variance from the autoregressive occasion factors; for depression construct there were 15.2% to 18.1% of the total variance from the autoregressive occasion factors. Additionally, results showed that when controlling initial symptom severity, the time-invariant components of all five dimensions of personality were predictive of change in depression (Extraversion: B= .32, Openness: B = -.21, Agreeableness: B = -.27, Conscientious: B = -.36, Neuroticism: B = .39). Because five dimensions of personality shared some variance, the models in which all five dimensions of personality were simultaneous to predict change in depression were investigated. The time-invariant components of five dimensions were still significant predictors for change in depression (Extraversion: B = .30, Openness: B = -.24, Agreeableness: B = -.28, Conscientious: B = -.35, Neuroticism: B = .42). In sum, the majority of the variability of personality was stable over 2 years. Individuals with the greater tendency of Extraversion and Neuroticism have higher degrees of depression; individuals with the greater tendency of Openness, Agreeableness and Conscientious have lower degrees of depression.

Keywords: assessment, depression, personality, trait-state-occasion model

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Authors: Dariush Jafari, Seyed Ali Jafari

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The recommended limit for cadmium concentration in potable water is less than 0.005 mg/L. A continuous biosorption process using indigenous red seaweed, Gracilaria corticata, was performed to remove cadmium from the potable water. The process was conducted under fixed conditions and the breakthrough curves were achieved for three consecutive sorption-desorption cycles. A modeling based on Artificial Neural Network (ANN) was employed to fit the experimental breakthrough data. In addition, a simplified semi empirical model, Thomas, was employed for this purpose. It was found that ANN well described the experimental data (R2>0.99) while the Thomas prediction were a bit less successful with R2>0.97. The adjusted design parameters using the nonlinear form of Thomas model was in a good agreement with the experimentally obtained ones. The results approve the capability of ANN to predict the cadmium concentration in potable water.

Keywords: ANN, biosorption, cadmium, packed-bed, potable water

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Authors: Vahid Ebrahimipour

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Word representation and context meaning of text-based documents play an essential role in knowledge modeling. Business procedures written in natural language are meant to store technical and engineering information, management decision and operation experience during the production system life cycle. Context meaning representation is highly dependent upon word sense, lexical relativity, and sematic features of the argument. This paper proposes a method for lexical semantic analysis and context meaning representation of maintenance activity in a mass production system. Our approach constructs a straightforward lexical semantic approach to analyze facilitates semantic and syntactic features of context structure of maintenance report to facilitate translation, interpretation, and conversion of human-readable interpretation into computer-readable representation and understandable with less heterogeneity and ambiguity. The methodology will enable users to obtain a representation format that maximizes shareability and accessibility for multi-purpose usage. It provides a contextualized structure to obtain a generic context model that can be utilized during the system life cycle. At first, it employs a co-occurrence-based clustering framework to recognize a group of highly frequent contextual features that correspond to a maintenance report text. Then the keywords are identified for syntactic and semantic extraction analysis. The analysis exercises causality-driven logic of keywords’ senses to divulge the structural and meaning dependency relationships between the words in a context. The output is a word contextualized representation of maintenance activity accommodating computer-based representation and inference using OWL/RDF.

Keywords: lexical semantic analysis, metadata modeling, contextual meaning extraction, ontology modeling, knowledge representation

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Authors: Jirod Chaisan, Somchai Maneewan, Chantana Punlek, Ninnart Rachapradit, Surapong Chirarattananon, Pattana Rakkwamsuk

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In this paper, simulation modeling of heat transfer, air flow and distribution emitted from CO2 was performed in a regenerated air. The study room was divided in 3 types: common room, small lecture room and large lecture room under evaluated condition in two case: released and unreleased CO2 including of used hybrid air ventilation system for regenerated air under Thailand climate conditions. The carbon dioxide was located on the center of the room and released rate approximately 900-1200 ppm corresponded with indoor air quality standard (IAQs). The indoor air in the thermal comfort zone was calculated and simulated with the numerical method that using real data from the handbook guideline. The results of the study showed that in the case of hybrid air ventilation system explained thermal and CO2 distribution due to the system was adapted significantly in the comfort zone. The results showed that when CO2 released on the center of the other room, the CO2 high concentration in comfort zone so used hybrid air ventilation that decreased CO2 with regeneration air including of reduced temperature indoor. However, the study is simulation modeling and guideline only so the future should be the experiment of hybrid air ventilation system for evaluated comparison of the systems.

Keywords: air ventilation, indoor air quality, thermal comfort, thermoelectric, photovoltaic, dehumidify

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Authors: A. Naamane, M. Hasnaoui

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Numerical modeling of fluid flows, whether compressible or incompressible, laminar or turbulent presents a considerable contribution in the scientific and industrial fields. However, the development of an approximate model of a supersonic flow requires the introduction of specific and more precise techniques and methods. For this purpose, the object of this paper is modeling a supersonic flow of inviscid fluid around a dihedral airfoil. Based on the thin airfoils theory and the non-dimensional stationary Steichen equation of a two-dimensional supersonic flow in isentropic evolution, we obtained a solution for the downstream velocity potential of the oblique shock at the second order of relative thickness that characterizes a perturbation parameter. This result has been dealt with by the asymptotic analysis and characteristics method. In order to validate our model, the results are discussed in comparison with theoretical and experimental results. Indeed, firstly, the comparison of the results of our model has shown that they are quantitatively acceptable compared to the existing theoretical results. Finally, an experimental study was conducted using the AF300 supersonic wind tunnel. In this experiment, we have considered the incident upstream Mach number over a symmetrical dihedral airfoil wing. The comparison of the different Mach number downstream results of our model with those of the existing theoretical data (relative margin between 0.07% and 4%) and with experimental results (concordance for a deflection angle between 1° and 11°) support the validation of our model with accuracy.

Keywords: asymptotic modelling, dihedral airfoil, supersonic flow, supersonic wind tunnel

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Authors: Michael Gerges, Ograbe Ahiakwo, Martin Jaeger, Ahmad Asaad

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Recent advances of Building Information Modeling (BIM) especially in the Middle East have increased remarkably. Dubai has been taking a lead on this by making it mandatory for BIM to be adopted for all projects that involve complex architecture designs. This is because BIM is a dynamic process that assists all stakeholders in monitoring the project status throughout different project phases with great transparency. It focuses on utilizing information technology to improve collaboration among project participants during the entire life cycle of the project from the initial design, to the supply chain, resource allocation, construction and all productivity requirements. In view of this trend, the paper examines the extent of applying BIM in the State of Kuwait, by exploring practitioners’ perspectives on BIM, especially their perspectives on main barriers and main advantages. To this end structured interviews were carried out based on questionnaires and with a range of different construction professionals. The results revealed that practitioners perceive improved communication and mitigated project risks by encouraged collaboration between project participants. However, it was also observed that the full implementation of BIM in the State of Kuwait requires concerted efforts to make clients demanding BIM, counteract resistance to change among construction professionals and offer more training for design team members. This paper forms part of an on-going research effort on BIM and its application in the State of Kuwait and it is on this basis that further research on the topic is proposed.

Keywords: building information modeling, BIM, construction industry, Kuwait

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Authors: Drashti G. Daraji, Rosa E. Moo-Puc, Hitesh D. Patel

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Substituted 2-Thioimidazole analogues have been synthesized and confirmed by advanced spectroscopic techniques. Among them, ten compounds have been selected and evaluated for their in vitro anti-cancer activity at the National Cancer Institute (NCI) for testing against a panel of 60 different human tumor cell lines derived from nine neoplastic cancer types. Furthermore, synthesized compounds were tested for their in vitro antiprotozoal activity, and none of them exhibited significant potency against antiprotozoans. It was observed that the tested all compounds seem effective on the UACC-62 melanoma cancer cell line as compared to other cancer cell lines and also exhibited the least potent in the Non-Small Cell Lung Cancer cell line in one-dose screening. In silico studies of these derivatives were carried out by molecular docking techniques and Absorption, Distribution, Metabolism, and Excretion (ADME) using Schrödinger software to find potent B-Raf kinase inhibitor (PDB ID: 3OG7). All the compounds have been performed for docking study; Compound D4 has a good docking score for melanoma cancer as compared with other.

Keywords: anticancer activity, cancer cell line, 2-thio imidazole, one-dose assay, molecular docking

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Authors: Marco Sewald

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Comparing present to past the numbers of Americans expatriating U. S. citizenship have risen. Even though these numbers are small compared to the immigrants, U. S. citizens expatriations have historically been much lower, making the uptick worrisome. In addition, the published lists and numbers from the U.S. government seems incomplete, with many not counted. Different branches of the U. S. government report different numbers and no one seems to know exactly how big the real number is, even though the IRS and the FBI both track and/or publish numbers of Americans who renounce. Since there is no single explanation, anecdotal evidence suggests this uptick is caused by global tax law and increased compliance burdens imposed by the U.S. lawmakers on U.S. citizens abroad. Within a research project the question arose about the reasons why a constant growing number of U.S. citizens are expatriating – the answers are believed helping to explain the underlying governmental policy rational, leading to such activities. While it is impossible to locate former U.S. citizens to conduct a survey on the reasons and the U.S. government is not commenting on the reasons given within the process of expatriation, the chosen methodology is Structural Equation Modeling (SEM), in the first step by re-using current surveys conducted by different researchers within the population of U. S. citizens residing abroad during the last years. Surveys questioning the personal situation in the context of tax, compliance, citizenship and likelihood to repatriate to the U. S. In general SEM allows: (1) Representing, estimating and validating a theoretical model with linear (unidirectional or not) relationships. (2) Modeling causal relationships between multiple predictors (exogenous) and multiple dependent variables (endogenous). (3) Including unobservable latent variables. (4) Modeling measurement error: the degree to which observable variables describe latent variables. Moreover SEM seems very appealing since the results can be represented either by matrix equations or graphically. Results: the observed variables (items) of the construct are caused by various latent variables. The given surveys delivered a high correlation and it is therefore impossible to identify the distinct effect of each indicator on the latent variable – which was one desired result. Since every SEM comprises two parts: (1) measurement model (outer model) and (2) structural model (inner model), it seems necessary to extend the given data by conducting additional research and surveys to validate the outer model to gain the desired results.

Keywords: expatriation of U. S. citizens, SEM, structural equation modeling, validating

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Authors: Ertuğ Yıldırım, Dile Kara, Salih Zeki Yıldız

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Metal containing polymers (MCPs) are macro molecules usually containing metal-ligand coordination units and are a multidisciplinary research field mainly based at the interface between coordination chemistry and polymer science. The progress of this area has also been reinforced by the growth of several other closely related disciplines including macro molecular engineering, crystal engineering, organic synthesis, supra molecular chemistry and colloidal and material science. Schiff base ligands are very effective in constructing supra molecular architectures such as coordination polymers, double helical and triple helical complexes. In addition, Schiff base derivatives incorporating a fluorescent moiety are appealing tools for optical sensing of metal ions. MCPs are well-known systems in which the combinations of local parameters are possible by means of fluoro metric techniques. Generally, without incorporation of the fluorescent groups with polymers is unspecific, and it is not useful to analyze their fluorescent properties. Therefore, it is necessary to prepare a new type epoxy polymers with fluorescent groups in terms of metal sensing prop and the other photo chemical applications. In the present study metal containing polymers were prepared via poly functional monomeric Schiff base metal chelate complexes in the presence of dis functional monomers such as diglycidyl ether Bisphenol A (DGEBA). The synthesized complexes and polymers were characterized by FTIR, UV-VIS and mass spectroscopies. The preparations of epoxy polymers have been carried out at 185 °C. The prepared composites having sharp and narrow excitation/emission properties are expected to be applicable in various systems such as heat-resistant polymers and photo voltaic devices. The prepared composite is also ideal for various applications, easily prepared, safe, and maintain good fluorescence properties.

Keywords: Schiff base ligands, crystal engineering, fluorescence properties, Metal Containing Polymers (MCPs)

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Authors: K. Żak, S. Przetocka, R. Kitel, K. Guzik, B. Musielak, S. Malicki, G. Dubin, T. A. Holak

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Studies on tumor genesis revealed a number of factors that may potentially serve as molecular targets for immunotherapies. One of such promising targets are PD1 and PDL1 proteins. PD1 (Programmed cell death protein 1) is expressed by activated T cells and plays a critical role in modulation of the host's immune response. One of the PD1 ligands -PDL1- is expressed by macrophages, monocytes and cancer cells which exploit it to avoid immune attack. The notion of the mechanisms used by cancer cells to block the immune system response was utilized in the development of therapies blocking PD1-PDL1 interaction. Up to date, human PD1-PDL1 complex has not been crystallized and structure of the mouse-human complex does not provide a complete view of the molecular basis of PD1-PDL1 interactions. The purpose of this study is to obtain crystal structure of the human PD1-PDL1 complex which shall allow rational design of small molecule inhibitors of the interaction. In addition, the study presents results of binding small-molecules to PD1 and fragment docking towards PD1 protein which will facilitate the design and development of small–molecule inhibitors of PD1-PDL1 interaction.

Keywords: PD1, PDL1, cancer, small molecule, drug discovery

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Authors: A. A. Hussen, I. N. Jleta

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Micro-electromechanical system (MEMS) accelerometers and gyroscopes are suitable for the inertial navigation system (INS) of many applications due to the low price, small dimensions and light weight. The main disadvantage in a comparison with classic sensors is a worse long term stability. The estimation accuracy is mostly affected by the time-dependent growth of inertial sensor errors, especially the stochastic errors. In order to eliminate negative effect of these random errors, they must be accurately modeled. Where the key is the successful implementation that depends on how well the noise statistics of the inertial sensors is selected. In this paper, the Allan variance technique will be used in modeling the stochastic errors of the inertial sensors. By performing a simple operation on the entire length of data, a characteristic curve is obtained whose inspection provides a systematic characterization of various random errors contained in the inertial-sensor output data.

Keywords: Allan variance, accelerometer, gyroscope, stochastic errors

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Authors: H. K. Ratre, M. Roy, S. Roy, M. S. Parmar, V. Bhagat

Abstract:

Mastitis is a common problem of dairy industries. Reduction in milk production and an irreparable damage to the udder associated with the disease are common causes of culling of dairy cows. Milk from infected animals is not suitable for drinking and for making different milk products. So, it has a major economic importance in dairy cattle. The aims of this study were to investigate the bacteriological panorama in milk from udder quarters with subclinical mastitis and to carried out for the molecular characterization of the major isolated organisms, from subclinical mastitis-affected cows in and around Durg and Rajnandgaon district of Chhattisgarh. Isolation and identification of bacteria from the milk samples of subclinical mastitis-affected cows were done by standard and routine culture procedures. A total of 78 isolates were obtained from cows and among the various bacteria isolated, Staphylococcus spp. occupied prime position with occurrence rate of 51.282%. However, other bacteria isolated includeStreptococcus spp. (20.512%), Micrococcus spp. (14.102%), E. coli (8.974%), Klebsiela spp. (2.564%), Salmonella spp. (1.282%) and Proteus spp. (1.282%). Staphylococcus spp. was isolated as the major causative agent of subclinical mastitis in the studied area. Molecular characterization of Staphylococus aureusisolates was done for genetic expression of the virulence genes like ‘nuc’ encoding thermonucleaseexoenzyme, coa and spa by PCR amplification of the respective genes in 25 Staphylococcus isolates. In the present study, 15 isolates (77.27%) out of 20 coagulase positive isolates were found to be genotypically positive for ‘nuc’ where as 20 isolates (52.63%) out of 38 CNS expressed the presence of the same virulence gene. In the present study, three Staphylococcus isolates were found to be genotypically positive for coa gene. The Amplification of the coa gene yielded two different products of 627, 710 bp. The amplification of the gene segment encoding the IgG binding region of protein A (spa) revealed a size of 220 and 253bp in twostaphylococcus isolates. The X-region binding of the spa gene produced an amplicon of 315 bp in one Staphylococcal isolates. Staphylococcus aureus was found to be major isolate (51.28%) responsible for causing subclinical mastitis in cows which also showed expression of virulence genesnuc, coa and spa.

Keywords: mastitis, bacteria, characterization, expression, gene

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Authors: Aymen Laadhari

Abstract:

We present in this paper a fully implicit finite element method tailored for the numerical modeling of inextensible fluidic membranes in a surrounding Newtonian fluid. We consider a highly simplified version of the Canham-Helfrich model for phospholipid membranes, in which the bending force and spontaneous curvature are disregarded. The coupled problem is formulated in a fully Eulerian framework and the membrane motion is tracked using the level set method. The resulting nonlinear problem is solved by a Newton-Raphson strategy, featuring a quadratic convergence behavior. A monolithic solver is implemented, and we report several numerical experiments aimed at model validation and illustrating the accuracy of the proposed method. We show that stability is maintained for significantly larger time steps with respect to an explicit decoupling method.

Keywords: finite element method, level set, Newton, membrane

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Authors: Jiahui Song

Abstract:

The use of electric fields with high intensity (~ 100kV/cm or higher) and ultra short pulse durations (nanosecond range) has been a recent development. Most of the studies of electroporation have ignored possible thermal effects because of the small duration of the applied voltage pulses. However, it has been predicted membrane temperature gradients ranging from 0.2×109 to 109 K/m. This research focuses on thermal effects that drive for electroporative enhancements, even though the actual temperature values might not have changed appreciably from their equilibrium levels. The dynamics of pore formation with the application of an externally applied electric field is studied on the basis of molecular dynamics (MD) simulations using the GROMACS package. MD simulations of a lipid layer with constant electric field strength of 0.5 V/nm at 25 °C and 47 °C are implemented to simulate the appropriate thermal effects. The GROMACS provides the force fields for the lipid membranes, which is taken to comprise of dipalmitoyl-phosphatidyl-choline (DPPC) molecules. The water model mimicks the aqueous environment surrounding the membrane. Velocities of water and membrane molecules are generated randomly at each simulation run according to a Maxwellian distribution. The high background electric field is typically used in MD simulations to probe electroporation. It serves as an accelerated test of the pore formation process since low electric fields would take inordinately long simulation time. MD simulation shows no pore is formed in a 1-ns snapshot for a DPPC membrane set at a temperature of 25°C after a 0.5 V/nm electric field is applied. A nano-sized pore is clearly seen in a 0.75-ns snapshot on the same geometry, but with the membrane surfaces kept at temperatures of 47°C. And the pore increases at 1 ns. The MD simulation results suggest the possibility that the increase in temperature can result in different degrees of electrically stimulated bio-effects. The results points to the role of thermal effects in facilitating and accelerating the electroporation process.

Keywords: high-intensity, ultra-short, electroporation, thermal effects, molecular dynamics

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Authors: Hyun-Woo Cho

Abstract:

Unexpected events may occur with serious impacts on industrial process. This work utilizes a data representation technique to model and to analyze process data pattern for the purpose of diagnosis. In this work, the use of triangular representation of process data is evaluated using simulation process. Furthermore, the effect of using different pre-treatment techniques based on such as linear or nonlinear reduced spaces was compared. This work extracted the fault pattern in the reduced space, not in the original data space. The results have shown that the non-linear technique based diagnosis method produced more reliable results and outperforms linear method.

Keywords: process monitoring, data analysis, pattern modeling, fault, nonlinear techniques

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Authors: Moataz M. Hamed, Khalid S. M. Al Hagla, Zeyad El Sayad

Abstract:

Thinking in design energy-efficiency and high-performance green buildings require a different design mechanism and design approach than conventional buildings to achieve more sustainable result. By reasoning about specific issues at the correct time in the design process, the design team can minimize negative impacts, maximize building performance and keep both first and operation costs low. This paper attempts to investigate and exploit the sustainable dimension of building information modeling (BIM) in designing high-performance green buildings that require less energy for operation, emit less carbon dioxide and provide a conducive indoor environment for occupants through early phases of the design process. This objective was attained by a critical and extensive literature review that covers the following issues: the value of considering green strategies in the early design stage, green design workflow, and BIM-based performance analysis. Then the research proceeds with a case study that provides an in-depth comparative analysis of building performance evaluation between an office building in Alexandria, Egypt that was designed by the conventional design process with the same building if taking into account sustainability consideration and BIM-based sustainable analysis integration early through the design process. Results prove that using sustainable capabilities of building information modeling (BIM) in early stages of the design process side by side with green design workflow promote buildings performance and sustainability outcome.

Keywords: BIM, building performance analysis, BIM-based sustainable analysis, green building design

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Authors: Fakhrosadat Sajjadian, Ramin Ghasemi Shayan

Abstract:

The tumor microenvironment plays an fundamental part in tumor start, movement, metastasis, and treatment resistance. It varies from ordinary tissue in terms of its extracellular network, vascular and lymphatic arrange, as well as physiological conditions. The clinical application of atomic cancer imaging is regularly prevented by the tall commercialization costs of focused on imaging operators as well as the constrained clinical applications and little showcase measure of a few operators. . Since numerous cancer types share comparable characteristics of the tumor microenvironment, the capacity to target these biomarkers has the potential to supply clinically translatable atomic imaging advances for numerous types encompassing cancer and broad clinical applications. Noteworthy advance has been made in focusing on the tumor microenvironment for atomic cancer imaging. In this survey, we summarize the standards and methodologies of later progresses in atomic imaging of the tumor microenvironment, utilizing distinctive imaging modalities for early discovery and conclusion of cancer. To conclude, The tumor microenvironment (TME) encompassing tumor cells could be a profoundly energetic and heterogeneous composition of safe cells, fibroblasts, forerunner cells, endothelial cells, flagging atoms and extracellular network (ECM) components.

Keywords: molecular, imaging, TME, medicine

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