Search results for: molecular simulation

Authors: Sanja O. Podunavac-Kuzmanović, Strahinja Z. Kovačević, Lidija R. Jevrić

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Prion is a protein substance whose certain form is considered as infectious agent. It is presumed to be the cause of the transmissible spongiform encephalopathies (TSEs). The protein it is composed of, called PrP, can fold in structurally distinct ways. At least one of those 3D structures is transmissible to other prion proteins. Prions can be found in brain tissue of healthy people and have certain biological role. The structure of prions naturally occurring in healthy organisms is marked as PrPc, and the structure of infectious prion is labeled as PrPSc. PrPc may play a role in synaptic plasticity and neuronal development. Also, it may be required for neuronal myelin sheath maintenance, including a role in iron uptake and iron homeostasis. PrPSc can be considered as an environmental pollutant. The main aim of this study was to carry out the molecular modeling and calculation of molecular descriptors (lipophilicity, physico-chemical and topological descriptors) of structurally diverse compounds which can be considered as anti-prion agents. Molecular modeling was conducted applying ChemBio3D Ultra version 12.0 software. The obtained 3D models were subjected to energy minimization using molecular mechanics force field method (MM2). The cutoff for structure optimization was set at a gradient of 0.1 kcal/Åmol. The Austin Model 1 (AM-1) was used for full geometry optimization of all structures. The obtained set of molecular descriptors is applied in analysis of similarities and dissimilarities among the tested compounds. This study is an important step in further development of quantitative structure-activity relationship (QSAR) models, which can be used for prediction of anti-prion activity of newly synthesized compounds.

Keywords: chemometrics, molecular modeling, molecular descriptors, prions, QSAR

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Authors: Ziraguen O. Williams, Shield B. Lin, Fouad N. Matari, Leslie J. Quiocho

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In a task to assist NASA in analyzing the dynamic forces caused by operational countermeasures of an astronaut’s exercise platform impacting the spacecraft, feedback delay, and signal noise were added to a simulation model of an active-controlled vibration isolation system to regulate the movement of the exercise platform. Previous simulation work was conducted primarily via MATLAB/Simulink. Two additional simulation tools used in this study were Trick and MBDyn, NASA co-developed software simulation environments. Simulation results obtained from these three tools were very similar. All simulation results support the hypothesis that an active-controlled vibration isolation system outperforms a passive-controlled system even with the addition of feedback delay and signal noise to the active-controlled system. In this paper, squat exercise was used in creating excited force to the simulation model. The exciter force from a squat exercise was calculated from the motion capture of an exerciser. The simulation results demonstrate much greater transmitted force reduction in the active-controlled system than the passive-controlled system.

Keywords: control, counterweight, isolation, vibration

Procedia PDF Downloads 101

Authors: Abdulmannan Fadel

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Arabinoxylan is a non-starch polysaccharide (NSP), which is one of the most important polysaccharides contained within cereal grains. Wheat endosperm pentosan and rice bran contain a significant amount of arabinoxylan (7% in rice bran and 10-12% in wheat endosperm pentosan). Several methods have been used for arabinoxylan extraction with varying degrees of success e.g. enzymatic and alkaline treatment. Yet, the use of extrusion alone as a pre-treatment to increase the yield and reduce the molecular weight in wheat endosperm pentosan and rice bran has not been investigated. The samples (wheat pentosan and rice bran) were extruded using a Twin-screw extruder at a range of screw speeds (80 and 160 rpm) and barrel temperatures range (80 to 140°C) with a throughput of 30 Kg hr-1 and moisture content of 25%. Arabinoxylans were extracted with water and the extraction yield and molecular weight was determined using size exclusion high-pressure liquid chromatography system. It was found that increasing screw speed from 80 rpm to 160 rpm, did not effect the extraction yield (p < 0.05) of arabinoxylan from either the wheat endosperm pentosan or the rice bran. However, the molecular weight of the extracted arabinoxylans from pentosan was found to decrease with increasing screw speed in wheat endosperm pentosan. These low molecular weight arabinoxylans have been suggested as immunomodulators.

Keywords: arabinoxylans, extrusion, wheat endosperm pentosan, rice bran

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Authors: Joseph E. Estevez, Mahdi Ghazizadeh, James G. Ryan, Ajit D. Kelkar

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Radiation shielding is an obstacle in long duration space exploration. Boron Nitride Nanotubes (BNNTs) have attracted attention as an additive to radiation shielding material due to B10’s large neutron capture cross section. The B10 has an effective neutron capture cross section suitable for low energy neutrons ranging from 10-5 to 104 eV and hydrogen is effective at slowing down high energy neutrons. Hydrogenated BNNTs are potentially an ideal nanofiller for radiation shielding composites. We use Molecular Dynamics (MD) Simulation via Material Studios Accelrys 6.0 to model the Young’s Modulus of Hydrogenated BNNTs. An extrapolation technique was employed to determine the Young’s Modulus due to the deformation of the nanostructure at its theoretical density. A linear regression was used to extrapolate the data to the theoretical density of 2.62g/cm3. Simulation data shows that the hydrogenated BNNTs will experience a 11% decrease in the Young’s Modulus for (6,6) BNNTs and 8.5% decrease for (8,8) BNNTs compared to non-hydrogenated BNNT’s. Hydrogenated BNNTs are a viable option as a nanofiller for radiation shielding nanocomposite materials for long range and long duration space exploration.

Keywords: boron nitride nanotube, radiation shielding, young modulus, atomistic modeling

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Authors: Mesbah Khaled, Bouraoui Ouissal, Benkiniouar Rachid, Belkhiri Lotfi

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Alstonia, which are tropical plants with a wide geographical distribution, have been divided into different sections by different authors based on previous studies of several species within the genus. Monachino divides Alstonia into 5 sections, while Pichon divides it into 3 sections. Several plants belonging to this genus, such as Alstonia brassii, have been used in traditional folk medicine to treat ailments such as fever, malaria and dysentery]. Previous studies focusing on the chemical composition of these plants have successfully identified indol alkaloids with cytotoxic, anti-diabetic and anti-inflammatory properties. The newly discovered monomers are structurally similar to the backbones of picralin, affinisin and macrolin. On the other hand, all recently isolated dimeric compounds have a macrolin moiety. In this study, a computational analysis was performed on a series of novel molecules, including both monomeric and dimeric compounds with different structural frameworks. This investigation represents the first computational study of these molecules using an in silico approach incorporating 2D-QSAR data. The analysis involved various computational techniques, including 2D-QSAR modelling, molecular docking studies and subsequent validation by molecular dynamics simulation and assessment of ADMET properties. The chemical composition was identified by 1D and 2D NMR. Eight new alkaloids were isolated, 5 monomers and 3 dimers. In this section, we focus on the biological activity of 4 new alkaloids belonging to two different skeletons, the affinisine skeleton.

Keywords: affinisine, talcarpine, macroline, cytotoxicity, alkaloids

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Authors: Tsai-Pei Liu, Zhi-Rou Zheng, Tzu-Tzu Wen

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Innovative logistics system simulation teaching is to extract the characteristics of the system through simulation methodology. The system has randomness and interaction problems in the execution time. Therefore, the simulation model can usually deal with more complex logistics process problems, giving students different learning modes. Students have more autonomy in learning time and learning progress. System simulation has become a new educational tool, but it still needs to accept many tests to use it in the teaching field. Although many business management departments in Taiwan have started to promote, this kind of simulation system teaching is still not popular, and the prerequisite for popularization is to be supported by students. This research uses an extension of Integration Unified Theory of Acceptance and Use of Technology (UTAUT2) to explore the acceptance of students in universities of science and technology to use system simulation as a learning tool. At the same time, it is hoped that this innovation can explore the effectiveness of the logistics system simulation after the introduction of teaching. The results indicated the significant influence of performance expectancy, social influence and learning value on students’ intention towards confirmed the influence of facilitating conditions and behavioral intention. The extended UTAUT2 framework helps in understanding students’ perceived value in the innovative logistics system teaching context.

Keywords: UTAUT2, logistics system simulation, learning value, Taiwan

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Authors: Jiří Barta, Josef Krahulec, Jiří F. Urbánek

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Education and practical training crisis management members are a topical issue nowadays. The paper deals with the perspectives and possibilities of ‘smart solutions’ to education for crisis management staff. Currently, there are a large number of simulation tools, which notes that they are suitable for practical training of crisis management staff. The first part of the paper is focused on the introduction of the technology simulation tools. The simulators aim is to create a realistic environment for the practical training of extending units of crisis staff. The second part of the paper concerns the possibilities of using the simulation technology to the education process. The aim of this section is to introduce the practical capabilities and potential of the simulation programs for practical training of crisis management staff.

Keywords: crisis management staff, computer simulation, software, technological education

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Authors: A. M. Naraghi, V. Gonzalez, M. O'Sullivan, C. G. Walker, M. Poshdar, F. Ying, M. Abdelmegid

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Discrete Event Simulation (DES) and Agent Based Simulation (ABS) are two simulation approaches that have been proposed to support decision-making in the construction industry. Despite the wide use of these simulation approaches in the construction field, their applications for production and material planning is still limited. This is largely due to the dynamic and complex nature of construction material supply chain systems. Moreover, managing the flow of construction material is not well integrated with site logistics in traditional construction planning methods. This paper presents a hybrid of DES and ABS to simulate on-site and off-site material supply processes. DES is applied to determine the best production scenarios with information of on-site production systems, while ABS is used to optimize the supply chain network. A case study of a construction piling project in New Zealand is presented illustrating the potential benefits of using the proposed hybrid simulation model in construction material flow planning. The hybrid model presented can be used to evaluate the impact of different decisions on construction supply chain management.

Keywords: construction supply-chain management, simulation modeling, decision-support tools, hybrid simulation

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Authors: Ki Hyun Park, Hye Min Park, Jeong Ho Kim, Chan Jong Park, Koan Sik Joo

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In the modern days, the use of radioactive substances is on the rise in the areas like chemical weaponry, industrial usage, and power plants. Although there are various technologies available to detect and monitor radioactive substances in the air, the technologies to detect underwater radioactive substances are scarce. In this study, computer simulation of the underwater detection system measuring beta-ray, a radioactive substance, has been done through MCNP. CaF₂, YAP(Ce) and YAG(Ce) have been used in the computer simulation to detect beta-ray as scintillator. Also, the source used in the computer simulation is Sr-90 and Y-90, both of them emitting only pure beta-ray. The distance between the source and the detector was shifted from 1mm to 10mm by 1 mm in the computer simulation. The result indicated that Sr-90 was impossible to measure below 1 mm since its emission energy is low while Y-90 was able to be measured up to 10mm underwater. In addition, the detector designed with CaF₂ had the highest efficiency among 3 scintillators used in the computer simulation. Since it was possible to verify the detectable range and the detection efficiency according to modeling through MCNP simulation, it is expected that such result will reduce the time and cost in building the actual beta-ray detector and evaluating its performances, thereby contributing the research and development.

Keywords: Beta-ray, CaF₂, detector, MCNP simulation, scintillator

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Authors: Nikolaos Simantiris, Markos Avlonitis

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This work builds a simulation platform, modeling the spatial diffusion of the invasive species Callinectes sapidus (blue crab) as a random walk, incorporating also generation, fatality, and fishing rates modeling the time evolution of its population. Antinioti lagoon in West Greece was used as a testbed for applying the simulation model. Field measurements from June 2020 to June 2021 on the lagoon’s setting, bathymetry, and blue crab juveniles provided the initial population simulation of blue crabs, as well as biological parameters from the current literature were used to calibrate simulation parameters. The scope of this study is to render the authors able to predict the evolution of the blue crab population in confined environments of the Ionian Islands region in West Greece. The first result of the simulation experiments shows the possibility for a robust prediction for blue crab population evolution in the Antinioti lagoon.

Keywords: antinioti lagoon, blue crab, stochastic simulation, random walk

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Authors: Hafiz Md. HasanBabu, Khandaker Mohammad Mohi Uddin, Md. IstiakJaman Ami, Rahat Hossain Faisal

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Computing in biomolecular programming performs through the different types of reactions. Proteins and nucleic acids are used to store the information generated by biomolecular programming. DNA (Deoxyribose Nucleic Acid) can be used to build a molecular computing system and operating system for its predictable molecular behavior property. The DNA device has clear advantages over conventional devices when applied to problems that can be divided into separate, non-sequential tasks. The reason is that DNA strands can hold so much data in memory and conduct multiple operations at once, thus solving decomposable problems much faster. Programmable Logic Array, abbreviated as PLA is a programmable device having programmable AND operations and OR operations. In this paper, a DNA PLA is designed by different molecular operations using DNA molecules with the proposed algorithms. The molecular PLA could take advantage of DNA's physical properties to store information and perform calculations. These include extremely dense information storage, enormous parallelism, and extraordinary energy efficiency.

Keywords: biological systems, DNA computing, parallel computing, programmable logic array, PLA, DNA

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Authors: Vigen Barkhudaryan

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The influence of external effects (γ-, UV–radiations, high temperature) in presence of air oxygen on structural transformations of low-density polyethylene (LDPE) have been investigated dependent on the polymers’ thickness, the intensity and the dose of external actions. The methods of viscosimetry, light scattering, turbidimetry and gelation measuring were used for this purpose. The comparison of influence of external effects on LDPE shows, that the destruction and cross-linking processes of macromolecules proceed simultaneously with all kinds of external effects. A remarkable growth of average molecular mass of LDPE along with the irradiation doses and heat treatment exposure growth was established. It was linear for the mass average molecular mass and at the initial doses is mainly the result of the increase of the macromolecular branching. As a result, the macromolecular hydrodynamic volumes have been changed, and therefore the dependence of viscosity average molecular mass on the doses was going through the minimum at initial doses. A significant change of molecular mass, sizes and shape of macromolecules of LDPE occurs under the influence of external effects. The influence is limited only by diffusion of oxygen during -irradiation and heat treatment. At UV–irradiation the influence is limited both by diffusion of oxygen and penetration of radiation. Consequently, the molecular transformations are deeper and evident in case of -irradiation, as soon as the polymer is transformed in a whole volume. It was also established, that the mechanism of molecular transformations in polymers from the surface layer distinctly differs from those of the sample deeper layer. A comparison of the results of these investigations allows us to conclude, that the mechanisms of influence of investigated external effects on polyethylene are similar.

Keywords: cross-linking, destruction, high temperature, LDPE, γ-radiations, UV-radiations

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Authors: Asho Ali

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Tuberculosis is a disease of grave concern which infects one-third of the global population. The high incidence of tuberculosis is further compounded by the increasing emergence of drug resistant strains including multi drug resistant (MDR). Global incidence MDR-TB is ~4%. Molecular epidemiological studies, based on the assumption that patients infected with clustered strains are epidemiologically linked, have helped understand the transmission dynamics of disease. It has also helped to investigate the basis of variation in Mycobacterium tuberculosis (MTB) strains, differences in transmission, and severity of disease or drug resistance mechanisms from across the globe. This has helped in developing strategies for the treatment and prevention of the disease including MDR.

Keywords: Mycobcaterium tuberculosis, molecular epidemiology, drug resistance, disease

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Authors: Jeong-Hwan Choi, Hyo-Sang Park, Tae-Hyung Lee

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The transmission tower is one of the crucial lifeline structures in a modern society, and it needs to be protected against extreme loading conditions. However, the transmission tower is a very complex structure and, therefore, it is very difficult to simulate the actual damage and the collapse behavior of the tower structure. In this study, the actual collapse behavior of the transmission tower due to lateral loading conditions such as wind load is evaluated through the computational simulation. For that, a progressive collapse procedure is applied to the simulation. In this procedure, after running the simulation, if a member of the tower structure fails, the failed member is removed and the simulation run again. The 154kV transmission tower is selected for this study. The simulation is performed by nonlinear static analysis procedure, namely pushover analysis, using OpenSEES, an earthquake simulation platform. Three-dimensional finite element models of those towers are developed.

Keywords: transmission tower, OpenSEES, pushover, progressive collapse

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Authors: Salem El-Tohami Ashoor

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A novel new vanadium (IV) complexes incorporating the chelating diamido cyclopentadienyl {ArN(CH2)3NAr)}2-((ηn-Cp)Cp)} (Ar = 2,6-Pri2C6H3)(Cp = C5H5 and n = 1,2,3,4 and 5) have been studied with calculation of the properties of species involved in various of cyclopentadienyl reaction. These were carried out under investigation of density functional theory (DFT) calculation, and comparing together. Other methods, explicitly including electron correlation, are necessary for more accurate calculations; MB3LYP (Becke) (Lee–Yang–Parr) level of theory often being used to obtain more exact results. These complexes were estimated of electronic energy for molecular system, because it accounts for all electron correlation interactions. The optimised of [V(ArN(CH2)3NAr)2Cl(η5-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) was found to be thermally more stable than others of vanadium cyclopentadienyl. In the meantime the complex [V(ArN(CH2)3NAr)2Cl(η1-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) which is showed a low thermal stability in case of the just one carbon of cyclopentadienyl can be insertion with vanadium metal centre. By using Dewar-Chatt-Duncanson model, as a basis of the molecular orbital (MO) analysis and showed the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital LUMO.

Keywords: vanadium (IV) cyclopentadienyl complexes, DFT, MO, HOMO, LUMO

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Authors: Justine Kiiza, Xu Jiafang

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The world’s demand for energy is increasing rapidly due to population growth and a reduction in shallow conventional oil and gas reservoirs, resorting to deeper and mostly unconventional reserves like shale oil and gas. Most shale formations contain a large amount of expansive sodium montmorillonite (Na-Mnt), due to high water adsorption, hydration, and when the drilling fluid filtrate enters the formation with high Mnt content, the wellbore wall can be unstable due to hydration and swelling, resulting to shrinkage, sticking, balling, time wasting etc., and well collapse in extreme cases causing complex downhole accidents and high well costs. Recently, polyamines like 1, 6 – hexane diamine (HEDA) have been used as typical drilling fluid shale inhibitors to minimize and/or cab clay mineral swelling and maintain the wellbore stability. However, their application is limited to shallow drilling due to their sensitivity to elevated temperature and pressure. Inorganic potassium salts i.e., KCl, have long been applied for restriction of shale formation hydration expansion in deep wells, but their use is limited due to toxicity. Understanding the adsorption behaviour of HEDA on Na-Mnt surfaces in present of organo-salts, organic K-salts e.g., HCO₂K - main component of organo-salt drilling fluid, is of great significance in explaining the inhibitory performance of polyamine inhibitors. Molecular dynamic simulations (MD) were applied to investigate the influence of HCO₂K and KCl on the adsorption mechanism of HEDA on the Na-Mnt surface. Simulation results showed that adsorption configurations of HEDA are mainly by terminal amine groups with a flat-lying alkyl hydrophobic chain. Its interaction with the clay surface decreased the H-bond number between H₂O-clay and neutralized the negative charge of the Mnt surface, thus weakening the surface hydration ability of Na-Mnt. The introduction of HCO₂K greatly improved inhibition ability, coordination of interlayer ions with H₂O as they were replaced by K+, and H₂O-HCOO- coordination reduced H₂O-Mnt interactions, mobility and transport capability of H₂O molecules were more decreased. While KCl showed little ability and also caused more hydration with time, HCO₂K can be used as an alternative for offshore drilling instead of toxic KCl, with a maximum concentration noted in this study as 1.65 wt%. This study provides a theoretical elucidation for the inhibition mechanism and adsorption characteristics of HEDA inhibitor on Na-Mnt surfaces in the presence of K+-salts and may provide more insight into the evaluation, selection, and molecular design of new clay-swelling high-performance WBDF systems used in oil and gas complex offshore drilling well sections.

Keywords: shale, hydration, inhibition, polyamines, organo-salts, simulation

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Authors: Juraj Camaj, Anna Dolinayova, Jana Lalinska, Miroslav Bariak

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Planning of infrastructure and processes in logistic center within the frame of various kinds of logistic hubs and technological activities in them represent quite complex problem. The main goal is to design appropriate layout, which enables to realize expected operation on the desired levels. The simulation software represents progressive contemporary experimental technique, which can support complex processes of infrastructure planning and all of activities on it. It means that simulation experiments, reflecting various planned infrastructure variants, investigate and verify their eligibilities in relation with corresponding expected operation. The inducted approach enables to make qualified decisions about infrastructure investments or measures, which derive benefit from simulation-based verifications. The paper represents simulation software for simulation infrastructural layout and technological activities in marshalling yard, intermodal terminal, warehouse and combination between them as the parts of logistic center.

Keywords: marshalling yard, intermodal terminal, warehouse, transport technology, simulation

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Authors: T. Rajamäki

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In clean room environment molecular contamination in very small concentrations can cause significant harm for the components and processes. This is commonly referred as airborne molecular contamination (AMC). There is a shortage of high sensitivity continuous measurement data for existence and behavior of several of these contaminants. Accordingly, in most cases correlation between concentration of harmful molecules and their effect on processes is not known. In addition, the formation and distribution of contaminating molecules are unclear. In this work sensitive optical techniques are applied in clean room facilities for investigation of concentrations, forming mechanisms and effects of contaminating molecules. Special emphasis is on reactive acid and base gases ammonia (NH3) and hydrogen fluoride (HF). They are the key chemicals in several operations taking place in clean room processes.

Keywords: AMC, clean room, concentration, reactive gas

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Authors: Mosaab A. Omara, Layla O. Elmajdoubb, Mohammad Saleh Al-Aboodyc, Ahmed ElSifyd, Ahmed O. Elkhtamd

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The aim of this study is to present the molecular characterization of cysticercus tenuicolis of Taenia hydatigena from livestock isolates in Egypt, using the amplification of sequencing of the mt-CO1 gene. We introduce a detailed image of the Cysticercus tenuicolis infection in ruminant animals in Upper Egypt. Cysticercus tenuicolis inhabits such organs in ruminants as the omentum, viscera, and liver. In the present study, the infection rate of Cysticercus tenuicolis was found to be 16% and 19% in sheep and goat sample respectively. Firstly we report one larval stage of Taenia hydatigena detected in the camel liver in Egypt. Cysticercus tenuicolis infection manifested a higher prevalence in females than in males. Those above 2 years of age manifested a higher infection rate than younger animals. The preferred site for the infection was the omentum: a 70% preference in sheep and a 68% preference in goat samples. The molecular characterization using the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene of isolates from sheep, goats and camels corresponded to T. hydatigena. For this study, molecular characterizations of T. hydatigena were done for the first time in Egypt. Molecular tools are of great assistance in characterizing the Cysticercus tenuicolis parasite especially when the morphological character cannot be detected because the metacestodes are frequently confused with infection by the Hydatid cyst, especially when these occur in the visceral organs. In the present study, Cysticercus tenuicolis manifested high identity in the goat and sheep samples, while differences were found more frequently in the camel samples (10 pairbase). Clearly molecular diagnosis for Cysticercus tenuicolis infection significantly helps to differentiate it from such other metacestodes.

Keywords: cysticercus tenuicolis, its2, genetic, qena, molecular and taenia hydatigena

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Authors: N. Massoum, B. Bouazza

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In this paper, we have developed a numerical simulation model to describe the electrical properties of GaInP MESFET with submicron gate (Lg = 0.5 µm). This model takes into account the three-dimensional (3D) distribution of the load in the short channel and the law effect of mobility as a function of electric field. Simulation software based on a stochastic method such as Monte Carlo has been established. The results are discussed and compared with those of the experiment. The result suggests experimentally that, in a very small gate length in our devices (smaller than 40 nm), short-channel tunneling explains the degradation of transistor performance, which was previously enhanced by velocity overshoot.

Keywords: Monte Carlo simulation, transient electron transport, MESFET device, simulation software

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Authors: Somayeh Akrami, Vali-Allah Mozaffarian, Habib Onsori

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The studied region in this research, watershed Kuhkamar river, is about 112.66 square kilometers, it is located between 45º 48' 9" to 45º 2' 20" N and 38º 34' 15" to 38º 40' 28" E. The gained results of the studies on flora combinations, proved 287 plant species in 190 genera and 51 families. Asteracea with 49 and Lamiaceae with 27 plant species are the major plant families. Among collected species one interesting plant was found and determined as a new record Anemone narcissiflora L. for flora of Iran. This plant is known as a complex species that shows intraspecific speciation and is classified into about 12 subspecies and 10 varieties in world. To identify the infraspecies taxons of this species, in addition to morphological characteristics, the use of appropriate molecular markers for the better isolation of the individuals were needed.

Keywords: Anemone narcissiflora, floristic Study, kuhkamar, molecular marker

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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 309

Authors: Ziraguen O. Williams, Shield B. Lin, Fouad N. Matari, Leslie J. Quiocho

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Simulation for seated row exercise was a continued task to assist NASA in analyzing a one-dimensional vibration isolation and stabilization system for astronaut’s exercise platform. Feedback delay and signal noise were added to the model as previously done in simulation for squat exercise. Simulation runs for this study were conducted in two software simulation tools, Trick and MBDyn, software simulation environments developed at the NASA Johnson Space Center. The exciter force in the simulation was calculated from the motion capture of an exerciser during a seated row exercise. The simulation runs include passive control, active control using a Proportional, Integral, Derivative (PID) controller, and active control using a Piecewise Linear Integral Derivative (PWLID) controller. Output parameters include displacements of the exercise platform, the exerciser, and the counterweight; transmitted force to the wall of spacecraft; and actuator force to the platform. The simulation results showed excellent force reduction in the actively controlled system compared to the passive controlled system, which showed less force reduction.

Keywords: control, counterweight, isolation, vibration.

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Authors: Usman Ghani

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Feedback is a vital element for improving student learning in a simulation-based training as it guides and refines learning through scaffolding. A number of studies in literature have shown that students’ learning is enhanced when feedback is provided with personalized tutoring that offers specific guidance and adapts feedback to the learner in a one-to-one environment. Thus, emulating these adaptive aspects of human tutoring in simulation provides an effective methodology to train individuals. This paper presents the results of a study that investigated the effectiveness of automating different types of feedback techniques such as Knowledge-of-Correct-Response (KCR) and Answer-Until- Correct (AUC) in software simulation for learning basic information technology concepts. For the purpose of comparison, techniques like simulation with zero or no-feedback (NFB) and traditional hands-on (HON) learning environments are also examined. The paper presents the summary of findings based on quantitative analyses which reveal that the simulation based instructional strategies are at least as effective as hands-on teaching methodologies for the purpose of learning of IT concepts. The paper also compares the results of the study with the earlier studies and recommends strategies for using feedback mechanism to improve students’ learning in designing and simulation-based IT training.

Keywords: simulation, feedback, training, hands-on, labs

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Authors: Jooyoung Park, Junkyeong Kim, Aoqi Zhang, Seunghee Park

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Non-destructive testing on cable is in great demand due to safety accidents at sites where many equipments using cables are installed. In this paper, the quantitative change of the obtained signal was analyzed using a magnetic flux leakage (MFL) method. A two-dimensional simulation was conducted with a FEM model replicating real elevator cables. The simulation data were compared for three parameters (depth of defect, width of defect and inspection velocity). Then, an experiment on same conditions was carried out to verify the results of the simulation. Signals obtained from both the simulation and the experiment were transformed to characterize the properties of the damage. Throughout the results, a cable damage detection based on an MFL method was confirmed to be feasible. In further study, it is expected that the MFL signals of an entire specimen will be gained and visualized as well.

Keywords: magnetic flux leakage (mfl), cable damage detection, non-destructive testing, numerical simulation

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Authors: Muchun Yu, Xue Gao, Qian Chen

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As a novel passive vibration isolation technology, molecular spring isolator (MSI) is investigated in this paper. An MSI consists of water and hydrophobic zeolites as working medium. Under periodic excitation, water molecules intrude into hydrophobic pores of zeolites when the pressure rises and water molecules extrude from hydrophobic pores when pressure drops. At the same time, energy is stored, released and dissipated. An MSI of piston-cylinder structure was designed in this work. Experiments were conducted to investigate the stiffness properties of MSI. The results show that MSI exhibits high-static-low dynamic (HSLD) stiffness. Furthermore, factors such as the quantity of zeolites, temperature, and ions in water are proved to have an influence on the stiffness properties of MSI.

Keywords: hydrophobic zeolites, molecular spring, stiffness, vibration isolation

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Authors: Rauan Sakenov, Peter Bukovics, Peter Gaszler, Veronika Tokacs-Kollar, Beata Bugyi

Abstract:

FH2 (formin homology-2) domains of several proteins, collectively known as formins, including DAAM, DAAM1 and mDia1, promote G-actin nucleation and elongation. FH2 domains of these formins exist as oligomers. Chain dimerization by ring structure formation serves as a structural basis for actin polymerization function of FH2 domain. Proper single chain configuration and specific interactions between its various regions are necessary for individual chains to form a dimer functional in G-actin nucleation and elongation. FH1 and WH2 domain-containing formins were shown to behave as intrinsically disordered proteins. Thus, the aim of this research was to study structural dynamics of FH2 domain of DAAM. To investigate structural features of FH2 domain of DAAM, molecular dynamics simulation of chain A of FH2 domain of DAAM solvated in water box in 50 mM NaCl was conducted at temperatures from 293.15 to 353.15K, with VMD 1.9.2, NAMD 2.14 and Amber Tools 21 using 2z6e and 1v9d PDB structures of DAAM was obtained on I-TASSER webserver. Calcium and ATP bound G-actin 3hbt PDB structure was used as a reference protein with well-described structural dynamics of denaturation. Topology and parameter information of CHARMM 2012 additive all-atom force fields for proteins, carbohydrate derivatives, water and ions were used in NAMD 2.14 and ff19SB force field for proteins in Amber Tools 21. The systems were energy minimized for the first 1000 steps, equilibrated and produced in NPT ensemble for 1ns using stochastic Langevin dynamics and the particle mesh Ewald method. Our root-mean square deviation (RMSD) analysis of molecular dynamics of chain A of FH2 domains of DAAM revealed similar insignificant changes of total molecular average RMSD values of FH2 domain of these formins at temperatures from 293.15 to 353.15K. In contrast, total molecular average RMSD values of G-actin showed considerable increase at 328K, which corresponds to the denaturation of G-actin molecule at this temperature and its transition from native, ordered, to denatured, disordered, state which is well-described in the literature. RMSD values of lasso and tail regions of chain A of FH2 domain of DAAM exhibited higher than total molecular average RMSD at temperatures from 293.15 to 353.15K. These regions are functional in intra- and interchain interactions and contain highly conserved tryptophan residues of lasso region, highly conserved GNYMN sequence of post region and amino acids of the shell of hydrophobic pocket of the salt bridge between Arg171 and Asp321, which are important for structural stability and ordered state of FH2 domain of DAAM and its functions in FH2 domain dimerization. In conclusion, higher than total molecular average RMSD values of lasso and post regions of chain A of FH2 domain of DAAM may explain disordered state of FH2 domain of DAAM at temperatures from 293.15 to 353.15K. Finally, absence of marked transition, in terms of significant changes in average molecular RMSD values between native and denatured states of FH2 domain of DAAM at temperatures from 293.15 to 353.15K, can make it possible to attribute these formins to the group of intrinsically disordered proteins rather than to the group of intrinsically ordered proteins such as G-actin.

Keywords: FH2 domain, DAAM, formins, molecular modelling, computational biophysics

Procedia PDF Downloads 130

Authors: Milica Karadžić, Lidija Jevrić, Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Anamarija Mandić, Aleksandar Oklješa, Andrea Nikolić, Marija Sakač, Katarina Penov Gaši

Abstract:

Using chemometric approach, the relationships between the chromatographic lipophilicity and in silico molecular descriptors for twenty-nine selected steroid derivatives were studied. The chromatographic lipophilicity was predicted using artificial neural networks (ANNs) method. The most important in silico molecular descriptors were selected applying stepwise selection (SS) paired with partial least squares (PLS) method. Molecular descriptors with satisfactory variable importance in projection (VIP) values were selected for ANN modeling. The usefulness of generated models was confirmed by detailed statistical validation. High agreement between experimental and predicted values indicated that obtained models have good quality and high predictive ability. Global sensitivity analysis (GSA) confirmed the importance of each molecular descriptor used as an input variable. High-quality networks indicate a strong non-linear relationship between chromatographic lipophilicity and used in silico molecular descriptors. Applying selected molecular descriptors and generated ANNs the good prediction of chromatographic lipophilicity of the studied steroid derivatives can be obtained. This article is based upon work from COST Actions (CM1306 and CA15222), supported by COST (European Cooperation and Science and Technology).

Keywords: artificial neural networks, chemometrics, global sensitivity analysis, liquid chromatography, steroids

Procedia PDF Downloads 339

Authors: Mahmoud A. Abdulhamid

Abstract:

Poly(ether-ether-ketone) (PEEK) has received increased attention due to its outstanding performance in different membrane applications including gas and liquid separation. However, it suffers from a semi-crystalline morphology, bad solubility and low porosity. To fabricate membranes from PEEK, the usage of harsh acid such as sulfuric acid is essential, regardless its hazardous properties. In this work, we report the molecular design of poly(ether-ether-ketones) (iPEEKs) with intrinsic porosity character, by incorporating kinked units into PEEK backbone such as spirobisindane, Tröger's base, and triptycene. The porous polymers were used to fabricate stable membranes for organic solvent nanofiltration application. To better understand the mechanism, we conducted molecular dynamics simulations to evaluate the possible interactions between the polymers and the solvents. Notable enhancement in separation performance was observed confirming the importance of molecular engineering of high-performance polymers. The iPEEKs demonstrated good solubility in polar aprotic solvents, a high surface area of 205–250 m² g⁻¹, and excellent thermal stability. Mechanically flexible nanofiltration membranes were prepared from N-methyl-2-pyrrolidone dope solution at iPEEK concentrations of 19–35 wt%. The molecular weight cutoff of the membranes was fine-tuned in the range of 450–845 g mol⁻¹ displaying 2–6 fold higher permeance (3.57–11.09 L m⁻² h⁻¹ bar⁻¹) than previous reports. The long-term stabilities were demonstrated by a 7 day continuous cross-flow filtration.

Keywords: molecular engineering, polymer synthesis, membrane fabrication, liquid separation

Procedia PDF Downloads 91

Authors: Jun-ichi Ochiai, Itsuki Noda, Ryo Kanamori, Keiji Hirata, Hitoshi Matsubara, Hideyuki Nakashima

Abstract:

We conducted exhaustive simulations for data assimilation and evaluation of service quality for various setting in a new shared transportation system, called SAVS. Computational social simulation is a key technology to design recent social services like SAVS as new transportation service. One open issue in SAVS was to determine the service scale through the social simulation. Using our exhaustive simulation framework, OACIS, we did data-assimilation and evaluation of effects of SAVS based on actual tax-use data at Tajimi city, Japan. Finally, we get the conditions to realize the new service in a reasonable service quality.

Keywords: on-demand bus sytem, social simulation, data assimilation, exhaustive simulation

Procedia PDF Downloads 311