Search results for: molecular modelling

Authors: Buruk Kitachew Wossenyeleh

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Groundwater is the largest freshwater reservoir in the world. Like the other reservoirs of the hydrologic cycle, it is a finite resource. This study focused on the groundwater modeling of the Ter Kamerenbos well field to understand the groundwater flow system and the impact of different scenarios. The study area covers 68.9Km2 in the Brussels Capital Region and is situated in two river catchments, i.e., Zenne River and Woluwe Stream. The aquifer system has three layers, but in the modeling, they are considered as one layer due to their hydrogeological properties. The catchment aquifer system is replenished by direct recharge from rainfall. The groundwater recharge of the catchment is determined using the spatially distributed water balance model called WetSpass, and it varies annually from zero to 340mm. This groundwater recharge is used as the top boundary condition for the groundwater modeling of the study area. During the groundwater modeling using Processing MODFLOW, constant head boundary conditions are used in the north and south boundaries of the study area. For the east and west boundaries of the study area, head-dependent flow boundary conditions are used. The groundwater model is calibrated manually and automatically using observed hydraulic heads in 12 observation wells. The model performance evaluation showed that the root means the square error is 1.89m and that the NSE is 0.98. The head contour map of the simulated hydraulic heads indicates the flow direction in the catchment, mainly from the Woluwe to Zenne catchment. The simulated head in the study area varies from 13m to 78m. The higher hydraulic heads are found in the southwest of the study area, which has the forest as a land-use type. This calibrated model was run for the climate change scenario and well operation scenario. Climate change may cause the groundwater recharge to increase by 43% and decrease by 30% in 2100 from current conditions for the high and low climate change scenario, respectively. The groundwater head varies for a high climate change scenario from 13m to 82m, whereas for a low climate change scenario, it varies from 13m to 76m. If doubling of the pumping discharge assumed, the groundwater head varies from 13m to 76.5m. However, if the shutdown of the pumps is assumed, the head varies in the range of 13m to 79m. It is concluded that the groundwater model is done in a satisfactory way with some limitations, and the model output can be used to understand the aquifer system under steady-state conditions. Finally, some recommendations are made for the future use and improvement of the model.

Keywords: Ter Kamerenbos, groundwater modelling, WetSpass, climate change, well operation

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Authors: E. H. N. Gashti, M. Zarrini, M. Irannezhad, J. R. Langroudi

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Using ETABS software, this study analyzed 23 buildings to evaluate effects of mistakes during construction phase on buildings structural behavior. For modelling, two different loadings were assumed: 1) design loading and 2) loading due to the effects of mistakes in construction phase. Research results determined that considering traditional construction methods for buildings resulted in a significant increase in dead loads and consequently intensified the displacements and base-shears of buildings under seismic loads.

Keywords: reinforced-concrete buildings, construction mistakes, base-shear, displacements, failure

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Authors: Kevin A. Droguett, Edwin G. Pérez, Denis Fuentealba, Margarita E. Aliaga, Angélica M. Fierro

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Supramolecular chemistry is a field of growing interest. Moreover, studying the formation of host-guest complexes between macrocycles and dyes is highly attractive due to their potential applications. Examples of the above are drug delivery, catalytic process, and sensing, among others. There are different dyes of interest in the literature; one example is the quinolinone derivatives. Those molecules have good optical properties and chemical and thermal stability, making them suitable for developing fluorescent probes. Secondly, several macrocycles can be seen in the literature. One example is the cucurbiturils. This water-soluble macromolecule family has a hydrophobic cavity and two identical carbonyl portals. Additionally, the thermodynamic analysis of those supramolecular systems could help understand the affinity between the host and guest, their interaction, and the main stabilization energy of the complex. In this work, two 7-(diethylamino) quinoline-2 (1H)-one derivative (QD1-2) and their interaction with cucurbit[7]uril (CB[7]) were studied from an experimental and in-silico point of view. For the experimental section, the complexes showed a 1:1 stoichiometry by HRMS-ESI and isothermal titration calorimetry (ITC). The inclusion of the derivatives on the macrocycle lends to an upward shift in the fluorescence intensity, and the pKa value of QD1-2 exhibits almost no variation after the formation of the complex. The thermodynamics of the inclusion complexes was investigated using ITC; the results demonstrate a non-classical hydrophobic effect with a minimum contribution from the entropy term and a constant binding on the order of 106 for both ligands. Additionally, dynamic molecular studies were carried out during 300 ns in an explicit solvent at NTP conditions. Our finding shows that the complex remains stable during the simulation (RMSD ~1 Å), and hydrogen bonds contribute to the stabilization of the systems. Finally, thermodynamic parameters from MMPBSA calculations were obtained to generate new computational insights to compare with experimental results.

Keywords: host-guest complexes, molecular dynamics, quinolin-2(1H)-one derivatives dyes, thermodynamics

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Authors: A. Daftari, W. Kudla

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Liquefaction is a phenomenon in which the strength and stiffness of a soil is reduced by earthquake shaking or other rapid cyclic loading. Liquefaction and related phenomena have been responsible for huge amounts of damage in historical earthquakes around the world. Modelling of soil behaviour is the main step in soil liquefaction prediction process. Nowadays, several constitutive models for sand have been presented. Nevertheless, only some of them can satisfy this mechanism. One of the most useful models in this term is UBCSAND model. In this research, the capability of this model is considered by using PLAXIS software. The real data of superstition hills earthquake 1987 in the Imperial Valley was used. The results of the simulation have shown resembling trend of the UBC3D-PLM model.

Keywords: liquefaction, plaxis, pore-water pressure, UBC3D-PLM

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Authors: Halim Djerroud, Arab Ali Cherif

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We assume that conscious functions are implemented automatically. In other words that consciousness as well as the non-consciousness aspect of human thought, planning, and perception, are produced by biologically adaptive algorithms. We propose that the mechanisms of consciousness can be produced using similar adaptive algorithms to those executed by the mechanism. In this paper, we propose a computational model of consciousness, the ”Global Abstraction Workspace” which is an internal environmental modelling perceived as a multi-agent system. This system is able to evolve and generate new data and processes as well as actions in the environment.

Keywords: artificial consciousness, cognitive architecture, global abstraction workspace, multi-agent system

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Authors: Kavitha Madhu, Karthik K. Srinivasan, R. Sivanandan

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Indian traffic can be considered as mixed and heterogeneous due to the presence of various types of vehicles that operate with weak lane discipline. Consequently, vehicles can position themselves anywhere in the traffic stream depending on availability of gaps. The choice of lateral positioning is an important component in representing and characterizing mixed traffic. The field data provides evidence that the trajectory of vehicles in Indian urban roads have significantly varying longitudinal and lateral components. Further, the notion of headway which is widely used for homogeneous traffic simulation is not well defined in conditions lacking lane discipline. From field data it is clear that following is not strict as in homogeneous and lane disciplined conditions and neighbouring vehicles ahead of a given vehicle and those adjacent to it could also influence the subject vehicles choice of position, speed and acceleration. Given these empirical features, the suitability of using headway distributions to characterize mixed traffic in Indian cities is questionable, and needs to be modified appropriately. To address these issues, this paper attempts to analyze the time gap distribution between consecutive vehicles (in a time-sense) crossing a section of roadway. More specifically, to characterize the complex interactions noted above, the influence of composition, manoeuvre types, and lateral placement characteristics on time gap distribution is quantified in this paper. The developed model is used for evaluating various performance measures such as link speed, midblock delay and intersection delay which further helps to characterise the vehicular fuel consumption and emission on urban roads of India. Identifying and analyzing exact interactions between various classes of vehicles in the traffic stream is essential for increasing the accuracy and realism of microscopic traffic flow modelling. In this regard, this study aims to develop and analyze time gap distribution models and quantify it by lead lag pair, manoeuvre type and lateral position characteristics in heterogeneous non-lane based traffic. Once the modelling scheme is developed, this can be used for estimating the vehicle kilometres travelled for the entire traffic system which helps to determine the vehicular fuel consumption and emission. The approach to this objective involves: data collection, statistical modelling and parameter estimation, simulation using calibrated time-gap distribution and its validation, empirical analysis of simulation result and associated traffic flow parameters, and application to analyze illustrative traffic policies. In particular, video graphic methods are used for data extraction from urban mid-block sections in Chennai, where the data comprises of vehicle type, vehicle position (both longitudinal and lateral), speed and time gap. Statistical tests are carried out to compare the simulated data with the actual data and the model performance is evaluated. The effect of integration of above mentioned factors in vehicle generation is studied by comparing the performance measures like density, speed, flow, capacity, area occupancy etc under various traffic conditions and policies. The implications of the quantified distributions and simulation model for estimating the PCU (Passenger Car Units), capacity and level of service of the system are also discussed.

Keywords: lateral movement, mixed traffic condition, simulation modeling, vehicle following models

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Authors: Qin Yang, Fan Zhang, Juan Du, Chongkui Sun, Krishna Kota, Yun-Ling Zheng

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Telomeres are specialized structures at chromosome ends consisting of tandem repetitive DNA sequences [(TTAGGG)n in humans] and associated proteins, which are necessary for telomere function. Telomere lengths are tightly regulated within a narrow range in normal human somatic cells, the basis of cellular senescence and aging. Previous studies have extensively focused on how short telomeres are extended and have demonstrated that telomerase plays a central role in telomere maintenance through elongating the short telomeres. However, the molecular mechanisms of regulating excessively long telomeres are unknown. Here, we found that telomerase enzymatic component hTERT plays a dual role in the regulation of telomeres length. We analyzed single telomere alterations at each chromosomal end led to the discoveries that hTERT shortens excessively long telomeres and elongates short telomeres simultaneously, thus maintaining the optimal telomere length at each chromosomal end for an efficient protection. The hTERT-mediated telomere shortening removes large segments of telomere DNA rapidly without inducing telomere dysfunction foci or affecting cell proliferation, thus it is mechanistically distinct from rapid telomere deletion. We found that expression of hTERT generates telomeric circular DNA, suggesting that telomere homologous recombination may be involved in this telomere shortening process. Moreover, the hTERT-mediated telomere shortening is required its enzymatic activity, but telomerase RNA component hTR is not involved in it. Furthermore, shelterin protein TPP1 interacts with hTERT and recruits it on telomeres to mediate telomere shortening. In addition, telomere-associated proteins, DKC1 and TCAB1 also play roles in this process. This novel hTERT-mediated telomere shortening mechanism not only exists in cancer cells, but also in primary human cells. Thus, the hTERT-mediated telomere shortening is expected to shift the paradigm on current molecular models of telomere length maintenance, with wide-reaching consequences in cancer and aging fields.

Keywords: aging, hTERT, telomerase, telomeres, human cells

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Authors: Mario Perez-Won, Roberto Lemus-Mondaca, Constanza Olivares-Rivera, Fernanda Marin-Monardez

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This research presents the simultaneous application of high hydrostatic pressure (HHP) and osmotic dehydration (DO) as a pretreatment to hot –air drying of jumbo squid (Dosidicus gigas) cubes. The drying time was reduced to 2 hours at 60ºC and 5 hours at 40°C as compared to the jumbo squid samples untreated. This one was due to osmotic pressure under high-pressure treatment where increased salt saturation what caused an increasing water loss. Thus, a more reduced time during convective drying was reached, and so water effective diffusion in drying would play an important role in this research. Different working conditions such as pressure (350-550 MPa), pressure time (5-10 min), salt concentration, NaCl (10 y 15%) and drying temperature (40-60ºC) were optimized according to kinetic parameters of each mathematical model. The models used for drying experimental curves were those corresponding to Weibull, Page and Logarithmic models, however, the latest one was the best fitted to the experimental data. The values for water effective diffusivity varied from 4.82 to 6.59x10-9 m2/s for the 16 curves (DO+HHP) whereas the control samples obtained a value of 1.76 and 5.16×10-9 m2/s, for 40 and 60°C, respectively. On the other hand, quality characteristics such as color, texture, non-enzymatic browning, water holding capacity (WHC) and rehydration capacity (RC) were assessed. The L* (lightness) color parameter increased, however, b * (yellowish) and a* (reddish) parameters decreased for the DO+HHP treated samples, indicating treatment prevents sample browning. The texture parameters such as hardness and elasticity decreased, but chewiness increased with treatment, which resulted in a product with a higher tenderness and less firmness compared to the untreated sample. Finally, WHC and RC values of the most treatments increased owing to a minor damage in tissue cellular compared to untreated samples. Therefore, a knowledge regarding to the drying kinetic as well as quality characteristics of dried jumbo squid samples subjected to a pretreatment of osmotic dehydration under high hydrostatic pressure is extremely important to an industrial level so that the drying process can be successful at different pretreatment conditions and/or variable processes.

Keywords: diffusion coefficient, drying process, high pressure, jumbo squid, modelling, quality aspects

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Authors: Oleg Reva, Ilya Korotetskiy, Marina Lankina, Murat Kulmanov, Aleksandr Ilin

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Molecular docking approaches are widely used for design of new antibiotics and modeling of antibacterial activities of numerous ligands which bind specifically to active centers of indispensable enzymes and/or key signaling proteins of pathogens. Widespread drug resistance among pathogenic microorganisms calls for development of new antibiotics specifically targeting important metabolic and information pathways. A generally recognized problem is that almost all molecular targets have been identified already and it is getting more and more difficult to design innovative antibacterial compounds to combat the drug resistance. A promising way to overcome the drug resistance problem is an induction of reversion of drug resistance by supplementary medicines to improve the efficacy of the conventional antibiotics. In contrast to well established computer-based drug design, modeling of drug resistance reversion still is in its infancy. In this work, we proposed an approach to identification of compensatory genetic variants reducing the fitness cost associated with the acquisition of drug resistance by pathogenic bacteria. The approach was based on an analysis of the population genetic of Mycobacterium tuberculosis and on results of experimental modeling of the drug resistance reversion induced by a new anti-tuberculosis drug FS-1. The latter drug is an iodine-containing nanomolecular complex that passed clinical trials and was admitted as a new medicine against MDR-TB in Kazakhstan. Isolates of M. tuberculosis obtained on different stages of the clinical trials and also from laboratory animals infected with MDR-TB strain were characterized by antibiotic resistance, and their genomes were sequenced by the paired-end Illumina HiSeq 2000 technology. A steady increase in sensitivity to conventional anti-tuberculosis antibiotics in series of isolated treated with FS-1 was registered despite the fact that the canonical drug resistance mutations identified in the genomes of these isolates remained intact. It was hypothesized that the drug resistance phenotype in M. tuberculosis requires an adjustment of activities of many genes to compensate the fitness cost of the drug resistance mutations. FS-1 cased an aggravation of the fitness cost and removal of the drug-resistant variants of M. tuberculosis from the population. This process caused a significant increase in genetic heterogeneity of the Mtb population that was not observed in the positive and negative controls (infected laboratory animals left untreated and treated solely with the antibiotics). A large-scale search for linkage disequilibrium associations between the drug resistance mutations and genetic variants in other genomic loci allowed identification of target proteins, which could be influenced by supplementary drugs to increase the fitness cost of the drug resistance and deprive the drug-resistant bacterial variants of their competitiveness in the population. The approach will be used to improve the efficacy of FS-1 and also for computer-based design of new drugs to combat drug-resistant infections.

Keywords: complete genome sequencing, computational modeling, drug resistance reversion, Mycobacterium tuberculosis

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Authors: Alberto Enrique Molina Lozano, María Teresa Cortés Montañez

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Polyaniline (PANI) photoelectrodes were electrochemically synthesized through electrodeposition employing three techniques: chronoamperometry (CA), cyclic voltammetry (CV), and potential pulse (PP) methods. The substrate used for electrodeposition was a fluorine-doped tin oxide (FTO) glass with dimensions of 2.5 cm x 1.3 cm. Subsequently, structural and optical characterization was conducted utilizing Fourier-transform infrared (FTIR) spectroscopy and UV-visible (UV-vis) spectroscopy, respectively. The FTIR analysis revealed variations in the molar ratio of benzenoid to quinonoid rings within the PANI polymer matrix, indicative of differing oxidation states arising from the distinct electropolymerization methodologies employed. In the optical characterization, differences in the energy band gap (Eg) values and positions of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) were observed, attributable to variations in doping levels and structural irregularities introduced during the electropolymerization procedures. To assess the charge transfer properties of the PANI photoelectrodes, electrochemical impedance spectroscopy (EIS) experiments were carried out within a 0.1 M sodium sulfate (Na₂SO₄) electrolyte. The results displayed a substantial decrease in charge transfer resistance with the PANI coatings compared to uncoated substrates, with PANI obtained through cyclic voltammetry (CV) presenting the lowest charge transfer resistance, contrasting PANI obtained via chronoamperometry (CA) and potential pulses (PP). Subsequently, the photoactive response of the PANI photoelectrodes was measured through linear sweep voltammetry (LSV) and chronoamperometry. The photoelectrochemical measurements revealed a discernible photoactivity in all PANI-coated electrodes. However, PANI electropolymerized through CV displayed the highest photocurrent. Interestingly, PANI derived from chronoamperometry (CA) exhibited the highest degree of stable photocurrent over an extended temporal interval.

Keywords: PANI, photocurrent, photoresponse, charge separation, recombination

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Authors: Anthony Usoro

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In this paper, two classes of bilinear time series model are obtained under certain conditions from the general bilinear autoregressive moving average model. Bilinear Autoregressive (BAR) and Bilinear Moving Average (BMA) Models have been identified. From the general bilinear model, BAR and BMA models have been proved to exist for q = Q = 0, => j = 0, and p = P = 0, => i = 0 respectively. These models are found useful in modelling most of the economic and financial data.

Keywords: autoregressive model, bilinear autoregressive model, bilinear moving average model, moving average model

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Authors: Luciana Abednego, Cecilia Nugraheni

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There are many approaches proposed for solving Sudoku puzzles. One of them is by modelling the puzzles as block world problems. There have been three model for Sudoku solvers based on this approach. Each model expresses Sudoku solver as a parameterized multi agent systems. In this work, we propose a new model which is an improvement over the existing models. This paper presents the development of a Sudoku solver that implements all the proposed models. Some experiments have been conducted to determine the performance of each model.

Keywords: Sudoku puzzle, Sudoku solver, block world problem, parameterized multi agent systems

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Authors: Ahmad Odeh, Ahmad Jrade

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Energy assessment is an evidently significant factor when evaluating the sustainability of structures especially at the early design stage. Today design practices revolve around the selection of material that reduces the operational energy and yet meets their displinary need. Operational energy represents a substantial part of the building lifecycle energy usage but the fact remains that embodied energy is an important aspect unaccounted for in the carbon footprint. At the moment, little or no consideration is given to embodied energy mainly due to the complexity of calculation and the various factors involved. The equipment used, the fuel needed, and electricity required for each material vary with location and thus the embodied energy will differ for each project. Moreover, the method and the technique used in manufacturing, transporting and putting in place will have a significant influence on the materials’ embodied energy. This anomaly has made it difficult to calculate or even bench mark the usage of such energies. This paper presents a model aimed at helping designers select the construction materials based on their embodied energy. Moreover, this paper presents a systematic approach that uses an efficient method of calculation and ultimately provides new insight into construction material selection. The model is developed in a BIM environment targeting the quantification of embodied energy for construction materials through the three main stages of their life: manufacturing, transportation and placement. The model contains three major databases each of which contains a set of the most commonly used construction materials. The first dataset holds information about the energy required to manufacture any type of materials, the second includes information about the energy required for transporting the materials while the third stores information about the energy required by tools and cranes needed to place an item in its intended location. The model provides designers with sets of all available construction materials and their associated embodied energies to use for the selection during the design process. Through geospatial data and dimensional material analysis, the model will also be able to automatically calculate the distance between the factories and the construction site. To remain within the sustainability criteria set by LEED, a final database is created and used to calculate the overall construction cost based on R.M.S. means cost data and then automatically recalculate the costs for any modifications. Design criteria including both operational and embodied energies will cause designers to revaluate the current material selection for cost, energy, and most importantly sustainability.

Keywords: building information modelling, energy, life cycle analysis, sustainablity

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Authors: Hacene Benkhoula, Mohamed Badreddine Benabdella, Hamid Bouzeboudja, Abderrahmane Asraoui

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The wind is a random variable difficult to master, for this, we developed a mathematical and statistical methods enable to modeling and forecast wind power. Gaussian Processes (GP) is one of the most widely used families of stochastic processes for modeling dependent data observed over time, or space or time and space. GP is an underlying process formed by unrecognized operator’s uses to solve a problem. The purpose of this paper is to present how to forecast wind power by using the GP. The Gaussian process method for forecasting are presented. To validate the presented approach, a simulation under the MATLAB environment has been given.

Keywords: wind power, Gaussien process, modelling, forecasting

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Authors: Shrawan Baghel, Helen Cathcart, Biall J. O'Reilly

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Amorphous drug formulations have great potential to enhance solubility and thus bioavailability of BCS class II drugs. However, the higher free energy and molecular mobility of the amorphous form lowers the activation energy barrier for crystallization and thermodynamically drives it towards the crystalline state which makes them unstable. Accurate determination of the crystallization tendency/kinetics is the key to the successful design and development of such systems. In this study, dipyridamole (DPM) and cinnarizine (CNZ) has been selected as model compounds. Thermodynamic fragility (m_T) is measured from the heat capacity change at the glass transition temperature (Tg) whereas dynamic fragility (m_D) is evaluated using methods based on extrapolation of configurational entropy to zero 〖(m〗_(D_CE )), and heating rate dependence of Tg 〖(m〗_(D_Tg)). The mean relaxation time of amorphous drugs was calculated from Vogel-Tammann-Fulcher (VTF) equation. Furthermore, the correlation between fragility and glass forming ability (GFA) of model drugs has been established and the relevance of these parameters to crystallization of amorphous drugs is also assessed. Moreover, the crystallization kinetics of model drugs under isothermal conditions has been studied using Johnson-Mehl-Avrami (JMA) approach to determine the Avrami constant ‘n’ which provides an insight into the mechanism of crystallization. To further probe into the crystallization mechanism, the non-isothermal crystallization kinetics of model systems was also analysed by statistically fitting the crystallization data to 15 different kinetic models and the relevance of model-free kinetic approach has been established. In addition, the crystallization mechanism for DPM and CNZ at each extent of transformation has been predicted. The calculated fragility, glass forming ability (GFA) and crystallization kinetics is found to be in good correlation with the stability prediction of amorphous solid dispersions. Thus, this research work involves a multidisciplinary approach to establish fragility, GFA and crystallization kinetics as stability predictors for amorphous drug formulations.

Keywords: amorphous, fragility, glass forming ability, molecular mobility, mean relaxation time, crystallization kinetics, stability

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Authors: S. Pradhan, V. Kumaran

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Centrifugal gas separation processes effect separation by utilizing the difference in the mole fraction in a high speed rotating cylinder caused by the difference in molecular mass, and consequently the centrifugal force density. These have been widely used in isotope separation because chemical separation methods cannot be used to separate isotopes of the same chemical species. More recently, centrifugal separation has also been explored for the separation of gases such as carbon dioxide and methane. The efficiency of separation is critically dependent on the secondary flow generated due to temperature gradients at the cylinder wall or due to inserts, and it is important to formulate accurate models for this secondary flow. The widely used Onsager model for secondary flow is restricted to very long cylinders where the length is large compared to the diameter, the limit of high stratification parameter, where the gas is restricted to a thin layer near the wall of the cylinder, and it assumes that there is no mass difference in the two species while calculating the secondary flow. There are two objectives of the present analysis of the rarefied gas flow in a rotating cylinder. The first is to remove the restriction of high stratification parameter, and to generalize the solutions to low rotation speeds where the stratification parameter may be O (1), and to apply for dissimilar gases considering the difference in molecular mass of the two species. Secondly, we would like to compare the predictions with molecular simulations based on the direct simulation Monte Carlo (DSMC) method for rarefied gas flows, in order to quantify the errors resulting from the approximations at different aspect ratios, Reynolds number and stratification parameter. In this study, we have obtained analytical and numerical solutions for the secondary flows generated at the cylinder curved surface and at the end-caps due to linear wall temperature gradient and external gas inflow/outflow at the axis of the cylinder. The effect of sources of mass, momentum and energy within the flow domain are also analyzed. The results of the analytical solutions are compared with the results of DSMC simulations for three types of forcing, a wall temperature gradient, inflow/outflow of gas along the axis, and mass/momentum input due to inserts within the flow. The comparison reveals that the boundary conditions in the simulations and analysis have to be matched with care. The commonly used diffuse reflection boundary conditions at solid walls in DSMC simulations result in a non-zero slip velocity as well as a temperature slip (gas temperature at the wall is different from wall temperature). These have to be incorporated in the analysis in order to make quantitative predictions. In the case of mass/momentum/energy sources within the flow, it is necessary to ensure that the homogeneous boundary conditions are accurately satisfied in the simulations. When these precautions are taken, there is excellent agreement between analysis and simulations, to within 10 %, even when the stratification parameter is as low as 0.707, the Reynolds number is as low as 100 and the aspect ratio (length/diameter) of the cylinder is as low as 2, and the secondary flow velocity is as high as 0.2 times the maximum base flow velocity.

Keywords: rotating flows, generalized onsager and carrier-Maslen model, DSMC simulations, rarefied gas flow

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Authors: Emin Gundogar, Burak Erkayman, Aysegul Yilmaz, Nusret Sazak

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When considering current competition conditions on the world, satisfying customer demands on time has become an important factor that enables the firms take a step further. Therefore, production process must be completed faster to take the competitive advantage. A balanced assembly line is the one of most important factors affecting the speed of production lines. The aim of this study is to build an assembly line to balance the assembly line and to simulate it for different scenarios through a refrigerator factory. The times of the operations is analyzed and grouped by the priorities. First, a Kilbridge & Wester heuristics is put to the model then a simulation approach is implemented to the model and the differences are observed.

Keywords: assembly line design, assembly line balancing, simulation modelling, refrigeration industry

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Authors: Deepshikha Verma, V. N. Rajasekharan Pillai

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The present study reports the synthesis of cyclic PNC-28 peptides with solid-phase peptide synthesis method. In the first step, we synthesize the linear PNC-28 Peptide and in the second step, we cyclize (N-to-C or head-to-tail cyclization) the linear PNC-28 peptide. The molecular formula of cyclic PNC-28 peptide is C64H88N12O16 and its m/z mass is ≈1233.64. Elemental analysis of cyclic PNC-28 is C, 59.99; H, 6.92; N, 13.12; O, 19.98. The characterization of LC-MS, CD, FT-IR, and 1HNMR has been done to confirm the successful synthesis and cyclization of linear PNC-28 peptides.

Keywords: CD, FTIR, 1HNMR, cyclic peptide

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Authors: Ranadhir Roy

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Inverse problems arise in medical (molecular) imaging. These problems are characterized by large in three dimensions, and by the diffusion equation which models the physical phenomena within the media. The inverse problems are posed as a nonlinear optimization where the unknown parameters are found by minimizing the difference between the predicted data and the measured data. To obtain a unique and stable solution to an ill-posed inverse problem, a priori information must be used. Mathematical conditions to obtain stable solutions are established in Tikhonov’s regularization method, where the a priori information is introduced via a stabilizing functional, which may be designed to incorporate some relevant information of an inverse problem. Effective determination of the Tikhonov regularization parameter requires knowledge of the true solution, or in the case of optical imaging, the true image. Yet, in, clinically-based imaging, true image is not known. To alleviate these difficulties we have applied the penalty/modified barrier function (PMBF) method instead of Tikhonov regularization technique to make the inverse problems well-posed. Unlike the Tikhonov regularization method, the constrained optimization technique, which is based on simple bounds of the optical parameter properties of the tissue, can easily be implemented in the PMBF method. Imposing the constraints on the optical properties of the tissue explicitly restricts solution sets and can restore uniqueness. Like the Tikhonov regularization method, the PMBF method limits the size of the condition number of the Hessian matrix of the given objective function. The accuracy and the rapid convergence of the PMBF method require a good initial guess of the Lagrange multipliers. To obtain the initial guess of the multipliers, we use a least square unconstrained minimization problem. Three-dimensional images of fluorescence absorption coefficients and lifetimes were reconstructed from contact and noncontact experimentally measured data.

Keywords: constrained minimization, ill-conditioned inverse problems, Tikhonov regularization method, penalty modified barrier function method

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Authors: William Kelly, Sorelle Veigne, Xianhua Li, Zuyi Huang, Shyamsundar Subramanian, Eugene Schaefer

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The ambr15™ bioreactor is a single-use microbioreactor for cell line development and process optimization. The ambr system offers fully automatic liquid handling with the possibility of fed-batch operation and automatic control of pH and oxygen delivery. With operating conditions for large scale biopharmaceutical production properly scaled down, micro bioreactors such as the ambr15™ can potentially be used to predict the effect of process changes such as modified media or different cell lines. In this study, gassing rates and dilution rates were varied for a semi-continuous cell culture system in the ambr15™ bioreactor. The corresponding changes to metabolite production and consumption, as well as cell growth rate and therapeutic protein production were measured. Conditions were identified in the ambr15™ bioreactor that produced metabolic shifts and specific metabolic and protein production rates also seen in the corresponding larger (5 liter) scale perfusion process. A Dynamic Flux Balance model was employed to understand and predict the metabolic changes observed. The DFB model-predicted trends observed experimentally, including lower specific glucose consumption when CO₂ was maintained at higher levels (i.e. 100 mm Hg) in the broth. A Computational Fluid Dynamic (CFD) model of the ambr15™ was also developed, to understand transfer of O₂ and CO₂ to the liquid. This CFD model predicted gas-liquid flow in the bioreactor using the ANSYS software. The two-phase flow equations were solved via an Eulerian method, with population balance equations tracking the size of the gas bubbles resulting from breakage and coalescence. Reasonable results were obtained in that the Carbon Dioxide mass transfer coefficient (kLa) and the air hold up increased with higher gas flow rate. Volume-averaged kLa values at 500 RPM increased as the gas flow rate was doubled and matched experimentally determined values. These results form a solid basis for optimizing the ambr15™, using both CFD and FBA modelling approaches together, for use in microscale simulations of larger scale cell culture processes.

Keywords: cell culture, computational fluid dynamics, dynamic flux balance analysis, microbioreactor

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Authors: D. M. Rey, V. Delgado, J. Zambrano Nájera

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Increases in urbanization during XX century, has produced changes in natural dynamics of the basins, which has resulted in increases in runoff volumes, peak flows and flow velocities, that in turn increases flood risk. Higher runoff volumes decrease sewerage networks hydraulic capacity and can cause its failure. This in turn generates increasingly recurrent floods causing mobility problems and general economic detriment in the cities. In Latin America, especially Colombia, this is a major problem because urban population at late XX century was more than 70% is in urban areas increasing approximately in 790% in 1940-1990 period. Besides, high slopes product of Andean topography and high precipitation typical of tropical climates increases velocities and volumes even more, causing stopping of cities during storms. Thus, it becomes very important to know hydrological behavior of Andean Urban Watersheds. This research aims to determine the impact of urbanization in high sloped urban watersheds in its hydrology. To this end, it will be used as study area experimental urban watershed named Palogrande-San Luis watershed, located in the city of Manizales, Colombia. Manizales is a city in central western Colombia, located in Colombian Central Mountain Range (part of Los Andes Mountains) with an abrupt topography (average altitude is 2.153 m). The climate in Manizales is quite uniform, but due to its high altitude it presents high precipitations (1.545 mm/year average) with high humidity (83% average). It was applied HEC-HMS Hydrologic model on the watershed. The inputs to the model were derived from Geographic Information Systems (GIS) theme layers of the Instituto de Estudios Ambientales –IDEA of Universidad Nacional de Colombia, Manizales (Institute of Environmental Studies) and aerial photography taken for the research in conjunction with available literature and look up tables. Rainfall data from a network of 4 rain gages and historical stream flow data were used to calibrate and validate runoff depth using the hydrologic model. Manual calibration was made, and the simulation results show that the model selected is able to characterize the runoff response of the watershed due to land use for urbanization in high mountain watersheds.

Keywords: Andean watersheds modelling, high mountain urban hydrology, urban planning, hydrologic modelling

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Authors: Nina V. Zaitseva, Pavel Z. Shur, Nina G. Atiskova

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Nowadays harmonization of sanitary and hygienic standards of environmental quality with international standards is crucial part of integration of Russia into the international community. Harmonization of Russian and international ambient air quality standards may be realized by risk-based standards development. In this paper approaches to risk-based standards development and examples of these approaches implementation are presented.

Keywords: harmonization, health risk assessment, evolutionary modelling, benchmark level, nickel, manganese

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Authors: Hannah O'Sullivan, Esther Quinn

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Purpose: The Architectural, Engineering, and Construction (AEC) industry has historically struggled to adapt to change. Although the ability to innovate and successfully implement organizational change has been demonstrated to be critical in achieving a sustainable competitive advantage in the industry, many AEC organizations continue to struggle when affecting organizational change. One prominent area of organizational change that presents many challenges in the industry is the adoption of new forms of technology, for example, Building Information Modelling (BIM). Certain Organisational Change Management (OCM) practices have been proven to be effective in supporting organizations to adopt change, but little research has been carried out on diverging employee attitudes to change relative to their roles within the organization. The purpose of this research study is to examine how OCM practices influence employee attitudes to change when adopting new forms of technology and to analyze the diverging employee perspectives within an organization on the importance of different OCM strategies. Methodology: Adopting an interview-based approach, a case study was carried out on a large-sized, prominent Irish construction organization who are currently adopting a new technology platform for its projects. Qualitative methods were used to gain insight into differing perspectives on the utilization of various OCM practices and their efficacy when adopting a new form of technology on projects. Change agents implementing the organizational change gave insight into their intentions with the technology rollout strategy, while other employees were interviewed to understand how this rollout strategy was received and the challenges that were encountered. Findings: The results of this research study are currently being finalized. However, it is expected that employees in different roles will value different OCM practices above others. Findings and conclusions will be determined within the coming weeks. Value: This study will contribute to the body of knowledge relating to the introduction of new technologies, including BIM, to AEC organizations. It will also contribute to the field of organizational change management, providing insight into methods of introducing change that will be most effective for different employees based on their roles and levels of experience within the industry. The focus of this study steers away from traditional studies of the barriers to adopting BIM in its first instance at an organizational level and centers on the direct effect on employees when a company changes the technology platform being used.

Keywords: architectural, engineering, and construction (AEC) industry, Building Information Modelling, case study, challenges, employee perspectives, organisational change management.

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Authors: Yonas Masresha Aymeku

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The purpose of capacity modelling at U-turns is to develop a relationship between capacity and its geometric characteristics. In fact, the few models available for the estimation of capacity at different transportation facilities do not provide specific guidelines for median openings. For this reason, an effort is made to estimate the capacity by collecting the data sets from median openings at different lane roads in Hyderabad City, India. Wide difference (43% -59%) among the capacity values estimated by the existing models shows the limitation to consider for mixed traffic situations. Thus, a distinct model is proposed for the estimation of the capacity of U-turn vehicles at median openings considering mixed traffic conditions, which would further prompt to investigate the effect of different factors that might affect the capacity.

Keywords: geometric, guiddelines, median, vehicles

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Authors: Hongkui Li, Tongli Lu , Jianwu Zhang

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This paper focuses on developing an estimation method of clutch drag torque in wet DCT. The modelling of clutch drag torque is investigated. As the main factor affecting the clutch drag torque, dynamic viscosity of oil is discussed. The paper proposes an estimation method of clutch drag torque based on recursive least squares by utilizing the dynamic equations of gear shifting synchronization process. The results demonstrate that the estimation method has good accuracy and efficiency.

Keywords: clutch drag torque, wet DCT, dynamic viscosity, recursive least squares

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Authors: Adeyi Akindele Oluwatosin, Mustapha Kaosarat Keji, Ajisebiola Babafemi Siji, Adeyi Olubisi Esther, Damilohun Samuel Metibemu, Raphael Emuebie Okonji

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Envenoming by Echis ocellatus is potentially life-threatening due to severe hemorrhage, renal failure, and capillary leakage. These effects are attributed to snake venom metalloproteinases (SVMPs). Due to drawbacks in the use of antivenom, natural inhibitors from plants are of interest in studies of new antivenom treatment. Antagonizing effects of bioactive compounds of Moringa oleifera, a known antisnake plant, are yet to be tested against SVMPs of E. ocellatus (SVMP-EO). Ethanol crude extract of M. oleifera was partitioned using n-hexane and ethyl acetate. Each partition was fractionated using column chromatography and tested against SVMP-EO purified through ion-exchange chromatography with EchiTab-PLUS polyvalent anti-venom as control. Phytoconstituents of ethyl acetate fraction were screened against the catalytic site of crystal of BaP1-SVMP, while drug-likeness and ADMET toxicity of compound were equally determined. The molecular weight of isolated SVMP-EO was 43.28 kDa, with a specific activity of 245 U/ml, a percentage yield of 62.83 %, and a purification fold of 0.920. The Vmax and Km values are 2 mg/ml and 38.095 μmol/ml/min, respectively, while the optimal pH and temperature are 6.0 and 40°C, respectively. Polyvalent anti-venom, crude extract, and ethyl acetate fraction of M. oleifera exhibited a complete inhibitory effect against SVMP-EO activity. The inhibitions of the P-1 and P-II metalloprotease’s enzymes by the ethyl acetate fraction are largely due to methanol, 6, 8, 9-trimethyl-4-(2-phenylethyl)-3-oxabicyclo[3.3.1]non-6-en-1-yl)- and paroxypropione, respectively. Both compounds are potential drug candidates with little or no concern of toxicity, as revealed from the in-silico predictions. The inhibitory effects suggest that this compound might be a therapeutic candidate for further exploration for treatment of Ocellatus’ envenoming.

Keywords: Echis ocellatus, Moringa oleifera, anti-venom, metalloproteases, snakebite, molecular docking

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Authors: Mona Alharbi

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Melioidosis has emerged as a lethal disease. Unfortunately, the molecular mechanisms of virulence and pathogenicity of Burkholderia pseudomallei remain unknown. However, proteomics research has selected putative targets in B. pseudomallei that might play roles in the B. pseudomallei virulence. BPSL 2418 putative protein has been predicted as a free methionine sulfoxide reductase and interestingly there is a link between the level of the methionine sulfoxide in pathogen tissues and its virulence. Therefore in this work, we describe the cloning expression, purification, and crystallization of BPSL 2418 and the solution of its 3D structure using X-ray crystallography. Also, we aimed to identify the substrate binding and reduced forms of the enzyme to understand the role of BPSL 2418. The gene encoding BPSL2418 from B. pseudomallei was amplified by PCR and reclone in pETBlue-1 vector and transformed into E. coli Tuner DE3 pLacI. BPSL2418 was overexpressed using E. coli Tuner DE3 pLacI and induced by 300μM IPTG for 4h at 37°C. Then BPS2418 purified to better than 95% purity. The pure BPSL2418 was crystallized with PEG 4000 and PEG 6000 as precipitants in several conditions. Diffraction data were collected to 1.2Å resolution. The crystals belonged to space group P2 21 21 with unit-cell parameters a = 42.24Å, b = 53.48Å, c = 60.54Å, α=γ=β= 90Å. The BPSL2418 binding MES was solved by molecular replacement with the known structure 3ksf using PHASER program. The structure is composed of six antiparallel β-strands and four α-helices and two loops. BPSL2418 shows high homology with the GAF domain fRMsrs enzymes which suggest that BPSL2418 might act as methionine sulfoxide reductase. The amino acids alignment between the fRmsrs including BPSL 2418 shows that the three cysteines that thought to catalyze the reduction are fully conserved. BPSL 2418 contains the three conserved cysteines (Cys⁷⁵, Cys⁸⁵ and Cys¹⁰⁹). The active site contains the six antiparallel β-strands and two loops where the disulfide bond formed between Cys⁷⁵ and Cys¹⁰⁹. X-ray structure of free methionine sulfoxide binding and native forms of BPSL2418 were solved to increase the understanding of the BPSL2418 catalytic mechanism.

Keywords: X-Ray Crystallography, BPSL2418, Burkholderia pseudomallei, Melioidosis

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Authors: Anicet Dansou

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Textile reinforced concrete (TRC)is increasingly used nowadays in various fields, in particular civil engineering, where it is mainly used for the reinforcement of damaged reinforced concrete structures. TRC is a composite material composed of multi- or uni-axial textile reinforcements coupled with a fine-grained cementitious matrix. The TRC composite is an alternative solution to the traditional Fiber Reinforcement Polymer (FRP) composite. It has good mechanical performance and better temperature stability but also, it makes it possible to meet the criteria of sustainable development better.TRCs are highly anisotropic composite materials with nonlinear hardening behavior; their macroscopic behavior depends on multi-scale mechanisms. The characterization of these materials through numerical simulation has been the subject of many studies. Since TRCs are multiscale material by definition, numerical multi-scale approaches have emerged as one of the most suitable methods for the simulation of TRCs. They aim to incorporate information pertaining to microscale constitute behavior, mesoscale behavior, and macro-scale structure response within a unified model that enables rapid simulation of structures. The computational costs are hence significantly reduced compared to standard simulation at a fine scale. The fine scale information can be implicitly introduced in the macro scale model: approaches of this type are called non-classical. A representative volume element is defined, and the fine scale information are homogenized over it. Analytical and computational homogenization and nested mesh methods belong to these approaches. On the other hand, in classical approaches, the fine scale information are explicitly introduced in the macro scale model. Such approaches pertain to adaptive mesh refinement strategies, sub-modelling, domain decomposition, and multigrid methods This research presents the main principles of numerical multiscale approaches. Advantages and limitations are identified according to several criteria: the assumptions made (fidelity), the number of input parameters required, the calculation costs (efficiency), etc. A bibliographic study of recent results and advances and of the scientific obstacles to be overcome in order to achieve an effective simulation of textile reinforced concrete in civil engineering is presented. A comparative study is further carried out between several methods for the simulation of TRCs used for the structural reinforcement of reinforced concrete structures.

Keywords: composites structures, multiscale methods, numerical modeling, textile reinforced concrete

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Authors: Oktay Emir

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The objective of this study is to determine how entrepreneurs perceive the economic, social and physical impacts of tourism. The study was conducted in the city of Afyonkarahisar, Turkey, which is rich in thermal tourism resources and investments. A survey was used as the data collection method, and the questionnaire was applied to 472 entrepreneurs. A simple random sampling method was used to identify the sample. Independent sampling t-tests and ANOVA tests were used to analyse the data obtained. Additionally, some statistically significant differences (p<0.05) were found based on the participants’ demographic characteristics regarding their opinions about the social, economic and physical impacts of tourism activities.

Keywords: tourism, perception, entrepreneurship, entrepreneurs, structural equation modelling

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Authors: Indunil Jayatilake, Warna Karunasena, Weena Lokuge

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An Australian manufacturer has fabricated an innovative GFRP sandwich panel made from E-glass fiber skin and a modified phenolic core for structural applications. Debonding, which refers to separation of skin from the core material in composite sandwiches, is one of the most common types of damage in composites. The presence of debonding is of great concern because it not only severely affects the stiffness but also modifies the dynamic behaviour of the structure. Generally, it is seen that the majority of research carried out has been concerned about the delamination of laminated structures whereas skin-core debonding has received relatively minor attention. Furthermore, it is observed that research done on composite slabs having multiple skin-core debonding is very limited. To address this gap, a comprehensive research investigating dynamic behaviour of composite panels with single and multiple debonding is presented. The study uses finite-element modelling and analyses for investigating the influence of debonding on free vibration behaviour of single and multilayer composite sandwich panels. A broad parametric investigation has been carried out by varying debonding locations, debonding sizes and support conditions of the panels in view of both single and multiple debonding. Numerical models were developed with Strand7 finite element package by innovatively selecting the suitable elements to diligently represent their actual behavior. Three-dimensional finite element models were employed to simulate the physically real situation as close as possible, with the use of an experimentally and numerically validated finite element model. Comparative results and conclusions based on the analyses are presented. For similar extents and locations of debonding, the effect of debonding on natural frequencies appears greatly dependent on the end conditions of the panel, giving greater decrease in natural frequency when the panels are more restrained. Some modes are more sensitive to debonding and this sensitivity seems to be related to their vibration mode shapes. The fundamental mode seems generally the least sensitive mode to debonding with respect to the variation in free vibration characteristics. The results indicate the effectiveness of the developed three-dimensional finite element models in assessing debonding damage in composite sandwich panels

Keywords: debonding, free vibration behaviour, GFRP sandwich panels, three dimensional finite element modelling

Procedia PDF Downloads 315