Search results for: molecular simulations

Authors: S. Chandrasekaran, S. Nandita, M. Shivathmika, Srikrishnan Shivakumar

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The objective of the research work is to analyze the computational chemical-composition of carbohydrates in the context of healthcare informatics. The computation involves the representation of complex chemical molecular structure of carbohydrate using graph theory and in a deployable Chemical Markup Language (CML). The parallel molecular structure of the chemical molecules with or without other adulterants for the sake of business profit can be analyzed in terms of robustness and derivatization measures. The rural healthcare program should create awareness in malnutrition to reduce ill-effect of decomposition and help the consumers to know the level of such energy storage mixtures in a quantitative way. The earlier works were based on the empirical and wet data which can vary from time to time but cannot be made to reuse the results of mining. The work is carried out on the quantitative computational chemistry on carbohydrates to provide a safe and secure right to food act and its regulations.

Keywords: carbohydrates, chemical-composition, chemical markup, robustness, food safety

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Authors: Rabia Korkmaz Tan, Şebnem Bora

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The major problem encountered when modeling complex systems with agent-based modeling and simulation techniques is the existence of large parameter spaces. A complex system model cannot be expected to reflect the whole of the real system, but by specifying the most appropriate parameters, the actual system can be represented by the model under certain conditions. When the studies conducted in recent years were reviewed, it has been observed that there are few studies for parameter tuning problem in agent based simulations, and these studies have focused on tuning parameters of a single model. In this study, an approach of parameter tuning is proposed by using metaheuristic algorithms such as Genetic Algorithm (GA), Particle Swarm Optimization (PSO), Artificial Bee Colonies (ABC), Firefly (FA) algorithms. With this hybrid structured study, the parameter tuning problems of the models in the different fields were solved. The new approach offered was tested in two different models, and its achievements in different problems were compared. The simulations and the results reveal that this proposed study is better than the existing parameter tuning studies.

Keywords: parameter tuning, agent based modeling and simulation, metaheuristic algorithms, complex systems

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Authors: S. Dargouthi, S. Boughdiri, B. Tangour

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This work invoked two complementary parts. In the first, we performed a theoretical study of various dimers of molecular of titanium dioxide. Five structures were examined. Three among them, the (T), (C) and (T/P) isomers, may be considered as stable compounds because they represent absolute minima on their potential energy surfaces. (T) and (C) may coexist because they are separted by only 6.5 kcal mol-1 but (T/P) dimer is in a metastable state from an energetic point of view. Non bonded dimer (P) transforms into its homologue (O) which has been considered as transitory specie with low lifetime which evolves to (T) structure. In the second part, we highlight the possible stabilization of (T), (C) and (P) dimers by encapsulation in carbon nanotubes. This indicates the probable role that plays this transitory specie the polymerization process of molecular TiO2. Confinement is suitable to control the fast evolution process and could towards the synthesis of new titanium dioxide nanostructured materials. An alternative description of TiO2 polymorphs (Rutie, anatase et Brookite) is proposed from (T), (C) and (T/P) dimmers motifs.

Keywords: titanium dioxide, carbon nanotube, confinement. encapsulation, transitory specie

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Authors: Hiroyuki Aoki

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The glass transition phenomenon has been extensively studied for a long time. The glass transition of polymer materials is assigned to the transition of the dynamics of the chain backbone segment. However, the detailed mechanism of the transition behavior of the segmental motion is still unclear. In the current work, the single molecule detection technique was employed to reveal the trajectory of the molecular motion of the single polymer chain. The center segment of poly(butyl methacrylate) chain was labeled by a perylenediimide dye molecule and observed by a highly sensitive fluorescence microscope in a defocus condition. The translational and rotational diffusion of the center segment in a single polymer chain was analyzed near the glass transition temperature. The direct observation of the individual polymer chains revealed the intermittent behavior of the segmental motion, indicating the spatial inhomogeneity.

Keywords: glass transition, molecular motion, polymer materials, single molecule

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Authors: Albina V. Moskvicheva, Gevorg G. Kazarian, Anna R. Valeeva, Marina A. Efimova, Malik N. Mukminov, Eduard A. Shuralev, Rustam Kh. Ravilov, Kamil S. Khaertynov

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Improving the early diagnosis of tuberculosis and solving a number of problems associated with the differential diagnosis of Mycobacterium bovis infection, nonspecific tuberculin reactions caused by sensitization of the body by non-tuberculosis mycobacteria, is urgent. The filtrates and extracts of M. bovis cell surface components are promising antigens with diagnostic potential. The purpose of this study was to isolate and characterize antigenic proteins and determine the dominant M. bovis antigens recognized by the humoral immune system. The mycobacterial cells were homogenized on FastPrep-24. Gel-filtration chromatography was used to fractionate the lysates of cell surface component extracts and proteins isolated from M. bovis culture supernatant. The separated fractions were analyzed using two-dimensional gel electrophoresis followed by determination of antigen serological activity using immunoblot with specific hyperimmune rabbit blood serum. As a result of electrophoretic separation of components by molecular weight, 23 antigen fractions were obtained. Analysis of densitograms showed that the fractions contained two zones of antigens with pronounced serological activity, corresponding to molecular weights of 28 and 21 kDa. The high serological activity of the 28 kDa antigen was established by immunoblot using hyperimmune blood sera. Separated and characterized by M. bovis specific antigen with a molecular weight of 28 kDa was added to the collection of specific marker antigens for M. bovis.

Keywords: antigen, gel-filtration chromatography, immunoblot, Mycobacterium bovis

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Authors: Nahla Elazab, Mohamed Aboudina, Ghada Ibrahim, Hossam Fahmy, Ahmed Khalil

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This paper presents the developed memristor based demodulators for eight circular Quadrature Amplitude Modulation (QAM) and Binary Frequency Shift Keying (BFSK) operating at relatively high frequency. In our implementations, the experimental-based ‘nonlinear’ dopant drift model is adopted along with the proposed circuits providing incorporation of all known non-idealities of practically realized memristor and gaining high operation frequency. The suggested designs leverage the distinctive characteristics of the memristor device, definitely, its changeable average memristance versus the frequency, phase and amplitude of the periodic excitation input. The proposed demodulators feature small integration area, low power consumption, and easy implementation. Moreover, the proposed QAM demodulator precludes the requirement for the carrier recovery circuits. In doing so, the designs were validated by transient simulations using the nonlinear dopant drift memristor model. The simulations results show high agreement with the theory presented.

Keywords: BFSK, demodulator, high frequency memristor applications, memristor based analog circuits, nonlinear dopant drift model, QAM

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Authors: Kishor T. Zingre, Seshadhri Srinivasan

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Energy consumption by the building sector is increasing at an alarming rate throughout the world and leading to more building-related CO₂ emissions into the environment. In buildings, the main contributors to energy consumption are heating, ventilation, and air-conditioning (HVAC) systems, lighting, and electrical appliances. It is hypothesised that the energy efficiency in buildings can be achieved by implementing sustainable technologies such as i) enhancing the thermal resistance of fabric materials for reducing heat gain (in hotter climates) and heat loss (in colder climates), ii) enhancing daylight and lighting system, iii) HVAC system and iv) occupant localization. Energy performance of various sustainable technologies is highly dependent on climatic conditions. This paper investigated the use of machine learning techniques for accurate prediction of air-conditioning energy in seasonal climates. The data required to train the machine learning techniques is obtained using the computational simulations performed on a 3-story commercial building using EnergyPlus program plugged-in with OpenStudio and Google SketchUp. The EnergyPlus model was calibrated against experimental measurements of surface temperatures and heat flux prior to employing for the simulations. It has been observed from the simulations that the performance of sustainable fabric materials (for walls, roof, and windows) such as phase change materials, insulation, cool roof, etc. vary with the climate conditions. Various renewable technologies were also used for the building flat roofs in various climates to investigate the potential for electricity generation. It has been observed that the proposed technique overcomes the shortcomings of existing approaches, such as local linearization or over-simplifying assumptions. In addition, the proposed method can be used for real-time estimation of building air-conditioning energy.

Keywords: building energy efficiency, energyplus, machine learning techniques, seasonal climates

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Authors: Jaber H. Almutairi, Hosny Z. Abou-Ziyan, Issa F. Almesri, Mosab A. Alrahmani

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The present work investigates the behavior of fluid flow inside tunnel kilns using 3D-CFD (Computational Fluid Dynamics) simulations. The CFD simulations are carried out with the FLUENT software and validated against experimental results on fluid flow and heat transfer in tunnel kilns. A grid dependency study is conducted in the current work to improve the accuracy of the results. Three turbulence models k–ω, standard k–ε, and RNG k–ε are tested where k–ω model gives the best results in comparison with the experiment. The numerical results reveal an intriguing phenomenon where a long flow separation zone behind the setting is observed under different geometric and operation conditions. It was found that the uniformity of flow distribution can be substantially improved by rearranging the geometrical parameters of brick setting relative to kiln/setting. This improvement of flow distribution plays a critical role to enhance the quality and quantity of the production. It can be concluded that a better design and operation of tunnel kilns in terms of productivity and energy consumption can be obtained by taking into consideration the flow uniformity inside the tunnel kilns using CFD modelling.

Keywords: tunnel kilns, flow separation, flow uniformity, computational fluid dynamics

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Authors: Kamal Hammad, Alexey Fedorenko, Ivan Sergeichev

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This study uses analytical modeling, experimental testing, and explicit numerical simulations to evaluate failure and spall damage in Carbon Fiber-Reinforced Polymer (CFRP) composite confinement vessels. It investigates the response of composite materials to explosive loading dynamic impact, revealing varied failure modes. Hashin damage was used to model inplane failure, while the Virtual Crack Closure Technique (VCCT) modeled inter-laminar damage. Results show moderate agreement between simulations and experiments regarding free surface velocity and failure stresses, with discrepancies due to wire alignment imperfections and wave reverberations in the experimental test. The findings can improve design and risk-reduction strategies in high-risk scenarios, leading to enhanced safety and economic efficiency in material assessment and structural design processes.

Keywords: explicit, numerical, spall, damage, CFRP, composite, vessels, explosive, dynamic, impact, Hashin, VCCT

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Authors: Tanja Kreitenweis

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Lifelong learning is increasingly seen as essential for coping with the rapidly changing work environment. To this end, serious games can provide convenient and straightforward access to complex knowledge for all age groups. However, learning achievements depend largely on a learner’s non-cognitive skill disposition (e.g., motivation, self-belief, playfulness, and openness). With the aim of combining the fields of serious games and non-cognitive skills, this research focuses in particular on the use of a business simulation, which conveys change management insights. Business simulations are a subset of serious games and are perceived as a non-traditional learning method. The presented objectives of this work are versatile: (1) developing a scale, which measures learners’ knowledge and skills level before and after a business simulation was played, (2) investigating the influence of non-cognitive skills on learning in this business simulation environment and (3) exploring the moderating role of team preference in this type of learning setting. First, expert interviews have been conducted to develop an appropriate measure for learners’ skills and knowledge assessment. A pretest-posttest experimental design with German management students was implemented to approach the remaining objectives. By using the newly developed, reliable measure, it was found that students’ skills and knowledge state were higher after the simulation had been played, compared to before. A hierarchical regression analysis revealed two positive predictors for this outcome: motivation and self-esteem. Unexpectedly, playfulness had a negative impact. Team preference strengthened the link between grit and playfulness, respectively, and learners’ skills and knowledge state after completing the business simulation. Overall, the data underlined the potential of business simulations to improve learners’ skills and knowledge state. In addition, motivational factors were found as predictors for benefitting most from the applied business simulation. Recommendations are provided for how pedagogues can use these findings.

Keywords: business simulations, change management, (experiential) learning, non-cognitive skills, serious games

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Authors: Md. Fazlul Karim, Ashik Sharfaraz, Aysha Ferdoushi

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Background: Computational medicinal chemistry approaches are used for designing and identifying new drug-like molecules, predicting properties and pharmacological activities, and optimizing lead compounds in drug development. SIRT7, a nicotinamide adenine dinucleotide (NAD+)-dependent deacylase which regulates aging, is an emerging target for cancer therapy with mounting evidence that SIRT7 downregulation plays important roles in reversing cancer phenotypes and suppressing tumor growth. Activation or altered expression of SIRT7 is associated with the progression and invasion of various cancers, including liver, breast, gastric, prostate, and non-small cell lung cancer. Objectives: The goal of this work was to identify potent and selective bioactive candidate inhibitors of SIRT7 by in silico screening of small molecule compounds obtained from Nigella sativa (N. sativa). Methods: SIRT7 structure was retrieved from The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), and its active site was identified using CASTp and metaPocket. Molecular docking simulation was performed with PyRx 0.8 virtual screening software. Drug-likeness properties were tested using SwissADME and pkCSM. In silico toxicity was evaluated by Osiris Property Explorer. Bioactivity was predicted by Molinspiration software. Antitumor activity was screened for Prediction of Activity Spectra for Substances (PASS) using Way2Drug web server. Molecular dynamics (MD) simulation was carried out by Desmond v3.6 package. Results: A total of 159 bioactive compounds from the N. Sativa were screened against the SIRT7 enzyme. Five bioactive compounds: chrysin (CID:5281607), pinocembrin (CID:68071), nigellidine (CID:136828302), nigellicine (CID:11402337), and epicatechin (CID:72276) were identified as potent SIRT7 anti-cancer candidates after docking score evaluation and applying Lipinski's Rule of Five. Finally, MD simulation identified Chrysin as the top SIRT7 anti-cancer candidate molecule. Conclusion: Chrysin, which shows a potential inhibitory effect against SIRT7, can act as a possible anti-cancer drug candidate. This inhibitor warrants further evaluation to check its pharmacokinetics and pharmacodynamics properties both in vitro and in vivo.

Keywords: SIRT7, antitumor, molecular docking, molecular dynamics simulation

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Authors: Chul Lee, Seoae Cho, Erich D. Jarvis, Heebal Kim

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Vocal learning, the ability to imitate vocalizations based on auditory experience, is a homoplastic character state observed in different independent lineages of animals such as songbirds, parrots, hummingbirds and human. It has now become possible to perform genome-wide molecular analyses across vocal learners and vocal non-learners with the recent expansion of avian genome data. It was analyzed the whole genomes of human and 48 avian species including those belonging to the three avian vocal learning lineages, to determine if behavior and neural convergence are associated with molecular convergence in divergent species of vocal learners. Analyses of 8295 orthologous genes across bird species revealed 141 genes with amino acid substitutions specific to vocal learners. Out of these, 25 genes have vocal learner specific genetic homoplasies, and their functions were enriched for learning. Several sites in these genes are estimated under convergent evolution and positive selection. A potential role for a subset of these genes in vocal learning was supported by associations with gene expression profiles in vocal learning brain regions of songbirds and human disease that cause language dysfunctions. The key candidate gene with multiple independent lines of the evidences specific to vocal learners was DRD5. Our findings suggest cAMP-based learning pathway in avian vocal learners, indicating molecular homoplastic changes associated with a complex behavioral trait, vocal learning.

Keywords: amino acid substitutions, convergent evolution, positive selection, vocal learning

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Authors: Siti Rafeah Md Rafei, Karen Wang Yanping, Park Mi Kyoung

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Tissue samples are precious supply for molecular studies or disease identification diagnosed using molecular assays, namely real-time PCR (qPCR). It is critical to establish the most favorable nucleic acid extraction that gives the PCR-amplifiable genomic DNA. Furthermore, automated nucleic acid extraction is an appealing alternative to labor-intensive manual methods. Operational complexity, defined as the number of steps required to obtain an extracted sample, is one of the criteria in the comparison. Here we are comparing the One BioMed’s automated X8 platform with the commercially available manual-operated kits from QIAGEN Mini Kit and Roche. We extracted DNA from rat fresh-frozen tissue (from different type of organs) in the matrices. After tissue pre-treatment, it is added to the One BioMed’s X8 pre-filled cartridge, and the QIAGEN QIAmp column respectively. We found that the results after subjecting the eluates to the Real Time PCR using BIORAD CFX are comparable.

Keywords: DNA extraction, frozen tissue, PCR, qPCR, rat

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Authors: Dmitry V. Fomichev, Vladimir I. Solonin

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In this paper, experimental and numerical study of hydrodynamic characteristics of the air coolant flow in the test wire-wrapped assembly is presented. The test assembly has 37 rods, which are similar to the real fuel pins of the BREST-OD-300 fuel assemblies geometrically. Air open loop test facility installed at the “Nuclear Power Plants and Installations” department of BMSTU was used to obtain the experimental data. The obtaining altitudinal distribution of static pressure in the near-wall test assembly as well as velocity and temperature distribution of coolant flow in the test sections can give us some new knowledge about the mechanism of formation of the turbulence flow structure in the wire wrapped fuel assemblies. Numerical simulations of the turbulence flow has been accomplished using ANSYS Fluent 14.5. Different non-local turbulence models have been considered, such as standard and RNG k-e models and k-w SST model. Results of numerical simulations of the flow based on the considered turbulence models give the best agreement with the experimental data and help us to carry out strong analysis of flow characteristics.

Keywords: wire-spaces fuel assembly, turbulent flow structure, computation fluid dynamics

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Authors: Nina Philipova

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The influence of the geometric parameters of trapezoidal labyrinth channel on the pressure losses along the labyrinth length is investigated in this work. The impact of the dentate height is studied at fixed values of the dentate angle and the dentate spacing. The objective of the work presented in this paper is to derive a mathematical model of the pressure losses along the labyrinth length depending on the dentate height. The numerical simulations of the water flow movement are performed by using Commercial codes ANSYS GAMBIT and FLUENT. Dripper inlet pressure is set up to be 1 bar. As a result, the mathematical model of the pressure losses is determined as a second-order polynomial by means Commercial code STATISTIKA. Bi-objective optimization is performed by using the mean algebraic function of utility. The optimum value of the dentate height is defined at fixed values of the dentate angle and the dentate spacing. The derived model of the pressure losses and the optimum value of the dentate height are used as a basis for a more successful emitter design.

Keywords: drip irrigation, labyrinth channel hydrodynamics, numerical simulations, Reynolds stress model

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Authors: Samira B. R. Prado, Paulo R. Melfi, Beatriz T. Minguzzi, João P. Fabi

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Fruit softening is the main change that occurs during papaya (Carica papaya L.) ripening. It is characterized by the depolymerization of cell wall polysaccharides, especially the pectic fractions, which causes cell wall disassembling. However, it is uncertain how the modification of the two main pectin polysaccharides fractions (water-soluble – WSF, and oxalate-soluble fractions - OSF) accounts for fruit softening. The aim of this work was to correlate molecular weight changes of WSF and OSF with the gene expression of pectin-solubilizing enzymes (pectinases) during papaya ripening. Papaya fruits obtained from a producer were harvest and storage under specific conditions. The fruits were divided in five groups according to days after harvesting. Cell walls from all groups of papaya pulp were isolated and fractionated (WSF and OSF). Expression profiles of pectinase genes were achieved according to the MIQE guidelines (Minimum Information for publication of Quantitative real-time PCR Experiments). The results showed an increased yield and a decreased molecular weight throughout ripening for WSF and OSF. Gene expression data support that papaya softening is achieved by polygalacturonases (PGs) up-regulation, in which their actions might have been facilitated by the constant action of pectinesterases (PMEs). Moreover, BGAL1 gene was up-regulated during ripening with a simultaneous galactose release, suggesting that galactosidases (GALs) could also account for pulp softening. The data suggest that a solubilization of galacturonans and a depolymerization of cell wall components were caused mainly by the action of PGs and GALs.

Keywords: carica papaya, fruit ripening, galactosidases, plant cell wall, polygalacturonases

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Authors: José Davi Oliveira De Moura, Chou Sin Chan

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In this study, the effect of convective momentum transport (CMT) on the life of cyclone systems and their organization is analyzed. A case of strong precipitation, in the southeast of Brazil, was simulated using Eta model with two kinds of convective parameterization: Kain-Fritsch without CMT and Kain-fritsch with CMT. Reanalysis data from CFSR were used to compare Eta model simulations. The Wind, mean sea level pressure, rain and temperature are included in analysis. The rain was evaluated by Equitable Threat Score (ETS) and Bias Index; the simulations were compared among themselves to detect the influence of CMT displacement on the systems. The result shows that CMT process decreases the intensity of meso cyclones (higher pressure values on nuclei) and change the positions and production of rain. The decrease of intensity in meso cyclones should be caused by the dissolution of momentum from lower levels from up levels. The rain production and rain distribution were altered because the displacement of the larger systems scales was changed. In addition, the inclusion of CMT process is very important to improve the simulation of life time of meteorological systems.

Keywords: convection, Kain-Fritsch, momentum, parameterization

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Authors: Emad A. Mohammed

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Utilizing the capabilities of Data Mining and Artificial Intelligence in the prediction of the minimum miscibility pressure (MMP) required for multi-contact miscible (MCM) displacement of reservoir petroleum by hydrocarbon gas flooding using Fuzzy Logic models and Artificial Neural Network models will help a lot in giving accurate results. The factors affecting the (MMP) as it is proved from the literature and from the dataset are as follows: XC2-6: Intermediate composition in the oil-containing C2-6, CO2 and H2S, in mole %, XC1: Amount of methane in the oil (%),T: Temperature (°C), MwC7+: Molecular weight of C7+ (g/mol), YC2+: Mole percent of C2+ composition in injected gas (%), MwC2+: Molecular weight of C2+ in injected gas. Fuzzy Logic and Neural Networks have been used widely in prediction and classification, with relatively high accuracy, in different fields of study. It is well known that the Fuzzy Inference system can handle uncertainty within the inputs such as in our case. The results of this work showed that our proposed models perform better with higher performance indices than other emprical correlations.

Keywords: MMP, gas flooding, artificial intelligence, correlation

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Authors: Teng Li, Kamran Mohseni

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This paper presents an inviscid regularization technique for the incompressible two-phase flow simulations. This technique is known as observable method due to the understanding of observability that any feature smaller than the actual resolution (physical or numerical), i.e., the size of wire in hotwire anemometry or the grid size in numerical simulations, is not able to be captured or observed. Differ from most regularization techniques that applies on the numerical discretization, the observable method is employed at PDE level during the derivation of equations. Difficulties in the simulation and analysis of realistic fluid flow often result from discontinuities (or near-discontinuities) in the calculated fluid properties or state. Accurately capturing these discontinuities is especially crucial when simulating flows involving shocks, turbulence or sharp interfaces. Over the past several years, the properties of this new regularization technique have been investigated that show the capability of simultaneously regularizing shocks and turbulence. The observable method has been performed on the direct numerical simulations of shocks and turbulence where the discontinuities are successfully regularized and flow features are well captured. In the current paper, the observable method will be extended to two-phase interfacial flows. Multiphase flows share the similar features with shocks and turbulence that is the nonlinear irregularity caused by the nonlinear terms in the governing equations, namely, Euler equations. In the direct numerical simulation of two-phase flows, the interfaces are usually treated as the smooth transition of the properties from one fluid phase to the other. However, in high Reynolds number or low viscosity flows, the nonlinear terms will generate smaller scales which will sharpen the interface, causing discontinuities. Many numerical methods for two-phase flows fail at high Reynolds number case while some others depend on the numerical diffusion from spatial discretization. The observable method regularizes this nonlinear mechanism by filtering the convective terms and this process is inviscid. The filtering effect is controlled by an observable scale which is usually about a grid length. Single rising bubble and Rayleigh-Taylor instability are studied, in particular, to examine the performance of the observable method. A pseudo-spectral method is used for spatial discretization which will not introduce numerical diffusion, and a Total Variation Diminishing (TVD) Runge Kutta method is applied for time integration. The observable incompressible Euler equations are solved for these two problems. In rising bubble problem, the terminal velocity and shape of the bubble are particularly examined and compared with experiments and other numerical results. In the Rayleigh-Taylor instability, the shape of the interface are studied for different observable scale and the spike and bubble velocities, as well as positions (under a proper observable scale), are compared with other simulation results. The results indicate that this regularization technique can potentially regularize the sharp interface in the two-phase flow simulations

Keywords: Euler equations, incompressible flow simulation, inviscid regularization technique, two-phase flow

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Authors: Qi Wu, Dian-Yong Chen, Feng-Kun Guo, Gang Li

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In the past decade, a growing number of new hadron states have been observed, which are dubbed as XYZ states in the heavy quarkonium mass regions. In this work, we present our study on the production of some new hadron states. In particular, we investigate the processes Υ(5S,6S)→ Zb (10610)/Zb (10650)π, Bc→ Zc (3900)/Zc (4020)π and Λb→ Pc (4312)/Pc (4440)/Pc (4457)K. (1) For the production of Zb (10610)/Zb (10650) from Υ(5S,6S) decay, two types of bottom-meson loops were discussed within a nonrelativistic effective field theory. We found that the loop contributions with all intermediate states being the S-wave ground state bottom mesons are negligible, while the loops with one bottom meson being the broad B₀* or B₁' resonance could provide the dominant contributions to the Υ(5S)→ Zb⁽'⁾ π. (2) For the production of Zc (3900)/Zc (4020) from Bc decay, the branching ratios of Bc⁺→ Z (3900)⁺ π⁰ and Bc⁺→ Zc (4020)⁺ π⁰ are estimated to be of order of 10⁽⁻⁴⁾ and 10⁽⁻⁷⁾ in an effective Lagrangian approach. The large production rate of Zc (3900) could provide an important source of the production of Zc (3900) from the semi-exclusive decay of b-flavored hadrons reported by D0 Collaboration, which can be tested by the exclusive measurements in LHCb. (3) For the production of Pc (4312), Pc (4440) and Pc (4457) from Λb decay, the ratio of the branching fraction of Λb→ Pc K was predicted in a molecular scenario by using an effective Lagrangian approach, which is weakly dependent on our model parameter. We also find the ratios of the productions of the branching fractions of Λb→ Pc K and Pc→ J/ψ p can be well interpreted in the molecular scenario. Moreover, the estimated branching fractions of Λb→ Pc K are of order 10⁽⁻⁶⁾, which could be tested by further measurements in LHCb Collaboration.

Keywords: effective Lagrangian approach, hadron loops, molecular states, new hadron states

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Authors: Katherine Madero Valencia, Carlos Jaramillo, Elida Dueñas, Carlos Torres, María Del Pilar Delgado

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Asthma, described as a chronic inflammatory condition of the airways, courses accompanied by episodes known as exacerbations, characterized by a worsening of symptoms. Among the triggers, some allergen-irritative and infectious agents are found, including Chlamydophila pneumoniae which seems to play an increasingly important role. In this paper a PCR was used to detect C. pneumoniae in order to estimate the frequency of infections caused by this agent in pediatric patients with asthma exacerbations. C. pneumoniae distribution throughout the study period was also evaluated. 175 nasopharyngeal aspirates from children with asthma exacerbations were analyzed by PCR and sequencing. A global prevalence of C. pneumoniae of 53.71% was obtained. This study highlights a high circulation of C. pneumoniae during the study period, in children of all ages and especially in children under 5 years old. Molecular tests applied permit a rapid detection and improved our knowledge about these infections in children with asthma.

Keywords: Chlamydophila pneumoniae, detection, molecular techniques, pediatric asthma

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Authors: Asima Shah, F. A. Masoodi, Adil Gani, Bilal Ahmad Ashwar

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The present study was designed to evaluate the effect of γ-rays on the antioxidant and antiproliferative potential of β-glucan isolated from oats. The β-glucan was irradiated with 0, 2, 6, and 10 kGy by gamma ray. The samples were characterized by FT-IR, GPC, and quantitative estimation by Megazyme β-glucan assay kit. The average molecular weight of non-irradiated β-glucan was 199 kDa that decreased to 70 kDa at 10 kGy. Both FT-IR spectrum and chemical analysis revealed that the extracted β-glucan was pure having minor impurities. Antioxidant activity was evaluated by DPPH, lipid peroxidation, reducing power, metal chelating ability and oxidative DNA damage assays. Results revealed that the antioxidant activity of β-glucan increased with the increase in irradiation dose. Irradiated β-glucan also exhibited dose dependent cancer cell growth inhibition with irradiation doses. The study revealed that low molecular weight β-glucan with enhanced antioxidant and antiproliferative activities can be produced by a simple irradiation method.

Keywords: γ-irradiation, antioxidant activity, antiproliferative activity, β-glucan, oats

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Authors: Alia Alghosoun, Michael Herty, Mohammed Seaid

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We present a new class of numerical techniques to solve shallow water flows over dry areas including run-up. Many recent investigations on wave run-up in coastal areas are based on the well-known shallow water equations. Numerical simulations have also performed to understand the effects of several factors on tsunami wave impact and run-up in the presence of coastal areas. In all these simulations the shallow water equations are solved in entire domain including dry areas and special treatments are used for numerical solution of singularities at these dry regions. In the present study we propose a new method to deal with these difficulties by reformulating the shallow water equations into a new system to be solved only in the wetted domain. The system is obtained by a change in the coordinates leading to a set of equations in a moving domain for which the wet/dry interface is the reconstructed using the wave speed. To solve the new system we present a finite volume method of Lax-Friedrich type along with a modified method of characteristics. The method is well-balanced and accurately resolves dam-break problems over dry areas.

Keywords: dam-break problems, finite volume method, run-up waves, shallow water flows, wet/dry interfaces

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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: Virendra Nath, Vipin Kumar

Abstract:

Background: TypeII Diabetes mellitus is a foremost health problem worldwide, predisposing to increased mortality and morbidity. Undesirable effects of the current medications have prompted the researcher to develop more potential drug(s) against the disease. The peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptors family and take part in a vital role in the regulation of metabolic equilibrium. They can induce or repress genes associated with adipogenesis, lipid, and glucose metabolism. Aims: Investigation of PPARα/γ agonistic hits were screened by hierarchical virtual screening followed by molecular dynamics simulation and knowledge-based structure-activity relation (SAR) analysis using approved PPAR α/γ dual agonist. Methods: The PPARα/γ agonistic activity of compounds was searched by using Maestro through structure-based virtual screening and molecular dynamics (MD) simulation application. Virtual screening of nuclear-receptor ligands was done, and the binding modes with protein-ligand interactions of newer entity(s) were investigated. Further, binding energy prediction, Stability studies using molecular dynamics (MD) simulation of PPARα and γ complex was performed with the most promising hit along with the structural comparative analysis of approved PPARα/γ agonists with screened hit was done for knowledge-based SAR. Results and Discussion: The silicone chip-based approach recognized the most capable nine hits and had better predictive binding energy as compared to the reference drug compound (Tesaglitazar). In this study, the key amino acid residues of binding pockets of both targets PPARα/γ were acknowledged as essential and were found to be associated in the key interactions with the most potential dual hit (ChemDiv-3269-0443). Stability studies using molecular dynamics (MD) simulation of PPARα and γ complex was performed with the most promising hit and found root mean square deviation (RMSD) stabile around 2Å and 2.1Å, respectively. Frequency distribution data also revealed that the key residues of both proteins showed maximum contacts with a potent hit during the MD simulation of 20 nanoseconds (ns). The knowledge-based SAR studies of PPARα/γ agonists were studied using 2D structures of approved drugs like aleglitazar, tesaglitazar, etc. for successful designing and synthesis of compounds PPARγ agonistic candidates with anti-hyperlipidimic potential.

Keywords: computational, diabetes, PPAR, simulation

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Authors: Moulay Driss Mellaoui, Abdallah Imjjad, Rachid Boutiddar, Haydar Mohammad-Salim, Nivedita Acharjee, Hassan Bourzi, Souad El Issami, Khalid Abbiche, Hanane Zejli

Abstract:

We have investigated the underlying molecular processes involved in the [3+2] cycloaddition (32CA) reactions between N-methyl-C-(2-furyl) nitrone and three acetylene derivatives: 4b, 5b, and 6b. For this investigation, we utilized molecular electron density theory (MEDT) and density functional theory (DFT) methods at the B3LYP-D3/6 31G (d) computational level. These 32CA reactions, which exhibit a zwitterionic (zw-type) nature, proceed through a one-step mechanism with activation enthalpies ranging from 8.80 to 14.37 kcal mol−1 in acetonitrile and ethanol solvents. When the nitrone reacts with phenyl methyl propiolate (4b), two regioisomeric pathways lead to the formation of two products: P1,5-4b and P1,4-4b. On the other hand, when the nitrone reacts with dimethyl acetylene dicarboxylate (5b) and acetylene dicarboxylic acid (but-2-ynedioic acid) (6b), it results in the formation of a single product. Through topological analysis, we can categorize the nitrone as a zwitterionic three-atom component (TAC). Furthermore, the analysis of conceptual density functional theory (CDFT) indices classifies the 32CA reactions of the nitrone with 4b, 5b, and 6b as forward electron density flux (FEDF) reactions. The study of bond evolution theory (BET) reveals that the formation of new C-C and C-O covalent bonds does not initiate in the transition states, as the intermediate stages of these reactions display pseudoradical centers of the atoms already involved in bonding.

Keywords: 4-isoxazoline, DFT/B3LYP-D3, regioselectivity, cycloaddition reaction, MEDT, ELF

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Authors: Drissi Mokhtaria, Chouaih Abdelkader, Fodil Hamzaoui

Abstract:

Our work is about a comparison of experimental and theoretical results of the electron charge density distribution and the electrostatic potential around the M-Nitrophenol Molecule (m-NPH) kwon for its interesting physical characteristics. The molecular experimental results have been obtained from a high-resolution X-ray diffraction study. Theoretical investigations were performed under the Gaussian program using the Density Functional Theory at B3LYP level of theory at 6-31G*. The multipolar model of Hansen and Coppens was used for the experimental electron charge density distribution around the molecule, while we used the DFT methods for the theoretical calculations. The electron charge density obtained in both methods allowed us to find out the different molecular properties such us the electrostatic potential and the dipole moment which were finally subject to a comparison leading to an outcome of a good matching results obtained in both methods.

Keywords: electron charge density, m-nitrophenol, nonlinear optical compound, electrostatic potential, optimized geometric

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Authors: Daniel Tscharnuter, Eliza Truszkiewicz, Gerald Pinter

Abstract:

High-quality surfaces of plastic parts can be achieved in a very cost-effective manner using in-mold processes, where e.g. scratch resistant or high gloss polymer films are pre-formed and subsequently receive their support structure by injection molding. The pre-forming may be done by high-pressure forming. In this process, a polymer sheet is heated and subsequently formed into the mold by pressurized air. Due to the heat transfer to the cooled mold the polymer temperature drops below its glass transition temperature. This ensures that the deformed microstructure is retained after depressurizing, giving the sheet its final formed shape. The development of a forming process relies heavily on the experience of engineers and trial-and-error procedures. Repeated mold design and testing cycles are however both time- and cost-intensive. It is, therefore, desirable to study the process using reliable computer simulations. Through simulations, the construction of the mold and the effect of various process parameters, e.g. temperature levels, non-uniform heating or timing and magnitude of pressure, on the deformation of the polymer sheet can be analyzed. Detailed knowledge of the deformation is particularly important in the forming of polymer films with integrated electro-optical functions. Care must be taken in the placement of devices, sensors and electrical and optical paths, which are far more sensitive to deformation than the polymers. Reliable numerical prediction of the deformation of the polymer sheets requires sophisticated material models. Polymer films are often either transversely isotropic or orthotropic due to molecular orientations induced during manufacturing. The anisotropic behavior affects the resulting strain field in the deformed film. For example, parts of the same shape but different strain fields may be created by varying the orientation of the film with respect to the mold. The numerical simulation of the high-pressure forming of such films thus requires material models that can capture the nonlinear anisotropic mechanical behavior. There are numerous commercial polymer grades for the engineers to choose from when developing a new part. The effort required for comprehensive material characterization may be prohibitive, especially when several materials are candidates for a specific application. We, therefore, propose a class of models for compressible hyperelasticity, which may be determined from basic experimental data and which can capture key features of the mechanical response. Invariant-based hyperelastic models with a reduced number of invariants are formulated in a semi-numerical way, such that the models are determined from a single uniaxial tensile tests for isotropic materials, or two tensile tests in the principal directions for transversely isotropic or orthotropic materials. The simulation of the high pressure forming of an orthotropic polymer film is finally done using an orthotropic formulation of the hyperelastic model.

Keywords: hyperelastic, anisotropic, polymer film, thermoforming

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Authors: Samir Al-Zobaidi

Abstract:

This study attempts to understand the effect of different UV irradiation methods on the intercalation of LDPE/MMT nanocomposites, and its molecular behavior at certain isothermal crystallization temperature. Three different methods of UV exposure were employed using single composition of LDPE/MMT nanocomposites. All samples were annealed for 5 hours at a crystallization temperature of 100°C. The crystallization temperature was chosen to be at large supercooling temperature to ensure quick and complete crystallization. The raw material of LDPE consisted of two stable monoclinic and orthorhombic phases according to XRD results. The thermal behavior of both phases acted differently when UV exposure method was changed. The monoclinic phase was more dependent on the method used compared to the orthorhombic phase. The intercalation of clay, as well as, the non-isothermal crystallization temperature, has also shown a clear dependency on the type of UV exposure. A third phase that is thermally less stable was also observed. Its respond to UV irradiation was greater since it contains low molecular weight entities which make it more vulnerable to any UV exposure.

Keywords: LDPE/MMt nanocomposites, crystallization, UV irradiation, intercalation

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Authors: K. Frahtia, I. Mihoubi, S. Picot

Abstract:

Leishmaniasis is a group of parasitic disease with a varied clinical expression caused by flagellate protozoa of the Leishmania genus. These diseases are transmitted to humans and animals by the sting of a vector insect, the female sandfly. Among the groups of dipteral disease vectors, Phlebotominae occupy a prime position and play a significant role in human pathology, such as leishmaniasis that affects nearly 350 million people worldwide. The vector control operation launched by health services throughout the country proves to be effective since despite the prevalence of the disease remains high especially in rural areas, leishmaniasis appears to be declining in Algeria. In this context, this study mainly concerns molecular detection of Leishmania from the vector. Furthermore, a molecular diagnosis has also been made on skin samples taken from patients in the region of Constantine, located in the North-East of Algeria. Concerning the vector, 5858 sandflies were captured, including 4360 males and 1498 females. Male specimens were identified based on their morphological. The morphological identification highlighted the presence of the Phlebotomus genus with a prevalence of 93% against 7% represented by the Sergentomyia genus. About the identified species, P. perniciosus is the most abundant with 59.4% of the male identified population followed by P. longicuspis with 24.7% of the workforce. P. perfiliewi is poorly represented by 6.7% of specimens followed by P. papatasi with 2.2% and 1.5% S. dreyfussi. Concerning skin samples, 45/79 (56.96%) collected samples were found positive by real-time PCR. This rate appears to be in sharp decline compared to previous years (alert peak of 30,227 cases in 2005). Concerning the detection of Leishmania from sandflies by RT-PCR, the results show that 3/60 PCR performed genus are positive with melting temperatures corresponding to that of the reference strain (84.1 +/- 0.4 ° C for L. infantum). This proves that the vectors were parasitized. On the other side, identification by RT-PCR species did not give any results. This could be explained by the presence of an insufficient amount of leishmanian DNA in the vector, and therefore support the hypothesis of the regression of leishmaniasis in Constantine.

Keywords: Algeria, molecular diagnostic, phlebotomus, real time PCR

Procedia PDF Downloads 258