Search results for: molecular simulations

Authors: Vemula Amalakrishna, S. Pushpavanam

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Change and motion characterize and persistently reshape the world around us, on scales from molecular to global. The subtle interplay between change (Reaction) and motion (Diffusion) gives rise to an astonishing intricate spatial or temporal pattern. These pattern formation in nature has been intellectually appealing for many scientists since antiquity. Periodic precipitation patterns, also known as Liesegang patterns (LP), are one of the stimulating examples of such self-assembling reaction-diffusion (RD) systems. LP formation has a great potential in micro and nanotechnology. So far, the research on LPs has been concentrated mostly on how these patterns are forming, retrieving information to build a universal mathematical model for them. Researchers have developed various theoretical models to comprehensively construct the geometrical diversity of LPs. To the best of our knowledge, simulation studies of LPs assume an arbitrary value of RD parameters to explain experimental observation qualitatively. In this work, existing models were studied to understand the mechanism behind this phenomenon and challenges pertaining to models were understood and explained. These models are not computationally effective due to the presence of discontinuous precipitation rate in RD equations. To overcome the computational challenges, smoothened Heaviside functions have been introduced, which downsizes the computational time as well. Experiments were performed using a conventional LP system (AgNO₃-K₂Cr₂O₇) to understand the effects of different gels and temperatures on formed LPs. The model is extended for real parameter values to compare the simulated results with experimental data for both 1-D (Cartesian test tubes) and 2-D(cylindrical and Petri dish).

Keywords: reaction-diffusion, spatio-temporal patterns, nucleation and growth, supersaturation

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Authors: Reza Talebi

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Wheat (Triticum aestivum) is one of the most important food staples in Iran. Understanding genetic variability among the landrace wheat germplasm is important for breeding. Landraces endemic to Iran are a genetic resource that is distinct from other wheat germplasm. In this study, 60 Iranian landrace wheat accessions were characterized AFLP and ISSR markers. Twelve AFLP primer pairs detected 128 polymorphic bands among the sixty genotypes. The mean polymorphism rate based on AFLP data was 31%; however, a wide polymorphism range among primer pairs was observed (22–40%). Polymorphic information content (PIC value) calculated to assess the informativeness of each marker ranged from 0.28 to 0.4, with a mean of 0.37. According to AFLP molecular data, cluster analysis grouped the genotypes in five distinct clusters. .ISSR markers generated 68 bands (average of 6 bands per primer), which 31 were polymorphic (45%) across the 60 wheat genotypes. Polymorphism information content (PIC) value for ISSR markers was calculated in the range of 0.14 to 0.48 with an average of 0.33. Based on data achieved by ISSR-PCR, cluster analysis grouped the genotypes in three distinct clusters. Both AFLP and ISSR markers able to showed that high level of genetic diversity in Iranian landrace wheat accessions has maintained a relatively constant level of genetic diversity during last years.

Keywords: wheat, genetic diversity, AFLP, ISSR

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Authors: Wei Zhao, Yuxuan Yao, Hao Chen

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In order to find out the mechanical properties and failure behavior of lithium-ion batteries, drop hammer impact experiments and finite element simulations are carried out on batteries with different packed angles. Firstly, a drop hammer impact experiment system, which is based on the DHR-1808 drop hammer and oscilloscope, is established, and then a drop test of individual batteries and packed angles of 180 ° and 120 ° are carried out. The image of battery deformation, force-time curve and voltage-time curve are recorded. Secondly, finite element models of individual batteries and two packed angles are established, and the results of the test and simulation are compared. Finally, the mechanical characteristics and failure behavior of lithium-ion battery modules with the packed arrangement of 6 * 6 and packing angles of 180 °, 120 °, 90 ° and 60 ° are analyzed under the same velocity with different battery packing angles, and the same impact energy with different impact velocity and different packing angles. The result shows that the individual battery is destroyed completely in the drop hammer impact test with an initial impact velocity of 3m/s and drop height of 459mm, and the voltage drops to close to 0V when the test ends. The voltage drops to 12V when packed angle of 180°, and 3.6V when packed angle of 120°. It is found that the trend of the force-time curve between simulation and experiment is generally consistent. The difference in maximum peak value is 3.9kN for a packing angle of 180° and 1.3kN for a packing angle of 120°. Under the same impact velocity and impact energy, the strain rate of the battery module with a packing angle of 180° is the lowest, and the maximum stress can reach 26.7MPa with no battery short-circuited. The research under our experiment and simulation shows that the lithium-ion battery module with a packing angle of 180 ° is the least likely to be damaged, which can sustain the maximum stress under the same impact load.

Keywords: battery module, finite element simulation, power battery, packing angle

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Authors: Palak J. Shukla, Atul K. Desai, Chentankumar D. Modhera

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For any country in the world, it has become a priority to protect the critical infrastructure from looming risks of terrorism. In any infrastructure system, the structural elements like lower floors, exterior columns, walls etc. are key elements which are the most susceptible to damage due to blast load. The present study revisits the state of art review of the design and analysis of reinforced concrete panels subjected to blast loading. Various aspects in association with blast loading on structure, i.e. estimation of blast load, experimental works carried out previously, the numerical simulation tools, various material models, etc. are considered for exploring the current practices adopted worldwide. Discussion on various parametric studies to investigate the effect of reinforcement ratios, thickness of slab, different charge weight and standoff distance is also made. It was observed that for the simulation of blast load, CONWEP blast function or equivalent numerical equations were successfully employed by many researchers. The study of literature indicates that the researches were carried out using experimental works and numerical simulation using well known generalized finite element methods, i.e. LS-DYNA, ABAQUS, AUTODYN. Many researchers recommended to use concrete damage model to represent concrete and plastic kinematic material model to represent steel under action of blast loads for most of the numerical simulations. Most of the studies reveal that the increase reinforcement ratio, thickness of slab, standoff distance was resulted in better blast resistance performance of reinforced concrete panel. The study summarizes the various research results and appends the present state of knowledge for the structures exposed to blast loading.

Keywords: blast phenomenon, experimental methods, material models, numerical methods

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Authors: H. M. D. Prabhashana Herath, M. D. Anuradha Wickramasinghe, A. M. C. Kalpani Polgolla, R. A. C. Prasad Ranasinghe, M. Anusha Wijewardane

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The demand for thermal comfort in buildings in hot and humid climates increases progressively. In general, buildings in hot and humid climates spend more than 60% of the total energy cost for the functionality of the air conditioning (AC) system. Hence, it is required to install energy efficient AC systems or integrate energy recovery systems for both new and/or existing AC systems whenever possible, to reduce the energy consumption by the AC system. Integrate a Rotary Thermal Wheel as the energy recovery device of an existing AC system has shown very promising with attractive payback periods of less than 5 years. A rotary thermal wheel can be located in the Air Handling Unit (AHU) of a central AC system to recover the energy available in the return air stream. During this study, a sensitivity analysis was performed using a CFD (Computational Fluid Dynamics) software to determine the optimum design parameters (i.e., rotary speed and parameters of the matrix profile) of a rotary thermal wheel for hot and humid climates. The simulations were performed for a sinusoidal matrix geometry. Variation of sinusoidal matrix parameters, i.e., span length and height, were also analyzed to understand the heat exchanging performance and the induced pressure drop due to the air flow. The results show that the heat exchanging performance increases when increasing the wheel rpm. However, the performance increment rate decreases when increasing the rpm. As a result, it is more advisable to operate the wheel at 10-20 rpm. For the geometry, it was found that the sinusoidal geometries with lesser spans and higher heights have higher heat exchanging capabilities. Considering the sinusoidal profiles analyzed during the study, the geometry with 4mm height and 3mm width shows better performance than the other combinations.

Keywords: air conditioning, computational fluid dynamics, CFD, energy recovery, heat exchangers

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Authors: Rahul Shrivastava, Manish Tripathi, Mohmmad Yasir, Shailesh Singh

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Life style changes and depletion in atmospheric ozone layer in recent decades lead to increase in skin cancer including both melanoma and nonmelanomas. Natural products which were obtained from different plant species have the potential of anti skin cancer activity. In regard of this, present study focuses the potential effect of Glycosmis pentaphylla against anti skin cancer activity. Different Phytochemical constituents which were present in the roots of Glycosmis pentaphylla were identified and were used as ligands after sketching of their structures with the help of ACD/Chemsketch. These ligands are screened for their anticancer potential with proteins which are involved in skin cancer effects with the help of pyrx software. After performing docking studies, results reveal that Noracronycine secondary metabolite of Glycosmis pentaphylla shows strong affinity of their binding energy with Ribosomal S6 Kinase 2 (2QR8) protein. Ribosomal S6 Kinase 2 (2QR8) has an important role in the cell proliferation and transformation mediated through by N-terminal kinase domain and was induced by the tumour promoters such as epidermal growth factor. It also plays a key role in the neoplastic transformation of human skin cells and in skin cancer growth. Noracronycine interact with THR-493 and MET-496 residue of Ribosomal S6 Kinase 2 protein with binding energy ΔG = -8.68 kcal/mole. Thus on the basis of this study we can say that Noracronycine which present in roots of Glycosmis pentaphylla can be used as lead compound against skin cancer.

Keywords: glycosmis pentaphylla, pyrx, ribosomal s6 kinase, skin cancer

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Authors: Harish Aryal

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The safe and reliable operation of nuclear reactors has always been one of the topmost priorities in the nuclear industry. Transient testing allows us to understand the time-dependent behavior of the neutron population in response to either a planned change in the reactor conditions or unplanned circumstances. These unforeseen conditions might occur due to sudden reactivity insertions, feedback, power excursions, instabilities, and accidents. To study such behavior, we need transient testing, which is like car crash testing, to estimate the durability and strength of a car design. In nuclear designs, such transient testing can simulate a wide range of accidents due to sudden reactivity insertions and helps to study the feasibility and integrity of the fuel to be used in certain reactor types. This testing involves a high neutron flux environment and real-time imaging technology with advanced instrumentation with appropriate accuracy and resolution to study the fuel slumping behavior. With the aid of transient testing and adequate imaging tools, it is possible to test the safety basis for reactor and fuel designs that serves as a gateway in licensing advanced reactors in the future. To that end, it is crucial to fully understand advanced imaging techniques both analytically and via simulations. This paper presents an innovative method of supporting real-time imaging of fuel pins and other structures during transient testing. The major fuel-motion detection device that is studied in this dissertation is the Hodoscope which requires collimators. This paper provides 1) an MCNP model and simulation of a Transient Reactor Test (TREAT) core with a central fuel element replaced by a slotted fuel element that provides an open path between test samples and a hodoscope detector and 2) a choice of good filter to improve image resolution.

Keywords: hodoscope, transient testing, collimators, MCNP, TREAT, hodogram, filters

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Authors: Angelica Salmeron Alcocer, Deifilia Ahuatzi Chacon, Felipe Rodriguez Casasola

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Polycyclic aromatic hydrocarbons (PAHs) are produced naturally (forest fires, volcanic eruptions) and human activity (burning fossil fuels). Concern for PAHs is due to their toxic, mutagenic and carcinogenic effects and so pose a potential risk to human health and ecology. Therefore these are considered the most toxic components of oil, they are highly hydrophobic, making them easily depositable on the floor, air and water. One method of removing PAHs of contaminated soil used surfactants such as Tween 80, which it has been reported as less toxic and also increases the solubility of the PAH compared to other surfactants, fluoranthene is a PAH with molecular formula C16H10, its name derives from the fluorescence which presents to UV light. In this paper, a study of the fluoranthene removal solubilized with Tween 80 in synthetic wastewater using a microbial community (isolated from soil of coffee plantations in the state of Veracruz, Mexico) and Fenton oxidation method was performed. The microbial community was able to use both tween 80 and fluoranthene as carbon sources for growth, when the biological treatment in batch culture was applied, 100% of fluoranthene was mineralized, this only occurred at an initial concentration of 100 ppm, but by increasing the initial concentration of fluoranthene the removal efficiencies decay and degradation time increases due to the accumulation of byproducts more toxic or less biodegradable, however when the Fenton oxidation was previously applied to the biological treatment, it was observed that removal of fluoranthene improved because it is consumed approximately 2.4 times faster.

Keywords: fluoranthene, polycyclic aromatic hydrocarbons, biological treatment, fenton oxidation

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Authors: Amir Sattari, Mac Panah, Naeim Rashidfarokhi

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To enhance the mixing of fluid in a rectangular enclosure with a circular inlet and outlet, an energy-efficient approach is further investigated through computational fluid dynamics (CFD). Particle image velocimetry (PIV) measurements help confirm that the pulsation of the inflow velocity improves the mixing performance inside the enclosure considerably without increasing energy consumption. In this study, multiple CFD simulations with different turbulent models were performed. The results obtained were compared with experimental PIV results. This study investigates small-scale representations of flow patterns in a ventilated rectangular room. The objective is to validate the concept of an energy-efficient ventilation strategy with improved thermal comfort and reduction of stagnant air inside the room. Experimental and simulated results confirm that through pulsation of the inflow velocity, strong secondary vortices are generated downstream of the entrance wall-jet. The pulsatile inflow profile promotes a periodic generation of vortices with stronger eddies despite a relatively low inlet velocity, which leads to a larger boundary layer with increased kinetic energy in the occupied zone. A real-scale study was not conducted; however, it can be concluded that a constant velocity inflow profile can be replaced with a lower pulsated flow rate profile while preserving the mixing efficiency. Among the turbulent CFD models demonstrated in this study, SST-kω is most advantageous, exhibiting a similar global airflow pattern as in the experiments. The detailed near-wall velocity profile is utilized to identify the wall-jet instabilities that consist of mixing and boundary layers. The SAS method was later applied to predict the turbulent parameters in the center of the domain. In both cases, the predictions are in good agreement with the measured results.

Keywords: CFD, PIV, pulsatile inflow, ventilation, wall-jet

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Authors: Nesrine Lenchi, Salima Kebbouche-Gana, Laddada Belaid, Mohamed Lamine Khelfaoui, Mohamed Lamine Gana

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Saline lakes are extreme hypersaline environments that are considered five to ten times saltier than seawater (150 – 300 g L-1 salt concentration). Hypersaline regions differ from each other in terms of salt concentration, chemical composition and geographical location, which determine the nature of inhabitant microorganisms. In order to explore the diversity of moderate and extreme halophiles Bacteria in Chott Tinsilt (East of Algeria), an isolation program was performed. In the first time, water samples were collected from the saltern during pre-salt harvesting phase. Salinity, pH and temperature of the sampling site were determined in situ. Chemical analysis of water sample indicated that Na +and Cl- were the most abundant ions. Isolates were obtained by plating out the samples in complex and synthetic media. In this study, seven halophiles cultures of Bacteria were isolated. Isolates were studied for Gram’s reaction, cell morphology and pigmentation. Enzymatic assays (oxidase, catalase, nitrate reductase and urease), and optimization of growth conditions were done. The results indicated that the salinity optima varied from 50 to 250 g L-1, whereas the optimum of temperature range from 25°C to 35°C. Molecular identification of the isolates was performed by sequencing the 16S rRNA gene. The results showed that these cultured isolates included members belonging to the Halomonas, Staphylococcus, Salinivibrio, Idiomarina, Halobacillus Thalassobacillus and Planococcus genera and what may represent a new bacterial genus.

Keywords: bacteria, Chott, halophilic, 16S rRNA

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Authors: Nidhi S. Chandra, Veena Agrawal, Debprasad Chattopadhyay

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Background: Hepatitis E virus (HEV) is a major cause of acute viral hepatitis in developing countries. It spreads feco orally mainly due to contamination of drinking water by sewage. There is limited data on the genotypic comparison of HEV isolates from sewage water and humans. The aim of this study was to identify genotype and conduct phylogenetic analysis of HEV isolates from sewage water and humans. Materials and Methods: 14 sewage water and 60 serum samples from acute sporadic hepatitis E cases (negative for hepatitis A, B, C) were tested for HEV-RNA by nested polymerase chain reaction (RTnPCR) using primers designed with in RdRp (RNA dependent RNA polymerase) region of open reading frame-1 (ORF-1). Sequencing was done by ABI prism 310. The sequences (343 nucleotides) were compared with each other and were aligned with previously reported HEV sequences obtained from GeneBank, using Clustal W software. A Phylogenetic tree was constructed by using PHYLIP version 3.67 software. Results: HEV-RNA was detected in 49/ 60 (81.67%) serum and 5/14 (35.71%) sewage samples. The sequences obtained from 17 serums and 2 sewage specimens belonged to genotype I with 85% similarity and clustering with previously reported human HEV sequences from India. HEV isolates from human and sewage in North West India are genetically closely related to each other. Conclusion: These finding suggest that sewage acts as reservoir of HEV. Therefore it is important that measures are taken for proper waste disposal and treatment of drinking water to prevent outbreaks and epidemics due to HEV.

Keywords: hepatitis E virus, nested polymerase chain reaction, open reading frame-1, nucleotidies

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Authors: Maninderjeet K. Grewal, Sakshi Bhatnor, Renu Chadha

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The composition of pharmaceutical entities and the molecular interactions can be altered to optimize drug properties such as solubility and bioavailability by the crystal engineering technique. The present work has emphasized on the preparation, characterization, and biopharmaceutical evaluation of co-crystal of BCS Class II anti-osteoarthritis drug, Oxaprozin (OXA) with aspartic acid (ASPA) as co-former. The co-crystals were prepared through the mechanochemical solvent drop grinding method. Characterization of the prepared co-crystal (OXA-ASPA) was done by using analytical tools such as differential scanning calorimetry (DSC), Fourier transform infrared spectroscopy (FT-IR), powder X-ray diffraction (PXRD). DSC thermogram of OXA-ASPA cocrystal showed a single sharp melting endotherm at 235 ºC, which was between the melting peaks of the drug and the counter molecules suggesting the formation of a new phase which is a co-crystal that was further confirmed by using other analytical techniques. FT-IR analysis of OXA-ASPA cocrystal showed a shift in a hydroxyl, carbonyl, and amine peaks as compared to pure drugs indicating all these functional groups are participating in cocrystal formation. The appearance of new peaks in the PXRD pattern of cocrystals in comparison to individual components showed that a new crystalline entity has been formed. The Crystal structure of cocrystal was determined using material studio software (Biovia) from PXRD. The equilibrium solubility study of OXA-ASPA showed improvement in solubility as compared to pure drug. Therefore, it was envisioned to prepare the co-crystal of oxaprozin with a suitable conformer to modulate its physiochemical properties and consequently, the biopharmaceutical parameters.

Keywords: cocrystals, coformer, oxaprozin, solubility

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Authors: Miriam Sosa-Díaz, Faustino Sánchez-Garduño

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In population dynamics the study of both, the abundance and the spatial distribution of the populations in a given habitat, is a fundamental issue a From ecological point of view, the determination of the factors influencing such changes involves important problems. In this paper a mathematical model to describe the temporal dynamic and the spatiotemporal dynamic of the interaction of three populations (pollinators, plants and herbivores) is presented. The study we present is carried out by stages: 1. The temporal dynamics and 2. The spatio-temporal dynamics. In turn, each of these stages is developed by considering three cases which correspond to the dynamics of each type of interaction. For instance, for stage 1, we consider three ODE nonlinear systems describing the pollinator-plant, plant-herbivore and plant-pollinator-herbivore, interactions, respectively. In each of these systems different types of dynamical behaviors are reported. Namely, transcritical and pitchfork bifurcations, existence of a limit cycle, existence of a heteroclinic orbit, etc. For the spatiotemporal dynamics of the two mathematical models a novel factor are introduced. This consists in considering that both, the pollinators and the herbivores, move towards those places of the habitat where the plant population density is high. In mathematical terms, this means that the diffusive part of the pollinators and herbivores equations depend on the plant population density. The analysis of this part is presented by considering pairs of populations, i. e., the pollinator-plant and plant-herbivore interactions and at the end the two mathematical model is presented, these models consist of two coupled nonlinear partial differential equations of reaction-diffusion type. These are defined on a rectangular domain with the homogeneous Neumann boundary conditions. We focused in the role played by the density dependent diffusion term into the coexistence of the populations. For both, the temporal and spatio-temporal dynamics, a several of numerical simulations are included.

Keywords: bifurcation, heteroclinic orbits, steady state, traveling wave

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Authors: Mallikarjunachari Gangapuram

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The design of stimuli-responsive hydrogel nanocomposite thin films is gaining significant attention in these days due to its wide variety of applications. Soft microrobots, drug delivery, biosensors, regenerative medicine, bacterial adhesion, energy storage and wound dressing are few advanced applications in different fields. In this research work, the nanomechanical properties of composite thin films of 20 microns were tuned by applying homogeneous external DC, and AC magnetic fields of magnitudes 0.05 T and 0.1 T. Polyvinyl alcohol (PVA) used as a matrix material and elliptical hematite nanoparticles (ratio of the length of the major axis to the length of the minor axis is 140.59 ± 1.072 nm/52.84 ± 1.072 nm) used as filler materials to prepare the nanocomposite thin films. Both quasi-static nanoindentation, Nano Dynamic Mechanical Analysis (Nano-DMA) tests were performed to characterize the viscoelastic properties of PVA, PVA+Hematite (0.1% wt, 2% wt and 4% wt) nanocomposites. Different properties such as storage modulus, loss modulus, hardness, and Er/H were carefully analyzed. The increase in storage modulus, hardness, Er/H and a decrease in loss modulus were observed with increasing concentration and DC magnetic field followed by AC magnetic field. Contact angle and ATR-FTIR experiments were conducted to understand the molecular mechanisms such as hydrogen bond formation, crosslinking density, and particle-particle interactions. This systematic study is helpful in design and modeling of magnetic responsive hydrogel nanocomposite thin films for biomedical applications.

Keywords: hematite, hydrogel, nanoindentation, nano-DMA

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Authors: Y. V. S. Annapurna, V. V. Lakshmi

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Urinary tract infection (UTI) is one of the most common infectious diseases at the community level with a high rate of morbidity . This is further augmented by increase in the number of resistant and multi resistant strains of bacteria particularly by those producing Extended spectrum of beta lactamases. The present study was aimed at analysis of antibiograms of E.coli and Klebsiella sp causing urinary tract infections. Between November 2011 and April 2013, a total of 1120 urine samples were analyzed,. Antibiotic sensitivity testing was done with 542(48%) isolates of E.coli and 446(39%) of Klebsiella sp using the standard disc diffusion method against eleven commonly used antibiotics .Organisms showed high susceptibility to Amikacin and Netilimicin and low susceptibility to Cephalosporins. MAR index was calculated for the multidrug resistant strains. Maximum MAR index detected among the isolates was 0.9. Phenotypic identification for ESBL production was confirmed by double disk synergy test (DDST) according to CLSI guidelines. Plasmid profile of the isolates was carried out using alkaline hydrolysis method. Agarose-gel electrophoresis showed presence of high-molecular weight plasmid DNA among the ESBL strains. This study emphasizes the importance of indiscriminate use of antibiotics which if discontinued, in turn would prevent further development of bacterial drug resistance. For this, a proper knowledge of susceptibility pattern of uropathogens is necessary before prescribing empirical antibiotic therapy and it should be made mandatory.

Keywords: escherichia coli, extended spectrum of beta lactamase, Klebsiella spp, Uropathogens

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Authors: Nacera Yassa, Abdelmalek Saidoune, Ghania Ouadfel, Hamza Houassine

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The rapid advancement in electrical technologies has underscored the increasing importance of multiphase machines across various industrial sectors. These machines offer significant advantages in terms of efficiency, compactness, and reliability compared to their single-phase counterparts. However, early detection and diagnosis of electrical faults remain critical challenges to ensure the durability and safety of these complex systems. This paper presents an advanced analytical model for multiphase machines, with a particular focus on dual stator asynchronous machines. The primary objective is to develop a robust diagnostic tool capable of effectively detecting and locating electrical faults in these machines, including short circuits, winding faults, and voltage imbalances. The proposed methodology relies on an analytical approach combining electrical machine theory, modeling of magnetic and electrical circuits, and advanced signal analysis techniques. By employing detailed analytical equations, the developed model accurately simulates the behavior of multiphase machines in the presence of electrical faults. The effectiveness of the proposed model is demonstrated through a series of case studies and numerical simulations. In particular, special attention is given to analyzing the dynamic behavior of machines under different types of faults, as well as optimizing diagnostic and recovery strategies. The obtained results pave the way for new advancements in the field of multiphase machine diagnostics, with potential applications in various sectors such as automotive, aerospace, and renewable energies. By providing precise and reliable tools for early fault detection, this research contributes to improving the reliability and durability of complex electrical systems while reducing maintenance and operation costs.

Keywords: faults, diagnosis, modelling, multiphase machine

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Authors: Ogbonnaya O. Iroanya, Samson T. Fakorede, Osamudiamen J. Edosa, Hadiat A. Azeez

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The human mitochondrial DNA (mtDNA) is about 17 kbp circular DNA fragments found within the mitochondria together with smaller fragments of 1200 bp known as the control region. Knowledge of variation within populations has been employed in forensic and molecular anthropology studies. The study was aimed at investigating the polymorphic nature of the two hypervariable segments (HVS) of the mtDNA, i.e., HVS1 and HVS2, and to determine the haplogroup distribution among individuals resident in Lagos, Southwestern Nigeria. Peripheral blood samples were obtained from sixty individuals who are not related maternally, followed by DNA extraction and amplification of the extracted DNA using primers specific for the regions under investigation. DNA amplicons were sequenced, and sequenced data were aligned and compared to the revised Cambridge Reference Sequence (rCRS) GenBank Accession number: NC_012920.1) using BioEdit software. Results obtained showed 61 and 52 polymorphic nucleotide positions for HVS1 and HVS2, respectively. While a total of three indels mutation were recorded for HVS1, there were seven for HVS2. Also, transition mutations predominate nucleotide change observed in the study. Genetic diversity (GD) values for HVS1 and HVS2 were estimated to be 84.21 and 90.4%, respectively, while random match probability was 0.17% for HVS1 and 0.89% for HVS2. The study also revealed mixed haplogroups specific to the African (L1-L3) and the Eurasians (U and H) lineages. New polymorphic sites obtained from the study are promising for human identification purposes.

Keywords: hypervariable region, indels, mitochondrial DNA, polymorphism, random match probability

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Authors: S. Altmeyer, B. Hof, F. Marques, J. M. Lopez

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We present numerical simulations concerning the reversal of spiraling vortices in short highly counter-rotating cylinders. Increasing the differential cylinder rotation results in global flow-inversion is which develops various different and complex flow dynamics of several quasi-periodic solutions that differ in their number of vortex cells in the bulk. The dynamics change from being dominated of the inner cylinder boundary layer with ’passive’ only responding outer one to be dominated by the outer cylinder boundary layer with only responding inner one. Solutions exist on either two or three tori invariant manifolds whereby they appear as symmetric or asymmetric states. We find for either moderate and high inner cylinder rotation speed the quasiperiodic flow to consist of only two vortex cells but differ as the vortices has opposite spiraling direction. These both flows live on 2-tori but differ in number of symmetries. While for the quasi-periodic flow (q^a_2) at lower rotation speed a pair of symmetrically related 2-tori T2 exists the quasi-periodic flow (q^s_2) at higher rotation speeds is symmetric living on a single 2-torus T2. In addition these both flows differ due to their dominant azimuthal m modes. The first is dominated by m=1 whereas for the latter m=3 contribution is largest. The 2-tori states are separated by a further quasi-periodic flow (q^a_3) living on pair of symmetrically related 3-tori T3. This flow offers a ’periodical’ competition between a two and three vortex cell states in the bulk. This flow is also an m=1 solution as for the quasiperiodic flows living on the pair of symmetrically-related 2-tori states. Moreover we find hysteresis resulting in coexisting regions of different quasiperiodic flows q^s_2 and q^a_3 with increasing and decreasing the differential rotation.

Keywords: transition, bifurcation, torus, symmetries

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Authors: Solaine Hachem, Frédéric Bourquin, Dominique Siegert

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The brutal collapse of bridges is mainly due to scour. Indeed, the soil erosion in the riverbed around a pier modifies the embedding conditions of the structure, reduces its overall stiffness and threatens its stability. Hence, finding an efficient technique that allows early scour detection becomes mandatory. Vibration analysis is an indirect method for scour detection that relies on real-time monitoring of the bridge. It tends to indicate the presence of a scour based on its consequences on the stability of the structure and its dynamic response. Most of the research in this field has focused on the dynamic behavior of a single pile and has examined the depth of the scour. In this paper, a bridge is fully modeled with all piles and spans and the scour is represented by a reduction in the foundation's stiffnesses. This work aims to identify the vibration modes sensitive to the rigidity’s loss in the foundations so that their variations can be considered as a scour indicator: the decrease in soil-structure interaction rigidity leads to a decrease in the natural frequencies’ values. By using the first-order perturbation method, the expression of sensitivity, which depends only on the selected vibration modes, is established to determine the deficiency of foundations stiffnesses. The solutions are obtained by using the singular value decomposition method for the regularization of the inverse problem. The propagation of uncertainties is also calculated to verify the efficiency of the inverse problem method. Numerical simulations describing different scenarios of scour are investigated on a simplified model of a real composite steel-concrete bridge located in France. The results of the modal analysis show that the modes corresponding to in-plane and out-of-plane piers vibrations are sensitive to the loss of foundation stiffness. While the deck bending modes are not affected by this damage.

Keywords: bridge’s piers, inverse problems, modal sensitivity, scour detection, vibration analysis

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Authors: Yung-Feng Yen, I-an Jen, Yi-Ming Arthur Chen

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The molecular mimicry between human immunodeficiency virus (HIV) protein and red blood cell (RBC) antigens could induce the production of anti-RBC autoantibodies. However, the association between HIV infection and subsequent development of autoimmune hemolytic anemia (AIHA) remains unclear. This nationwide population-based cohort study aimed to determine the association between incident AIHA and HIV in Taiwan. From 2000–2012, we identified adult people living with HIV/AIDS (PLWHA) from the Taiwan centers for disease control HIV Surveillance System. HIV-infected individuals were defined by positive HIV-1 western blot. Age- and sex-matched controls without HIV infection were selected from the Taiwan National Health Insurance Research Database for comparison. All patients were followed until Dec. 31, 2012, and observed for occurrence of AIHA. Of 171,468 subjects (19,052 PLWHA, 152,416 controls), 30 (0.02%) had incident AIHA during a mean follow-up of 5.45 years, including 23 (0.12%) PLWHA and 7 (0.01%) controls. After adjusting for potential confounders, HIV infection was found to be an independent risk factor of incident AIHA (adjusted hazard ratio [AHR], 20.9; 95% confidence interval [CI], 8.34-52.3). Moreover, PLWHA receiving HAART were more likely to develop AIHA than those not receiving HAART (AHR, 10.8; 95% CI, 2.90-40.1). Additionally, the risk of AIHA was significantly increased in those taking efavirenz (AHR, 3.15; 95% CI, 1.18-8.43) or atazanavir (AHR, 6.58; 95% CI, 1.88-22.9) component of the HAART. In conclusion, HIV infection is an independent risk factor for incident AIHA. Clinicians need to be aware of the higher risk of AIHA in PLWHA.

Keywords: autoimmune disease , hemolytic anemia, HIV, highly active antiretroviral treatment

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Authors: Mohammed N. Al Kindi, Mazin Al Khabouri, Khalsa Al Lamki, Tommasso Pappuci, Giovani Romeo, Nadia Al Wardy

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Hereditary hearing loss is a heterogeneous group of complex disorders with an overall incidence of one in every five hundred newborns presented as syndromic and non-syndromic forms. Cadherin-related 23 (CDH23) is one of the listed deafness causative genes. CDH23 is found to be expressed in the stereocilia of hair cells and the retina photoreceptor cells. Defective CDH23 has been associated mostly with prelingual severe-to-profound sensorineural hearing loss (SNHL) in either syndromic (USH1D) or non-syndromic SNHL (DFNB12). An Omani family diagnosed clinically with severe-profound sensorineural hearing loss was genetically analysed by whole exome sequencing technique. A novel homozygous missense variant, c.A7451C (p.D2484A), in exon 53 of CDH23 was detected. One hundred and thirty control samples were analysed where all were negative for the detected variant. The variant was analysed in silico for pathogenicity verification using several mutation prediction software. The variant proved to be a pathogenic mutation and is reported for the first time in Oman and worldwide. It is concluded that in silico mutation prediction analysis might be used as a useful molecular diagnostics tool benefiting both genetic counseling and mutation verification. The aspartic acid 2484 alanine missense substitution might be the main disease-causing mutation that damages CDH23 function and could be used as a genetic hearing loss marker for this particular Omani family.

Keywords: Cdh23, d2484a, in silico, Oman

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Authors: Reza Miresmaeili, Asghar Heydari Astaraee, Fereshteh Dolati

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In the present study, an analytical model based on dislocation density model was developed to simulate grain refinement in surface mechanical attrition treatment (SMAT). The correlation between SMAT time and development in plastic strain on one hand, and dislocation density evolution, on the other hand, was established to simulate the grain refinement in SMAT. A dislocation density-based constitutive material law was implemented using VUHARD subroutine. A random sequence of shots is taken into consideration for multiple impacts model using Python programming language by utilizing a random function. The simulation technique was to model each impact in a separate run and then transferring the results of each run as initial conditions for the next run (impact). The developed Finite Element (FE) model of multiple impacts describes the coverage evolution in SMAT. Simulations were run to coverage levels as high as 4500%. It is shown that the coverage implemented in the FE model is equal to the experimental coverage. It is depicted that numerical SMAT coverage parameter is adequately conforming to the well-known Avrami model. Comparison between numerical results and experimental measurements for residual stresses and depth of deformation layers confirms the performance of the established FE model for surface engineering evaluations in SMA treatment. X-ray diffraction (XRD) studies of grain refinement, including resultant grain size and dislocation density, were conducted to validate the established model. The full width at half-maximum in XRD profiles can be used to measure the grain size. Numerical results and experimental measurements of grain refinement illustrate good agreement and show the capability of established FE model to predict the gradient microstructure in SMA treatment.

Keywords: dislocation density, grain refinement, severe plastic deformation, simulation, surface mechanical attrition treatment

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Authors: Raeed Alanazi

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Introduction: Nursing students have a crucial role to play in the inhibition of infectious diseases and, therefore, must be trained in infection control and prevention modules prior to entering clinical settings. Simulations have been found to have a positive impact on infection control skills and the use of standard precautions. Aim: The purpose of this study was to use the four sources of self-efficacy in explaining the level of clinical self-efficacy and adherence to infection control practices in Saudi nursing students during simulation practice. Method: A cross-sectional design with convenience sampling was used. This study was conducted in all Saudi nursing schools, with a total number of 197 students participated in this study. Three scales were used simulation self- efficacy Scale (SSES), the four sources of self-efficacy scale (SSES), and Compliance with Standard Precautions Scale (CSPS). Multiple linear regression was used to test the use of the four sources of self-efficacy (SSES) in explaining level of clinical self-efficacy and adherence to infection control in nursing students. Results: The vicarious experience subscale (p =.044) was statistically significant. The regression model indicated that for every one unit increase in vicarious experience (observation and reflection in simulation), the participants’ adherence to infection control increased by .13 units (β =.22, t = 2.03, p =.044). In addition, the regression model indicated that for every one unit increase in education level, the participants’ adherence to infection control increased by 1.82 units (beta=.34= 3.64, p <.001). Also, the mastery experience subscale (p <.001) and vicarious experience subscale (p = .020) were shared significant associations with clinical self-efficacy. Conclusion: The findings of this research support the idea that simulation-based learning can be a valuable teaching-learning method to help nursing students develop clinical competence, which is essential in providing quality and safe nursing care.

Keywords: simulation-based learning, clinical self-efficacy, infection control, nursing students

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Authors: L. C. Ansanelli, P. Alfredini

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The article presents the evaluation of the effectiveness of two groins located at Gonzaguinha and Milionários Beaches, situated on the southeast coast of Brazil. The effectiveness of these coastal defense structures is evaluated in terms of sedimentary dynamics, which is one of the most important environmental processes to be assessed in coastal engineering studies. The applied method is based on the implementation of the Delft3D numerical model system tools. Delft3D-WAVE module was used for waves modelling, Delft3D-FLOW for hydrodynamic modelling and Delft3D-SED for sediment transport modelling. The calibration of the models was carried out in a way that the simulations adequately represent the region studied, evaluating improvements in the model elements with the use of statistical comparisons of similarity between the results and waves, currents and tides data recorded in the study area. Analysis of the maximum wave heights was carried to select the months with higher accumulated energy to implement these conditions in the engineering scenarios. The engineering studies were performed for two scenarios: 1) numerical simulation of the area considering only the two existing groins; 2) conception of breakwaters coupled at the ends of the existing groins, resulting in two “T” shaped structures. The sediment model showed that, for the simulated period, the area is affected by erosive processes and that the existing groins have little effectiveness in defending the coast in question. The implemented T structures showed some effectiveness in protecting the beaches against erosion and provided the recovery of the portion directly covered by it on the Milionários Beach. In order to complement this study, it is suggested the conception of further engineering scenarios that might recover other areas of the studied region.

Keywords: coastal engineering, coastal erosion, Sao Vicente bay, Delft3D, coastal engineering works

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Authors: Nafiseh Noormohammadi, Ahmad Sobhani Najafabadi

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Hypericins (hypericin and pseudohypericin) are natural napthodianthrone derivatives produced by Hypericum perforatum (St. John’s Wort), which have many medicinal properties such as antitumor, antineoplastic, antiviral, and antidepressant activities. Production and accumulation of hypericin in the plant are influenced by both genetic and environmental conditions. Despite the existence of different high-throughput data on the plant, genetic dimensions of hypericin biosynthesis have not yet been completely understood. In this research, 21 high-quality RNA-seq data on different parts of the plant were integrated into metabolic data to reconstruct a coexpression network. Results showed that a cluster of 30 transcripts was correlated with total hypericin. The identified transcripts were divided into three main groups based on their functions, including hypericin biosynthesis genes, transporters, detoxification genes, and transcription factors (TFs). In the biosynthetic group, different isoforms of polyketide synthase (PKSs) and phenolic oxidative coupling proteins (POCPs) were identified. Phylogenetic analysis of protein sequences integrated into gene expression analysis showed that some of the POCPs seem to be very important in the biosynthetic pathway of hypericin. In the TFs group, six TFs were correlated with total hypericin. qPCR analysis of these six TFs confirmed that three of them were highly correlated. The identified genes in this research are a rich resource for further studies on the molecular breeding of H. perforatum in order to obtain varieties with high hypericin production.

Keywords: hypericin, St. John’s Wort, data mining, transcription factors, secondary metabolites

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Authors: Andres Piña, Amy Meléndez, Pablo Cano, Tomas Cahuich

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The purpose of this project is to propose a quick and environmentally friendly alternative to measure the quality of oils used in food industry. There is evidence that repeated and indiscriminate use of oils in food processing cause physicochemical changes with formation of potentially toxic compounds that can affect the health of consumers and cause organoleptic changes. In order to assess the quality of oils, non-destructive optical techniques such as Interferometry offer a rapid alternative to the use of reagents, using only the interaction of light on the oil. Through this project, we used interferograms of samples of oil placed under different heating conditions to establish the changes in their quality. These interferograms were obtained by means of a Mach-Zehnder Interferometer using a beam of light from a HeNe laser of 10mW at 632.8nm. Each interferogram was captured, analyzed and measured full width at half-maximum (FWHM) using the software from Amcap and ImageJ. The total of FWHMs was organized in three groups. It was observed that the average obtained from each of the FWHMs of group A shows a behavior that is almost linear, therefore it is probable that the exposure time is not relevant when the oil is kept under constant temperature. Group B exhibits a slight exponential model when temperature raises between 373 K and 393 K. Results of the t-Student show a probability of 95% (0.05) of the existence of variation in the molecular composition of both samples. Furthermore, we found a correlation between the Iodine Indexes (Physicochemical Analysis) and the Interferograms (Optical Analysis) of group C. Based on these results, this project highlights the importance of the quality of the oils used in food industry and shows how Interferometry can be a useful tool for this purpose.

Keywords: food industry, interferometric, oils, quality control

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Authors: Sabir Khan, Sajjad Hussain, Ademar Wong, Maria Del Pilar Taboada Sotomayor

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The present work aims to develop magnetic molecularly imprinted polymers (MMIPs) for determination of a selected pesticide (ametryne) using high-performance liquid chromatography (HPLC). Computational simulation can assist the choice of the most suitable monomer for the synthesis of polymers. The (MMIPs) were polymerized at the surface of Fe3O4@SiO2 magnetic nanoparticles (MNPs) using 2-vinylpyradine as functional monomer, ethylene-glycol-dimethacrylate (EGDMA) is a cross-linking agent and 2,2-Azobisisobutyronitrile (AIBN) used as radical initiator. Magnetic non-molecularly imprinted polymer (MNIPs) was also prepared under the same conditions without analyte. The MMIPs were characterized by scanning electron microscopy (SEM), Brunauer, Emmett and Teller (BET) and Fourier transform infrared spectroscopy (FTIR). Pseudo first-order and pseudo second order model were applied to study kinetics of adsorption and it was found that adsorption process followed the pseudo-first-order kinetic model. Adsorption equilibrium data was fitted to Freundlich and Langmuir isotherms and the sorption equilibrium process was well described by Langmuir isotherm mode. The selectivity coefficients (α) of MMIPs for ametryne with respect to atrazine, ciprofloxacin and folic acid were 4.28, 12.32 and 14.53 respectively. The spiked recoveries ranged between 91.33 and 106.80% were obtained. The results showed high affinity and selectivity of MMIPs for pesticide ametryne in the food samples.

Keywords: molecularly imprinted polymer, pesticides, magnetic nanoparticles, adsorption

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Authors: Srinivasan Chandrasekaran, Shihas A. Khader

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Motion response of floating structures is of great concern in marine engineering. Nonlinearity is an inherent property of any floating bodies subjected to irregular waves. These floating structures are continuously subjected to environmental loadings from wave, current, wind etc. This can result in undesirable motions of the vessel which may challenge the operability. For a floating body to remain in its position, it should be able to induce a restoring force when displaced. Mooring is provided to enable this restoring force. This paper discuss the hydrodynamic performance and motion characteristics of an 8 point spread mooring system applied to a pipe laying barge operating in the West African sea. The modelling of the barge is done using a computer aided-design (CAD) software RHINOCEROS. Irregular waves are generated using a suitable wave spectrum. Both frequency domain and time domain analysis is done. Numerical simulations based on potential theory are carried out to find the responses and hydrodynamic performance of the barge in both free floating as well as moored conditions. Initially, potential flow frequency domain analysis is done to obtain the Response Amplitude Operator (RAO) which gives an idea about the structural motion in free floating state. RAOs for different wave headings are analyzed. In the following step, a time domain analysis is carried out to obtain the responses of the structure in the moored condition. In this study, wave induced motions are only taken into consideration. Wind and current loads are ruled out and shall be included in future studies. For the current study, 5000 seconds simulation is taken. The results represent wave-induced motion responses, mooring line tensions and identifies critical mooring lines.

Keywords: irregular wave, moored barge, time domain analysis, numerical simulation

Procedia PDF Downloads 239

Authors: Nikolaos Papadimas, Joanna Bennett, Amir Sakhaei, Timothy Dodwell

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Composite modeling of consolidation processes is playing an important role in the process and part design by indicating the formation of possible unwanted prior to expensive experimental iterative trial and development programs. Composite materials in their uncured state display complex constitutive behavior, which has received much academic interest, and this with different models proposed. Errors from modeling and statistical which arise from this fitting will propagate through any simulation in which the material model is used. A general hyperelastic polynomial representation was proposed, which can be readily implemented in various nonlinear finite element packages. In our case, FEniCS was chosen. The coefficients are assumed uncertain, and therefore the distribution of parameters learned using Markov Chain Monte Carlo (MCMC) methods. In engineering, the approach often followed is to select a single set of model parameters, which on average, best fits a set of experiments. There are good statistical reasons why this is not a rigorous approach to take. To overcome these challenges, A hierarchical Bayesian framework was proposed in which population distribution of model parameters is inferred from an ensemble of experiments tests. The resulting sampled distribution of hyperparameters is approximated using Maximum Entropy methods so that the distribution of samples can be readily sampled when embedded within a stochastic finite element simulation. The methodology is validated and demonstrated on a set of consolidation experiments of AS4/8852 with various stacking sequences. The resulting distributions are then applied to stochastic finite element simulations of the consolidation of curved parts, leading to a distribution of possible model outputs. With this, the paper, as far as the authors are aware, represents the first stochastic finite element implementation in composite process modelling.

Keywords: data-driven , material consolidation, stochastic finite elements, surrogate models

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Authors: Bibin Sagaram, Ronith Stanly, S. S. Suneesh

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Due to the dwindling supply of fuel reserves, engineers and designers now focus on fuel efficient designs for the solution of any problem; the transportation industry is not new to this kind of approach. Though the aerodynamic benefits of the dimples on a Golf-ball are known, it has never been scientifically tested on how such a design philosophy can improve the fuel efficiency of a real-life vehicle by imparting better aerodynamic performance. The main purpose of the paper is to establish the aerodynamic benefits of the Golf-ball-Inspired Dimpled Design in improving the fuel efficiency of a Super-mileage vehicle, constructed by Team Go Viridis for ‘Shell Eco Marathon Asia 2015’, and to predict the extent to which the results can be held valid for a road car. The body design was modeled in Autodesk Inventor and the Computational Fluid Dynamics (CFD) simulations were carried out using Ansys Fluent software. The aerodynamic parameters of designs (with and without the Golf-ball-Inspired Dimples) have been studied and the results are experimentally validated against those obtained from wind tunnel tests carried out on a 1:10 scaled-down 3D printed model. Test drives of the Super-mileage vehicle were carried out, under various conditions, to compare the variation in fuel efficiency with and without the Golf-ball-Inspired design. Primary investigations reveal an aerodynamic advantage of 25% for the vehicle with the Golf Ball Inspired Dimpled Design as opposed to the normal design. Initial tests conducted by ‘Mythbusters’ on Discovery Network using a modified road car has shown positive results which has motivated us to conduct such a research work using a custom-built experimental Super-Mileage vehicle. The content of the paper becomes relevant to the present Automotive and Energy industry where improving the fuel efficiency is of the top most priority.

Keywords: aerodynamics, CFD, fuel efficiency, golf ball

Procedia PDF Downloads 319