Search results for: Loop-Mediated Isothermal Amplification (LAMP)

Authors: Muhaned Zaidi, Ian Grout, Abu Khari bin A’ain

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In this paper, a two-stage op-amp design is considered using both Miller and negative Miller compensation techniques. The first op-amp design uses Miller compensation around the second amplification stage, whilst the second op-amp design uses negative Miller compensation around the first stage and Miller compensation around the second amplification stage. The aims of this work were to compare the gain and phase margins obtained using the different compensation techniques and identify the ability to choose either compensation technique based on a particular set of design requirements. The two op-amp designs created are based on the same two-stage rail-to-rail output CMOS op-amp architecture where the first stage of the op-amp consists of differential input and cascode circuits, and the second stage is a class AB amplifier. The op-amps have been designed using a 0.35mm CMOS fabrication process.

Keywords: op-amp, rail-to-rail output, Miller compensation, Negative Miller capacitance

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Authors: Fathul Mubin, Budi E. Nurcahya

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In 2006, a large earthquake ever occurred in the province of Yogyakarta, which caused considerable damage. This is the basis need to investigate the seismic vulnerability index in around of the earthquake zone. This research is called microzonation of earthquake hazard. This research has been conducted at the site and surrounding of Prambanan Temple, includes homes and civil buildings. The reason this research needs to be done because in the event of an earthquake in 2006, there was damage to the temples at Prambanan temple complex and its surroundings. In this research, data collection carried out for 60 minutes using three component seismograph measurements at 165 points with spacing of 1000 meters. The data recorded in time function were analyzed using the spectral ratio method, known as the Horizontal to Vertical Spectral Ratio (HVSR). Results from this analysis are dominant frequency (Fg) and maximum amplification factor (Ag) are used to obtain seismic vulnerability index. The results of research showed the dominant frequency range from 0.5 to 30 Hz and the amplification is in interval from 0.5 to 9. Interval value for seismic vulnerability index is 0.1 to 50. Based on distribution maps of seismic vulnerability index and impact of buildings damage seemed for suitability. For further research, it needs to survey to the east (klaten) and south (Bantul, DIY) to determine a full distribution maps of seismic vulnerability index.

Keywords: amplification factor, dominant frequency, microzonation analysis, seismic vulnerability index

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Authors: Cheng-Yen Lu, Chin-Yuan Hsu

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Ambient temperature reduction (ATR) can extend the lifespan of an annual fish (Nothobranchius rachovii), but the underlying mechanism is unknown. In this study, the expression, concentration, and activity of cellular-degraded molecules were evaluated in the muscle of N. rachovii reared under high (30 °C), moderate (25 °C), and low (20 °C) ambient temperatures by biochemical techniques. The results showed that (i) the activity of the 20S proteasome, the expression of microtubule-associated protein 1 light chain 3-II (LC3-II), the expression of lysosome-associated membrane protein type 2a (Lamp 2a), and lysosome activity increased with ATR; (ii) the expression of the 70 kD heat shock cognate protein (Hsc 70) decreased with ATR; (iii) the expression of the 20S proteasome, the expression of lysosome-associated membrane protein type 1 (Lamp 1), the expression of molecular target of rapamycin (mTOR), the expression of phosphorylated mTOR (p-mTOR), and the p-mTOR/mTOR ratio did not change with ATR. These findings indicated that ATR activated the activity of proteasome, macroautophagy, and chaperone-mediated autophagy. Taken together these data reveal that ATR likely activates cellular degradation activity to extend the lifespan of N. rachovii.

Keywords: ambient temperature reduction, autophagy, degradation activity, lifespan, proteasome

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Authors: P. G. Siddheshwar, T. N. Sakshath

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In the paper we make linear and non-linear stability analyses of Rayleigh-Bénard convection of a Newtonian nanoliquid in a rotating medium (called as Rayleigh-Bénard-Taylor convection). Rigid-rigid isothermal boundaries are considered for investigation. Khanafer-Vafai-Lightstone single phase model is used for studying instabilities in nanoliquids. Various thermophysical properties of nanoliquid are obtained using phenomenological laws and mixture theory. The eigen boundary value problem is solved for the Rayleigh number using an analytical method by considering trigonometric eigen functions. We observe that the critical nanoliquid Rayleigh number is less than that of the base liquid. Thus the onset of convection is advanced due to the addition of nanoparticles. So, increase in volume fraction leads to advanced onset and thereby increase in heat transport. The amplitudes of convective modes required for estimating the heat transport are determined analytically. The tri-modal standard Lorenz model is derived for the steady state assuming small scale convective motions. The effect of rotation on the onset of convection and on heat transport is investigated and depicted graphically. It is observed that the onset of convection is delayed due to rotation and hence leads to decrease in heat transport. Hence, rotation has a stabilizing effect on the system. This is due to the fact that the energy of the system is used to create the component V. We observe that the amount of heat transport is less in the case of rigid-rigid isothermal boundaries compared to free-free isothermal boundaries.

Keywords: nanoliquid, rigid-rigid, rotation, single phase

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Authors: Tsutomu Iwayama, Takayuki Hama

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Si ion implantation was widely used to synthesize specimens of SiO2 containing supersaturated Si and subsequent high temperature annealing induces the formation of embedded luminescent Si nanocrystals. In this work, the potentialities of excimer UV-light (172 nm, 7.2 eV) irradiation and rapid thermal annealing (RTA) to enhance the photoluminescence and to achieve low temperature formation of Si nanocrystals have been investigated. The Si ions were introduced at acceleration energy of 180 keV to fluence of 7.5 x 1016 ions/cm2. The implanted samples were subsequently irradiated with an excimer-UV lamp. After the process, the samples were rapidly thermal annealed before furnace annealing (FA). Photoluminescence spectra were measured at various stages at the process. We found that the luminescence intensity is strongly enhanced with excimer-UV irradiation and RTA. Moreover, effective visible photoluminescence is found to be observed even after FA at 900 oC, only for specimens treated with excimer-UV lamp and RTA. We also prepared specimens of Si nanocrystals embedded in a SiO2 by reactive pulsed laser deposition (PLD) in an oxygen atmosphere. We will make clear the similarities and differences with the way of preparation.

Keywords: Ion implantation, photoluminescence, pulsed laser deposition, rapid thermal anneal, Si nanocrystals

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Authors: Samir Al-Zobaidi

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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: Gurmail Singh

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Effective supply chain is the main priority of every organization which is the outcome of strategic corporate investments with deliberate management action. Value-driven supply chain is defined through development, procurement and by configuring the appropriate resources, metrics and processes. However, responsiveness of the supply chain can be improved by proper coordination. So the Bullwhip effect (BWE) and Net stock amplification (NSAmp) values were anticipated and used for the control of inventory in organizations by both discrete wavelet transform-Artificial neural network (DWT-ANN) and Adaptive Network-based fuzzy inference system (ANFIS). This work presents a comparative methodology of forecasting for the customers demand which is non linear in nature for a multilevel supply chain structure using hybrid techniques such as Artificial intelligence techniques including Artificial neural networks (ANN) and Adaptive Network-based fuzzy inference system (ANFIS) and Discrete wavelet theory (DWT). The productiveness of these forecasting models are shown by computing the data from real world problems for Bullwhip effect and Net stock amplification. The results showed that these parameters were comparatively less in case of discrete wavelet transform-Artificial neural network (DWT-ANN) model and using Adaptive network-based fuzzy inference system (ANFIS).

Keywords: bullwhip effect, hybrid techniques, net stock amplification, supply chain flexibility

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Authors: M. Zielinska, B. Daniels, J. Gabel, A. Paletko

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A common nickel based superalloy Inconel625 was brazed with Ni-base braze filler material (AMS4777) containing melting-point-depressants such as B and Si. Different braze gaps, brazing times and forms of braze filler material were tested. It was determined that the melting point depressants B and Si tend to form hard and brittle phases in the joint during the braze cycle. Brittle phases significantly reduce mechanical properties (e. g. tensile strength) of the joint. Therefore, it is important to define optimal process parameters to achieve high strength joints, free of brittle phases. High ultimate tensile strength (UTS) values can be obtained if the joint area is free of brittle phases, which is equivalent to a complete isothermal solidification of the joint. Isothermal solidification takes place only if the concentration of the melting point depressant in the braze filler material of the joint is continuously reduced by diffusion into the base material. For a given brazing temperature, long brazing times and small braze filler material volumes (small braze gaps) are beneficial for isothermal solidification. On the base of the obtained results it can be stated that the form of the braze filler material has an additional influence on the joint quality. Better properties can be achieved by the use of braze-filler-material in form of foil instead of braze-filler-material in form of paste due to a reduced amount of voids and a more homogeneous braze-filler-material-composition in the braze-gap by using foil.

Keywords: diffusion brazing, microstructure, superalloy, tensile strength

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Authors: K. Mehmood, Muhammad Asif Rafiq, A. Nasir Khan, M. Mudassar Rauf

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Air plasma spraying system was utilized to deposit Ni3Al coatings on AISI 321 steel samples. After thermal spraying, the nickel aluminide intermetallic coatings were isothermal heat treated at various temperatures. In this regard, temperatures from 500 °C to 800 °C with 100 °C increments were selected. The coatings were soaked for 10, 30, 60 and 100 hours at the mentioned temperatures. These coatings were then tested by a pin on disk method. It was observed that the coatings exposed at comparatively higher temperature experienced lower wear rate. The decrease in wear rate is due to the formation of NiO phase. Further, the as sprayed and heat treated coatings were characterized by other tools such as Microhardness testing, optical and scanning electron microscopy (SEM) and X-Ray diffraction analysis. After isothermal heat treatment, NiO was observed the main phase by X-Ray diffraction technique. Moreover, the surface hardness was also determined higher than cross sectional hardness.

Keywords: air plasma spraying, Ni -20Al, tribometer, intermetallic coating, nickel aluminide

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Authors: Donatien Niragira

Abstract:

The progress of technology creates new expectations for patients. The world of deafness is no exception. In recent years, there have been considerable advances in the field of technologies aimed at assisting failing hearing. According to the usual medical vocabulary, hearing aids are actually orthotics. They do not replace an organ but compensate for a functional impairment. The Amplifier Hearing amplification is useful for a large number of people with hearing loss. Hearing aids restore speech audibility. However, their benefits vary depending on the quality of residual hearing. The hearing aid is not a "cure" for deafness. It cannot correct all affected hearing abilities. It should be considered as an aid to communication. The urge to judge from the audiogram alone should be resisted here, as audiometry only indicates the ability to detect non-verbal sounds. To prevent hearing aids from ending up in the drawer, it is important to ensure that the patient's disability situations justify the use of this type of orthosis. If the problems of receptive Pre-fitting counseling are crucial: the person with hearing loss must be informed of the advantages and disadvantages of amplification in his or her case. Their expectations must be realistic. They also need to be aware that the adaptation process requires a good deal of patience and perseverance. They should be informed about the various models and types of hearing aids, including all the aesthetic, functional and financial considerations. If the person's motivation "survives" pre-fitting counseling, we are in the presence of a good candidate for amplification. In addition to its relevance, it shows that the results found in this study significantly improve the quality of audibility in the patient, from where this technology must be made accessible everywhere in the world.

Keywords: auditives protheses, hearing, aids, no medicaly treatable deafnes

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Authors: Yash M. Gupta, Kittisak Buddhachat, Surin Peyachoknagul, Somjit Homchan

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The house cricket, Acheta domesticus is one of the commonly found species of field crickets. Although it is very commonly used as food and feed, the genomic information of house cricket is still missing for genetic investigation. DNA sequencing technology has evolved over the decades, and it has also revolutionized the molecular marker development for genetic analysis. In the present study, we have sequenced the whole genome of A. domesticus using illumina platform based HiSeq X Ten sequencing technology for searching simple sequence repeats (SSRs) in DNA to develop polymorphic microsatellite markers for population genetic analysis. A total of 112,157 SSRs with primer pairs were identified, 91 randomly selected SSRs used to check DNA amplification, of which nine primers were polymorphic. These microsatellite markers have shown cross-amplification with other three species of crickets which are Gryllus bimaculatus, Gryllus testaceus and Brachytrupes portentosus. These nine polymorphic microsatellite markers were used to check genetic variation for forty-five individuals of A. domesticus, Phitsanulok population, Thailand. For nine loci, the number of alleles was ranging from 5 to 15. The observed heterozygosity was ranged from 0.4091 to 0.7556. These microsatellite markers will facilitate population genetic analysis for future studies of A. domesticus populations. Moreover, the transferability of these SSR makers would also enable researchers to conduct genetic studies for other closely related species.

Keywords: cross-amplification, microsatellite markers, observed heterozygosity, population genetic, simple sequence repeats

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Authors: Mina Kalantarzadeh, Claire Lockie-Williams, Caroline Howard

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DNA barcoding is increasingly used for identification of medicinal plants worldwide. In the last decade, a large number of DNA barcodes have been generated, and their application in species identification explored. The success of DNA barcoding process relies on the accuracy of the results from polymerase chain reaction (PCR) amplification step which could be negatively affected due to a presence of inhibitors or degraded DNA in herbal samples. An established DNA reference material can be used to support molecular characterisation protocols and prove system suitability, for fast and accurate identification of plant species. The present study describes the use of a novel reference material, the trnH-psbA British Pharmacopoeia Nucleic Acid Reference Material (trnH-psbA BPNARM), which was produced to aid in the identification of Ocimum tenuiflorum L., a widely used herb. During DNA barcoding of O. tenuiflorum, PCR amplifications of isolated DNA produced inconsistent results, suggesting an issue with either the method or DNA quality of the tested samples. The trnH-psbA BPNARM was produced and tested to check for the issues caused during PCR amplification. It was added to the plant material as control DNA before extraction and was co-extracted and amplified by PCR. PCR analyses revealed that the amplification was not as successful as expected which suggested that the amplification is affected by presence of inhibitors co-extracted from plant materials. Various potential issues were assessed during DNA extraction and optimisations were made accordingly. A DNA barcoding protocol for O. tenuiflorum was published in the British Pharmacopoeia 2016, which included the reference sequence. The trnH-psbA BPNARM accelerated degradation test which investigates the stability of the reference material over time demonstrated that it has been stable when stored at 56 °C for a year. Using this protocol and trnH-psbA reference material provides a fast and accurate method for identification of O. tenuiflorum. The optimisations of the DNA extraction using the trnH-psbA BPNARM provided a signposting method which can assist in overcoming common problems encountered when using molecular methods with medicinal plants.

Keywords: degradation, DNA extraction, nucleic acid reference material, trnH-psbA

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Authors: Mohammad Reza Ghaani, Michele Catti

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The reduction of CoO/Fe₂O₃ oxides supported on carbon xerogels was studied to elucidate the effect of nano-size distribution of the catalyst in carbon matrices. Resorcinol formaldehyde xerogels were synthesized, impregnated with iron and cobalt nitrates, and subsequently heated to obtain the oxides. The mechanism of oxide reduction to metal was investigated by in-situ synchrotron X-ray diffraction in dynamic, non-isothermal conditions. Kinetic profiles of the reactions were obtained by plotting the diffraction intensities of selected Bragg peaks vs. temperature. The extracted Temperature-Programmed-Reduction (TPR) diagrams were analyzed by appropriate kinetic models, leading to best results with the Avrami-Erofeev model for all reduction reactions considered. The activation energies for the two-step reduction of iron oxide were 65 and 37 kJmol⁻¹, respectively. The average value for the reduction of CoO to Co was found to be around 21 kJ mol⁻¹. Such results may contribute to develop efficient and inexpensive non-noble metal-based catalysts in element form, e.g., Fe, Co, via heterogenization of metal complexes on mesoporous supports.

Keywords: non-isothermal kinetics, carbon aerogel, in-situ synchrotron X-ray diffraction, reduction mechanisms

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Authors: Niragira Donatien

Abstract:

The progress of technology creates new expectations for patients. The world of deafness is no exception. In recent years, there have been considerable advances in the field of technologies aimed at assisting failing hearing. According to the usual medical vocabulary, hearing aids are actually orthotics. They do not replace an organ but compensate for a functional impairment. The amplifier hearing amplification is useful for a large number of people with hearing loss. Hearing aids restore speech audibility. However, their benefits vary depending on the quality of residual hearing. The hearing aid is not a "cure" for deafness. It cannot correct all affected hearing abilities. It should be considered as an aid to communicate who the best candidates for hearing aids are. The urge to judge from the audiogram alone should be resisted here, as audiometry only indicates the ability to detect non-verbal sounds. To prevent hearing aids from ending up in the drawer, it is important to ensure that the patient's disability situations justify the use of this type of orthosis. If the problems of receptive pre-fitting counselling are crucial, the person with hearing loss must be informed of the advantages and disadvantages of amplification in his or her case. Their expectations must be realistic. They also need to be aware that the adaptation process requires a good deal of patience and perseverance. They should be informed about the various models and types of hearing aids, including all the aesthetic, functional, and financial considerations. If the person's motivation "survives" pre-fitting counselling, we are in the presence of a good candidate for amplification. In addition to its relevance, hearing aids raise other questions: Should one or both ears be fitted? In short, all these questions show that the results found in this study significantly improve the quality of audibility in the patient, from where this technology must be made accessible everywhere in the world. So we want to progress with the technology.

Keywords: audiology, influence, hearing, madicaly, treatable

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Authors: Avdhesh K. Sharma

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Formulation for drying and pyrolysis process in packed beds at slow heating rates is presented. Drying of biomass particles bed is described by mass diffusion equation and local moisture-vapour-equilibrium relations. In gasifiers, volatilization rate during pyrolysis of biomass is modeled by using apparent kinetic rate expression, while product compositions at slow heating rates is modeled using empirical fitted mass ratios (i.e., CO/CO₂, ME/CO₂, H₂O/CO₂) in terms of pyrolysis temperature. The drying module is validated fairly with available chemical kinetics scheme and found that the testing zone in gasifier bed constituted of relatively smaller particles having high airflow with high isothermal temperature expedite the drying process. Further, volatile releases more quickly within the shorter zone height at high temperatures (isothermal). Both, moisture loss and volatile release profiles are found to be sensitive to temperature, although the influence of initial moisture content on volatile release profile is not so sensitive.

Keywords: modeling downdraft gasifier, drying, pyrolysis, moist woody biomass

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Authors: M. Fares, S. Mameri, I. Abdlani, K. Negara

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Neutron detectors in general, proportional counters gas filling based isotope 3He in particular are going to be essential for monitoring and control of certain nuclear facilities, monitoring of experimentation around neutron beams and channels nuclear research reactors, radiation protection instruments and other tools multifaceted exploration and testing of materials, etc. This work consists of a measurement campaign features two Proportional Counters 3He (3He: LND252/USA CP, CP prototype: 3He LND/DDM). This is to make a comparison study of a CP 3He LND252/USA reference one hand, and in the context of routine periodic monitoring of the characteristics of the detectors for controlling the operation especially for laboratory prototypes. In this paper, we have described the different characteristics of the detectors and the experimental protocols used. Tables of measures have been developed and the different curves were plotted. The experimental campaign at stake: 2 PC 3He were thus characterized: Their characteristics (sensitivity, energy pulse height distribution spectra, gas amplification etc.) Were identified: 01 PC 3He 1'' Type: prototype DEDIN/DDM, 01 PC 3He 1'' Type: LND252/USA.

Keywords: PC 3He, sensitivity, pulse height distribution spectra, gas amplification

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Authors: A. Delimitsou, C. Gouedard, E. Konstanta, A. Koletis, S. Patera, E. Manou, K. Spaho, S. Murray

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Background: There remains a lack of International Standard Control Reference materials for Next Generation Sequencing-based approaches or device calibration. We have designed and validated dsDNA biomimetic reference materials for targeted such approaches incorporating proprietary motifs (patent pending) for device/test calibration. They enable internal single-sample calibration, alleviating sample comparisons to pooled historical population-based data assembly or statistical modelling approaches. We have validated such an approach for BRCA Copy Number Variation analytics using iQRS™-CNVSUITE versus Mixed Ligation-dependent Probe Amplification. Methods: Standard BRCA Copy Number Variation analysis was compared between mixed ligation-dependent probe amplification and next generation sequencing using a cohort of 198 breast/ovarian cancer patients. Next generation sequencing based copy number variation analysis of samples spiked with iQRS™ dsDNA biomimetics were analysed using proprietary CNVSUITE software. Mixed ligation-dependent probe amplification analyses were performed on an ABI-3130 Sequencer and analysed with Coffalyser software. Results: Concordance of BRCA – copy number variation events for mixed ligation-dependent probe amplification and CNVSUITE indicated an overall sensitivity of 99.88% and specificity of 100% for iQRS™-CNVSUITE. The negative predictive value of iQRS-CNVSUITE™ for BRCA was 100%, allowing for accurate exclusion of any event. The positive predictive value was 99.88%, with no discrepancy between mixed ligation-dependent probe amplification and iQRS™-CNVSUITE. For device calibration purposes, precision was 100%, spiking of patient DNA demonstrated linearity to 1% (±2.5%) and range from 100 copies. Traditional training was supplemented by predefining the calibrator to sample cut-off (lock-down) for amplicon gain or loss based upon a relative ratio threshold, following training of iQRS™-CNVSUITE using spiked iQRS™ calibrator and control mocks. BRCA copy number variation analysis using iQRS™-CNVSUITE™ was successfully validated and ISO15189 accredited and now enters CE-IVD performance evaluation. Conclusions: The inclusion of a reference control competitor (iQRS™ dsDNA mimetic) to next generation sequencing-based sequencing offers a more robust sample-independent approach for the assessment of copy number variation events compared to mixed ligation-dependent probe amplification. The approach simplifies data analyses, improves independent sample data analyses, and allows for direct comparison to an internal reference control for sample-specific quantification. Our iQRS™ biomimetic reference materials allow for single sample copy number variation analytics and further decentralisation of diagnostics to single patient sample assessment.

Keywords: validation, diagnostics, oncology, copy number variation, reference material, calibration

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Authors: Taru Singh, Shukla Das, V. G. Ramachandran

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Objectives: To develop SYBR green based real-time PCR assay to detect carbapenemases (NDM, IMP) genes in E. coli. Methods: A total of 40 E. coli from stool samples were tested. Six were previously characterized as resistant to carbapenems and documented by PCR. The remaining 34 isolates previously tested susceptible to carbapenems and were negative for these genes. Bacterial RNA was extracted using manual method. The real-time PCR was performed using the Light Cycler III 480 instrument (Roche) and specific primers for each carbapenemase target were used. Results: Each one of the two carbapenemase gene tested presented a different melting curve after PCR amplification. The melting temperature (Tm) analysis of the amplicons identified was as follows: blaIMP type (Tm 82.18°C), blaNDM-1 (Tm 78.8°C). No amplification was detected among the negative samples. The results showed 100% concordance with the genotypes previously identified. Conclusions: The new assay was able to detect the presence of two different carbapenemase gene type by real-time PCR.

Keywords: resistance, b-lactamases, E. coli, real-time PCR

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Authors: Tauhidur Rahman, Kasturi Bhuyan

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In the present paper, Ground Response Analysis at the Rukni irrigation project has been thoroughly investigated. Surface level seismic hazard is mainly used by the practical Engineers for designing the important structures. Surface level seismic hazard can be obtained accounting the soil factor. Structures on soft soil will show more ground shaking than the structure located on a hard soil. The Surface level ground motion depends on the type of soil. Density and shear wave velocity is different for different types of soil. The intensity of the soil amplification depends on the density and shear wave velocity of the soil. Rukni irrigation project is located in the North Eastern region of India, near the Dauki fault (550 Km length) which has already produced earthquakes of magnitude (Mw= 8.5) in the past. There is a probability of a similar type of earthquake occuring in the future. There are several faults also located around the project site. There are 765 recorded strong ground motion time histories available for the region. These data are used to determine the soil amplification factor by incorporation of the engineering properties of soil. With this in view, three of soil bore holes have been studied at the project site up to a depth of 30 m. It has been observed that in Soil bore hole 1, the shear wave velocity vary from 99.44 m/s to 239.28 m/s. For Soil Bore Hole No 2 and 3, shear wave velocity vary from 93.24 m/s to 241.39 m/s and 93.24m/s to 243.01 m/s. In the present work, surface level seismic hazard at the project site has been calculated based on the Probabilistic seismic hazard approach accounting the soil factor.

Keywords: Ground Response Analysis, shear wave velocity, soil amplification, surface level seismic hazard

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Authors: Mohammed S. Razali, Kamel Khimeche, Dahah Hichem, Ammar Boudjellal, Djamel E. Kaderi, Nourddine Ramdani

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The use of additive manufacturing technologies has revolutionized various aspects of our daily lives. In particular, 3D printing has greatly advanced biomedical applications. While fused filament fabrication (FFF) technologies have made it easy to produce or prototype various medical devices, it is crucial to minimize the risk of contamination. New materials with antibacterial properties, such as those containing compounded silver nanoparticles, have emerged on the market. In a previous study, we prepared a newly sintered seashell filler (SSh) from bio-based seashells found along the Mediterranean coast using a suitable heat treatment process. We then prepared a series of polylactic acid (PLA) and polybutylene succinate (PBS) biocomposites filled with these SSh particles using a melt mixing technique with a twin-screw extruder to use them as feedstock filaments for 3D printing. The study consisted of two parts: evaluating the antibacterial activity of newly prepared biocomposites made of PLA and PBS reinforced with a sintered seashell in the first part and experimental and modeling analysis of the non-isothermal crystallization kinetics of these biocomposites in the second part. In the first part, the bactericidal activity of the biocomposites against three different bacteria, including Gram-negative bacteria such as (E. coli and Pseudomonas aeruginosa), as well as Gram-positive bacteria such as (Staphylococcus aureus), was examined. The PLA-based biocomposite containing 20 wt.% of SSh particles exhibited an inhibition zone with radial diameters of 8mm and 6mm against E. coli and Pseudo. Au, respectively, while no bacterial activity was observed against Staphylococcus aureus. In the second part, the focus was on investigating the effect of the sintered seashell filler particles on the non-isothermal crystallization kinetics of PLA and PBS 3D-printing composite materials. The objective was to understand the impact of the filler particles on the crystallization mechanism of both PLA and PBS during the cooling process of a melt-extruded filament in (FFF) to manage the dimensional accuracy and mechanical properties of the final printed part. We conducted a non-isothermal melt crystallization kinetic study of a series of PLA-SS and PBS-SS composites using differential scanning calorimetry at various cooling rates. We analyzed the obtained kinetic data using different crystallization kinetic models such as modified Avrami, Ozawa, and Mo's methods. Dynamic mode describes the relative crystallinity as a function of temperature; it found that time half crystallinity (t1/2) of neat PLA decreased from 17 min to 7.3 min for PLA+5 SSh and the (t1/2) of virgin PBS was reduced from 3.5 min to 2.8 min for the composite containing 5wt.% of SSh. We found that the coated SS particles with stearic acid acted as nucleating agents and had a nucleation activity, as observed through polarized optical microscopy. Moreover, we evaluated the effective energy barrier of the non-isothermal crystallization process using the Iso conversional methods of Flynn-Wall-Ozawa (F-W-O) and Kissinger-Akahira-Sunose (K-A-S). The study provides significant insights into the crystallization behavior of PLA and PBS biocomposites.

Keywords: avrami model, bio-based reinforcement, dsc, gram-negative bacteria, gram-positive bacteria, isoconversional methods, non-isothermal crystallization kinetics, poly(butylene succinate), poly(lactic acid), antbactirial activity

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Authors: Jaco Oosthuizen, Nerina C. Van Der Merwe

Abstract:

The National Health Laboratory Services in Bloemfontien has been the diagnostic testing facility for 1830 patients for familial breast cancer since 1997. From the cohort, 540 were comprehensively screened using High-Resolution Melting Analysis or Next Generation Sequencing for the presence of point mutations and/or indels. Approximately 90% of these patients stil remain undiagnosed as they are BRCA1/2 negative. Multiplex ligation-dependent probe amplification was initially added to screen for copy number variation detection, but with the introduction of next generation sequencing in 2017, was substituted and is currently used as a confirmation assay. The aim was to investigate the viability of utilizing internationally designed copy number variation detection assays based on mostly European/Caucasian genomic data for use within a South African context. The multiplex ligation-dependent probe amplification technique is based on the hybridization and subsequent ligation of multiple probes to a targeted exon. The ligated probes are amplified using conventional polymerase chain reaction, followed by fragment analysis by means of capillary electrophoresis. The experimental design of the assay was performed according to the guidelines of MRC-Holland. For BRCA1 (P002-D1) and BRCA2 (P045-B3), both multiplex assays were validated, and results were confirmed using a secondary probe set for each gene. The next generation sequencing technique is based on target amplification via multiplex polymerase chain reaction, where after the amplicons are sequenced parallel on a semiconductor chip. Amplified read counts are visualized as relative copy numbers to determine the median of the absolute values of all pairwise differences. Various experimental parameters such as DNA quality, quantity, and signal intensity or read depth were verified using positive and negative patients previously tested internationally. DNA quality and quantity proved to be the critical factors during the verification of both assays. The quantity influenced the relative copy number frequency directly whereas the quality of the DNA and its salt concentration influenced denaturation consistency in both assays. Multiplex ligation-dependent probe amplification produced false positives due to ligation failure when ligation was inhibited due to a variant present within the ligation site. Next generation sequencing produced false positives due to read dropout when primer sequences did not meet optimal multiplex binding kinetics due to population variants in the primer binding site. The analytical sensitivity and specificity for the South African population have been proven. Verification resulted in repeatable reactions with regards to the detection of relative copy number differences. Both multiplex ligation-dependent probe amplification and next generation sequencing multiplex panels need to be optimized to accommodate South African polymorphisms present within the genetically diverse ethnic groups to reduce the false copy number variation positive rate and increase performance efficiency.

Keywords: familial breast cancer, multiplex ligation-dependent probe amplification, next generation sequencing, South Africa

Procedia PDF Downloads 191

Authors: Irina S. Kolesnikova, Alexander A. Dolskiy, Natalya A. Lemskaya, Yulia V. Maksimova, Asia R. Shorina, Alena S. Telepova, Alexander S. Graphodatsky, Dmitry V. Yudkin

Abstract:

A cytogenetic and molecular genetic study of the family with a male child who had mental retardation and autistic features revealed an abnormal chromosome 13 bearing an enlarged p-arm with amplified ribosomal DNA (rDNA) in a boy and his father. Cytogenetic analysis using standard G-banding and FISH with labeled rDNA probes revealed an abnormal chromosome 13 with an enlarged p-arms due to rDNA amplification in a male child, who had clinically confirmed mental retardation and an autistic behavior. This chromosome is evidently inherited from the father, who has morphologically the same chromosome, but is healthy. The karyotype of the mother was normal. Ag-NOR staining showed brightly stained large whole-p-arm nucleolus organizer regions (NORs) in a child and normal-sized NORs in his father with 13p+-NOR-amount mosaicism. qRT-PCR with specific primers showed highly increased levels of 18S, 28S and 5,8 S ribosomal RNA (rRNA) in the patient’s blood samples compared to a normal healthy control donor. Both patient’s father and mother had no elevated levels of rRNAs expression. Thus, in this case, rRNA level seems to correlate with mental retardation in familial individuals with 13p+. Our findings of rRNA overexpression in a patient with mental retardation and his parents may show a possible link between the karyotype (p-arm enlargement due to rDNA amplification), rDNA functionality (rRNA overexpression), functional changes in the brain and mental retardation. The study is supported by Russian Science Foundation Grant 15-15-10001.

Keywords: mental retardation, ribosomal DNA–rDNA, ribosomal RNA–rRNA, nucleolus organizer region–NOR, chromosome 13

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Authors: M. Omer Faruk, A. M. A. M. Zonaed Siddiki, M. Fazal Karim, Md. Masuduzzaman, S. Chowdhury, Md. Shafiqul Islam, M. Alamgir Hossain

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The dog tapeworms Echinococcus granulosus develop hydatid cysts in various organs in human and domestic animals worldwide including Bangladesh. The aim of this study was to identify and characterize the genotype of E. granulosus isolated from cattle using 12S rRNA and Cytochrome oxidase 1 (COX 1) genes. A total of 43 hydatid cyst samples were collected from 390 examined cattle samples derived from slaughterhouses. Among them, three cysts were fertile. Genomic DNA was extracted from germinal membrane and/or protoscoleces followed by PCR amplification of mitochondrial 12S rRNA and Cytochrome oxidase 1 gene fragments. The sequence data revealed existence of G1 (64.28%) and possible G3 (21.43%) genotypes for the first time in Bangladesh. The study indicates that common sheep strain G1 is the dominant subtype of E. granulosus in Chittagong region of Bangladesh. This will increase our understanding of the epidemiology of hydatidosis in the southern part of the country and will be useful to plan suitable control measures in the long run.

Keywords: Echinococcus granulosus, Cox1, 12S rRNA, molecular characterization, Bangladesh

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Authors: Meimei Shi

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Objectives: The identification of endangered species, especially simultaneous detection of multiple species in complex samples, plays a critical role in alleged wildlife crime incidents and prevents illegal trade. This study was to develop a multi-locus DNA metabarcoding method for endangered animal species identification. Methods: Several pairs of universal primers were designed according to the mitochondria conserved gene regions. Experimental mixtures were artificially prepared by mixing well-defined species, including endangered species, e.g., forest musk, bear, tiger, pangolin, and sika deer. The artificial samples were prepared with 1-16 well-characterized species at 1% to 100% DNA concentrations. After multiplex-PCR amplification and parameter modification, the amplified products were analyzed by capillary electrophoresis and used for NGS library preparation. The DNA metabarcoding was carried out based on Illumina MiSeq amplicon sequencing. The data was processed with quality trimming, reads filtering, and OTU clustering; representative sequences were blasted using BLASTn. Results: According to the parameter modification and multiplex-PCR amplification results, five primer sets targeting COI, Cytb, 12S, and 16S, respectively, were selected as the NGS library amplification primer panel. High-throughput sequencing data analysis showed that the established multi-locus DNA metabarcoding method was sensitive and could accurately identify all species in artificial mixtures, including endangered animal species Moschus berezovskii, Ursus thibetanus, Panthera tigris, Manis pentadactyla, Cervus nippon at 1% (DNA concentration). In conclusion, the established species identification method provides technical support for customs and forensic scientists to prevent the illegal trade of endangered animals and their products.

Keywords: DNA metabarcoding, endangered animal species, mitochondria nucleic acid, multi-locus

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Authors: B. Donkova, M. Nedyalkova, D. Mehandjiev

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Sparingly soluble manganese oxalate is an appropriate precursor for the preparation of nanosized manganese oxides, which have a wide range of technological application. During the precipitation of manganese oxalate, three crystal forms could be obtained – α-MnC₂O₄.2H₂O (SG C2/c), γ-MnC₂O₄.2H₂O (SG P212121) and orthorhombic MnC₂O₄.3H₂O (SG Pcca). The thermolysis of α-MnC₂O₄.2H₂O has been extensively studied during the years, while the literature data for the other two forms has been quite scarce. The aim of the present communication is to highlight the influence of the initial crystal structure on the decomposition mechanism of these three forms, their magnetic properties, the structure of the anhydrous oxalates, as well as the nature of the obtained oxides. For the characterization of the samples XRD, SEM, DTA, TG, DSC, nitrogen adsorption, and in situ magnetic measurements were used. The dehydration proceeds in one step with α-MnC₂O₄.2H2O and γ-MnC₂O₄.2H₂O, and in three steps with MnC₂O₄.3H2O. The values of dehydration enthalpy are 97, 149 and 132 kJ/mol, respectively, and the last two were reported for the first time, best to our knowledge. The magnetic measurements show that at room temperature all samples are antiferomagnetic, however during the dehydration of α-MnC₂O₄.2H₂O the exchange interaction is preserved, for MnC₂O₄.3H₂O it changes to ferromagnetic above 35°C, and for γ-MnC₂O₄.2H₂O it changes twice from antiferomagnetic to ferromagnetic above 70°C. The experimental results for magnetic properties are in accordance with the computational results obtained with Wien2k code. The difference in the initial crystal structure of the forms used determines different changes in the specific surface area during dehydration and different extent of Mn(II) oxidation during decomposition in the air; both being highest at α-MnC₂O₄.2H₂O. The isothermal decomposition of the different oxalate forms shows that the type and physicochemical properties of the oxides, obtained at the same annealing temperature depend on the precursor used. Based on the results from the non-isothermal and isothermal experiments, and from different methods used for characterization of the sample, a comparison of the nature, mechanism and peculiarities of the thermolysis of the different crystal forms of manganese oxalate was made, which clearly reveals the influence of the initial crystal structure. Acknowledgment: 'Science and Education for Smart Growth', project BG05M2OP001-2.009-0028, COST Action MP1306 'Modern Tools for Spectroscopy on Advanced Materials', and project DCOST-01/18 (Bulgarian Science Fund).

Keywords: crystal structure, magnetic properties, manganese oxalate, thermal behavior

Procedia PDF Downloads 139

Authors: Ercan Kızılay, Mustafa Demi̇rel, Selçuk Coşkun

Abstract:

Railway signaling systems consist of vital products that regulate railway traffic and provide safe route arrangements and maneuvers of trains. SIL 4 signal lamps are produced by many manufacturers today. There is a need for systems that enable these signal lamps to be controlled by commands from the interlocking. These systems should act as fail-safe and give error indications to the interlocking system when an unexpected situation occurs for the safe operation of railway systems from the RAMS perspective. In the past, driving and proving the lamp in relay-based systems was typically done via signaling relays. Today, the proving of lamps is done by comparing the current values read over the return circuit, the lower and upper threshold values. The purpose is an analog electronic object controller with the possibility of easy integration with vital systems and the signal lamp itself. During the study, the EN50126 standard approach was considered, and the concept, definition, risk analysis, requirements, architecture, design, and prototyping were performed throughout this study. FMEA (Failure Modes and Effects Analysis) and FTA (Fault Tree) Analysis) have been used for safety analysis in accordance with EN 50129. Concerning these analyzes, the 1oo2D reactive fail-safe hardware design of a controller has been researched. Electromagnetic compatibility (EMC) effects on the functional safety of equipment, insulation coordination, and over-voltage protection were discussed during hardware design according to EN 50124 and EN 50122 standards. As vital equipment for railway signaling, railway signal object controllers should be developed according to EN 50126 and EN 50129 standards which identify the steps and requirements of the development in accordance with the SIL 4(Safety Integrity Level) target. In conclusion of this study, an analog railway signal object controller, which takes command from the interlocking system, is processed in driver cards. Driver cards arrange the voltage level according to desired visibility by means of semiconductors. Additionally, prover cards evaluate the current upper and lower thresholds. Evaluated values are processed via logic gates which are composed as 1oo2D by means of analog electronic technologies. This logic evaluates the voltage level of the lamp and mitigates the risks of undue dimming.

Keywords: object controller, railway electronic, analog electronic, safety, railway signal

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Authors: Babak Rezavand

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Pneumocystis carinii pneumonia (PCP) is one of the main causes of morbidity and mortality among immunocompromised and HIV-positive patients and remained one of the most important common opportunistic infections in these individuals in the world. Pneumocystis infection has been reported in many mammals. The aim of this study was to determine the Pneumocystis infection in wild rats as natural reservoirs of this organism in Tehran city, Iran. Fifty three rats (Rattus rattus) were live trapped in different areas of Tehran city, Iran. After isolation of their lung tissues and homogenization in sterile conditions, DNA was extracted. DNAs from all of the Pneumocystis species were amplified by pAZ102-H and pAZ102-E primers, and Nested PCR was performed using pAZ102-X and pAZ102-W primers from the initial PCR product for all the species of Pneumocystis. Amplification of the genome revealed the presence of Pneumocystis in the lungs of 17 rats (32%) through a PCR product with a bandwidth of 346 bp. In the Nested PCR amplification, from the PCR product of 53 rats, 64.2% of the samples were positive with a bandwidth of 261bp. Pneumocystis SPP infestation is highly prevalent among wild rats in Tehran city, indicating the existence of infection in the natural ecosystem of these rodents. As a host, rat plays an important role in the transmission of the microorganism in the world.

Keywords: pneumocystis SPP, rattus rattus, nested PCR, Tehran

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Authors: Mudawamah Mudawamah, Muhammad Z. Fadli, Gatot Ciptadi, Aulanni’am

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Canary breeders have spread throughout Indonesian regions for the low-middle society and become an income source for them. The interesting phenomenon of the canary market is the feather colours become one of determining factor for the price. The advantages of this research were contributed to the molecular database as a base of selection and mating for the Indonesia canary breeder. The research method was experiment with the genome obtained from canary blood isolation. The genome did the PCR amplification with PMEL marker followed by sequencing. Canaries were used 24 heads of light and dark colour feathers. Research data analyses used BioEdit and Network 4.6.0.0 software. The results showed that all samples were amplification with PMEL gene with 500 bp fragment length. In base sequence of 40 was found Cytosine(C) in the light colour canaries, while the dark colour canaries was obtained Thymine (T) in same base sequence. Sequence results had 286-415 bp fragment and 10 haplotypes. The conclusions were the PMEL gene (gene of white pigment) was likely to be used PMEL gene to detect molecular genetic variation of dark and light colour feather.

Keywords: canary, haplotype, PMEL, sequence

Procedia PDF Downloads 207

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

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

Keywords: mastitis, bacteria, characterization, expression, gene

Procedia PDF Downloads 190

Authors: Romulo D. C. Santos, Silvio M. A. Gama, Ramiro G. R. Camacho

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In this present paper, the thermos-fluid dynamics considering the mixed convection (natural and forced convections) and the principles of turbulence flow around complex geometries have been studied. In these applications, it was necessary to analyze the influence between the flow field and the heated immersed body with constant temperature on its surface. This paper presents a study about the Newtonian incompressible two-dimensional fluid around isothermal geometry using the immersed boundary method (IBM) with the virtual physical model (VPM). The numerical code proposed for all simulations satisfy the calculation of temperature considering Dirichlet boundary conditions. Important dimensionless numbers such as Strouhal number is calculated using the Fast Fourier Transform (FFT), Nusselt number, drag and lift coefficients, velocity and pressure. Streamlines and isothermal lines are presented for each simulation showing the flow dynamics and patterns. The Navier-Stokes and energy equations for mixed convection were discretized using the finite difference method for space and a second order Adams-Bashforth and Runge-Kuta 4th order methods for time considering the fractional step method to couple the calculation of pressure, velocity, and temperature. This work used for simulation of turbulence, the Smagorinsky, and Spalart-Allmaras models. The first model is based on the local equilibrium hypothesis for small scales and hypothesis of Boussinesq, such that the energy is injected into spectrum of the turbulence, being equal to the energy dissipated by the convective effects. The Spalart-Allmaras model, use only one transport equation for turbulent viscosity. The results were compared with numerical data, validating the effect of heat-transfer together with turbulence models. The IBM/VPM is a powerful tool to simulate flow around complex geometries. The results showed a good numerical convergence in relation the references adopted.

Keywords: immersed boundary method, mixed convection, turbulence methods, virtual physical model

Procedia PDF Downloads 91