Search results for: rolling circle amplification (RCA)

Authors: Burdin Louise, Brulez Anne-Catherine, Mazurcyk Radoslaw, Leclercq Jean-louis, Benayoun Stéphane

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By using a biomimetic approach, an investigation was conducted to determine the connections between morphology and wetting. The interest is focused on the Morpho peleides butterfly. This butterfly is already well-known among researchers for its brilliant iridescent color and has inspired numerous innovations. The intricate structure of its wings is responsible for such color. However, this multiscale structure exhibits a multitude of other features, such as hydrophobicity. Given the limited research on the wetting properties of Morpho butterfly, a detailed analysis of its wetting behavior is proposed. Multiscale surface topographies of the Morpho peleides butterfly were analyzed using scanning electron microscope and atomic force microscopy. To understand the relationship between morphology and wettability, a goniometer was employed to measured static and dynamic contact angle. Since several studies have consistently demonstrated that superhydrophobic surfaces can effectively delay freezing, icing delay time the Morpho’s wings was also measured. The results revealed contact angles close to 136°, indicating a high degree of hydrophobicity. Moreover, sliding angles (SA) were measured in different directions, including along and against the rolling-outward direction. The findings suggest anisotropic wetting. Specifically, when the wing was tilted along the rolling outward direction (i.e., away from the insect’s body) SA was about 7°. While, when the wing was tilted against the rolling outward direction, SA was about 29°. This phenomenon is directly linked to the butterfly’s survival strategy. To investigate the exclusive morphological impact on anti-icing properties, PDMS replicas of the Morpho butterfly were obtained. When compared to flat PDMS and microscale textured PDMS, Morpho replications exhibited a longer freezing time. Therefore, this could be a source of inspiration for designing superhydrophobic surfaces with anti-icing applications or functional surfaces with controlled wettability.

Keywords: biomimetic, anisotropic wetting, anti-icing, multiscale roughness

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Authors: Hasan Bulent Kantarci

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This paper examine how Zakat provide a fair income redistribution and struggle with poverty. To provide a fair income redistribution and struggle with poverty take place among the fundamental tasks of all countries. Each country seeks a solution for this problem according to their political, economical and administrative styles through applying various economic and financial policies. The same situation gets handled via zakat association in the Islam. Nowadays, we observe different versions of zakat in developed countries. The applications such as negative income tax denote merely a difference from the zakat being applied almost the same way under changed names. But the minimum values to donate the zakat (e.g. 85 gr. gold and 40 animals) get altered and various amounts are put into practice. It might be named as negative income tax instead of zakat, nonetheless, these applications are based on the Holy Koran and the hadith released 1400 years ago. Besides, considering the savage and slavery in the world at those times, we might easily recognize the true value of the zakat applied the first time then in Islamic system. Through zakat is enabled an income transfer by the government so that the poor could reach the minimum level of life standard. To whom the zakat would be donated was not left to people’s heart and encouraged to determine according to objective criteria. Since the zakat is obligatory, the transfer do not get forward by hand but via the government and get distributed, which requires a vast government organization. Through applying the zakat as it must be would achieve to reduce the poverty mostly and ensuring the fair income redistribution.

Keywords: Islamic finance, zakat, income redistribution, circle of poverty, negatif income tax

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Authors: Dawit Gebreegzabher Hagos, Yazezew Kebede Kiro, Mahmud Abdulkader, Henk H. D. F. Schallig, Dawit Wolday

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Rapid and accurate visceral leishmaniasis (VL) diagnosis is needed to initiate prompt treatment to reduce morbidity and mortality. Here, we evaluated the performance of loop-mediated isothermal amplification (LAMP) assay for the diagnosis of VL from blood in an endemic area in Ethiopia. LAMP was positive in 117/122 confirmed VL cases and negative in 149/152 controls, resulting in a sensitivity of 95.9% (95% CI: 90.69–98.66) and a specificity of 98.0% (95% CI: 94.34–99.59), respectively. The sensitivity of the LAMP assay was 95.0% (95% CI: 88.61–98.34) in HIV-negatives and 100% (95% CI: 85.18–100.0) in HIV-positives. Compared with microscopy, LAMP detected 82/87 (94.3%, 95% CI: 87.10–98.11) of the microscopy1 cases and was negative in 11/27 (40.7%, 95% CI: 22.39–61.20) of the microscopy2 cases. Compared with the rK39 serology, LAMP detected 113/120 (94.2%, 95% CI: 88.35–97.62) of the rK391 cases and was negative in 149/154 (96.8%, 95% CI: 92.59–98.94) of the rK392 cases. However, when compared with microscopy only, rK39 detected 83/87 (95.4%, 95% CI: 88.64–98.73) of the microscopy1 cases and negative in only 12/27 (44.4%, 95% CI: 25.48–64.67) of the microscopy– cases. There was an excellent agreement between rK39 and LAMP (Kappa 5 0.91, 95% CI: 0.86–0.96). Furthermore, an algorithm using rK39 followed by LAMP would yield a sensitivity of 99.2% (95%CI: 95.52–99.89) and a specificity of 98.0% (95% CI: 94.34–99.59). The findings demonstrate that the LAMP assay is an accurate and rapid molecular assay for VL diagnosis, including in HIV-1 co-infected patients, in an endemic setting.

Keywords: visceral leishmaniasis, HIV, diagnosis, LAMP, Ethiopia

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Authors: Peter Antwi Buah, Yingbin Zhang, Jianxian He, Chenlin Xiang, Delali Atsu Y. Bakah

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Near-fault ground motions with velocity pulses are considered to cause significant damage to structures or slopes compared to ordinary ground motions without velocity pulses. The double pulsed pulse-like ground motion is as well known to be stronger than the single pulse. This study has numerically justified this perspective by studying the dynamic response of a homogeneous rock slope subjected to four pulse-like and two non-pulse-like ground motions using the Fast Lagrangian Analysis of Continua in 3 Dimensions (FLAC3D) software. Two of the pulse-like ground motions just have a single pulse. The results show that near-fault ground motions with velocity pulses can cause a higher dynamic response than regular ground motions. The amplification of the peak ground acceleration (PGA) in horizontal direction increases with the increase of the slope elevation. The seismic response of the slope under double pulse ground motion is stronger than that of the single pulse ground motion. The PGV amplification factor under the effect of the non-pulse-like records is also smaller than those under the pulse-like records. The velocity pulse strengthens the earthquake damage to the slope, which results in producing a more strong dynamic response.

Keywords: velocity pulses, dynamic response, PGV magnification effect, elevation effect, double pulse

Procedia PDF Downloads 176

Authors: Morteza Hadi

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This research investigates the potential enhancement of the rollability of Cu-Ge-Ni alloy through the mitigation of microstructural and compositional inhomogeneities via two distinct heat treatment methods: homogenization and solution treatment. To achieve this objective, the alloy with the desired composition was fabricated using a vacuum arc remelting furnace (VAR), followed by sample preparation for microstructural, compositional, and heat treatment analyses at varying temperatures and durations. Characterization was conducted employing optical and scanning electron microscopy (SEM), X-ray diffraction (XRD), and Vickers hardness testing. The results obtained indicate that a minimum duration of 10 hours is necessary for adequate homogenization of the alloy at 750°C. This heat treatment effectively removes coarse dendrites from the casting microstructure and significantly reduces elemental separations. However, despite these improvements, the presence of a second phase with markedly different hardness from the matrix results in poor rolling ability for the alloy. The optimal time for solution treatment at various temperatures was determined, with the most effective cycle identified as 750°C for 2 hours, followed by rapid quenching in water. This process induces the formation of a single-phase microstructure and complete elimination of the second  phase, as confirmed by X-ray diffraction analysis. Results demonstrate a reduction in hardness by 30 Vickers, and the elimination of microstructural unevenness enables successful thickness reduction by up to 50% through rolling without encountering cracking.

Keywords: Cu-Ge-Ni alloy, homogenization. solution treatment, rollability

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Authors: Suharni Mohamad Suharni Mohamad, Nurul Izzati Hamzan Nurul Izzati Hamzan, Norhayu Abdul Rahman Norhayu Abdul Rahman, Siti Suraiya Md Noor Siti Suraiya Md Noor

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Human papillomavirus (HPV) is an important risk factor for development of oral cancer. HPV16 is the most common type found in HPV-positive squamous cell carcinoma. In the present study, we established a real-time loop-mediated isothermal amplification (real-time LAMP) for detection of HPV16. A set of six primers was specially designed to recognize eight distinct sequences of HPV16-E6. Detection and quantification was achieved by real-time monitoring using a real-time turbidimeter based on threshold time required for turbidity in the LAMP reaction. LAMP reagents (MgSO4, dNTPs, Bst polymerase concentrations) and various incubation times and temperatures were optimized. The sensitivity was determined using 10-fold serial dilutions of HPV16 standard strain. The specificity of was evaluated using other HPV genotypes. The optimized method was established with specifically designed primers by real-time detection in approximately 30 min at 65°C. The limit of detection of HPV16 using the LAMP assay was 10 pg/ml that could be detected in 30 min. The LAMP assay was 10 times more sensitive than the conventional PCR in detecting HPV16. No cross-reactivity with other HPV genotypes was observed. This quantitative real-time LAMP assay may improve diagnostic potential for the detection and quantification of HPV16 in clinical samples and epidemiological studies due to its rapidity, simplicity, high sensitivity and specificity. This assay will be further evaluated with HPV DNAs of saliva from patients with oral squamous cell carcinoma. Acknowledgement: This study was financially supported by the ScienceFund Grant, Ministry of Science, Technology and Innovation (305/PPSG/6113219).

Keywords: Oral Squamous Cell Carcinoma (OSCC), Human Papillomavirus 16 (HPV16), Loop-Mediated Isothermal Amplification (LAMP), rapid detection

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Authors: Nipun Manirajan, Heeralal Gargama, Sushil Guhe, Manoj Prabhakaran

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In railway industry, train sets are designed based on contractual requirements (mission profile), where reliability targets are measured in terms of mean distance between failures (MDBF). However, during the beginning of revenue services, trains do not achieve the designed mission profile distance (mileage) within the timeframe due to infrastructure constraints, scarcity of commuters or other operational challenges thereby not respecting the original design inputs. Since trains do not run sufficiently and do not achieve the designed mileage within the specified time, car builder has a risk of not achieving the contractual MDBF target. This paper proposes a constant failure rate based model to deal with the situations where mileage accumulation is not a part of the design mission profile. The model provides appropriate MDBF target to be demonstrated based on actual accumulated mileage. A case study of rolling stock running in the field is undertaken to analyze the failure data and MDBF target demonstration during low mileage accumulation. The results of case study prove that with the proposed method, reliability targets are achieved under low mileage accumulation.

Keywords: mean distance between failures, mileage-based reliability, reliability target appropriations, rolling stock reliability

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Authors: Ayalew Yimam Ali

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The T-shaped microchannel is used to mix both miscible or immiscible fluids with different viscosities. However, mixing at the entrance of the T-junction microchannel can be difficult mixing phenomena due to micro-scale laminar flow aspects with the two miscible high-viscosity water-glycerol fluids. One of the most promising methods to improve mixing performance and diffusion mass transfer in laminar flow phenomena is acoustic streaming (AS), which is a time-averaged, second-order steady streaming that can produce rolling motion in the microchannel by oscillating a low-frequency range acoustic transducer and inducing an acoustic wave in the flow field. The newly developed 3D trapezoidal, triangular structure spine used in this study was created using sophisticated CNC machine cutting tools used to create microchannel mold with a 3D trapezoidal triangular structure spine alone the T-junction longitudinal mixing region. In order to create the molds for the 3D trapezoidal structure with the 3D sharp edge tip angles of 30° and 0.3mm trapezoidal, triangular sharp edge tip depth from PMMA glass (Polymethylmethacrylate) with advanced CNC machine and the channel manufactured using PDMS (Polydimethylsiloxane) which is grown up longitudinally on the top surface of the Y-junction microchannel using soft lithography nanofabrication strategies. Flow visualization of 3D rolling steady acoustic streaming and mixing enhancement with high-viscosity miscible fluids with different trapezoidal, triangular structure longitudinal length, channel width, high volume flow rate, oscillation frequency, and amplitude using micro-particle image velocimetry (μPIV) techniques were used to study the 3D acoustic streaming flow patterns and mixing enhancement. The streaming velocity fields and vorticity flow fields show 16 times more high vorticity maps than in the absence of acoustic streaming, and mixing performance has been evaluated at various amplitudes, flow rates, and frequencies using the grayscale value of pixel intensity with MATLAB software. Mixing experiments were performed using fluorescent green dye solution with de-ionized water in one inlet side of the channel, and the de-ionized water-glycerol mixture on the other inlet side of the T-channel and degree of mixing was found to have greatly improved from 67.42% without acoustic streaming to 0.96.83% with acoustic streaming. The results show that the creation of a new 3D steady streaming rolling motion with a high volume flowrate around the entrance was enhanced by the formation of a new, three-dimensional, intense streaming rolling motion with a high-volume flowrate around the entrance junction mixing zone with the two miscible high-viscous fluids which are influenced by laminar flow fluid transport phenomena.

Keywords: micro fabrication, 3d acoustic streaming flow visualization, micro-particle image velocimetry, mixing enhancement.

Procedia PDF Downloads 20

Authors: Ayalew Yimam Ali

Abstract:

The Y-shaped microchannel is used to mix both miscible or immiscible fluids with different viscosities. However, mixing at the entrance of the Y-junction microchannel can be a difficult mixing phenomena due to micro-scale laminar flow aspects with the two miscible high-viscosity water-glycerol fluids. One of the most promising methods to improve mixing performance and diffusion mass transfer in laminar flow phenomena is acoustic streaming (AS), which is a time-averaged, second-order steady streaming that can produce rolling motion in the microchannel by oscillating a low-frequency range acoustic transducer and inducing an acoustic wave in the flow field. The developed 3D trapezoidal, triangular structure spine used in this study was created using sophisticated CNC machine cutting tools used to create microchannel mold with a 3D trapezoidal triangular structure spine alone the Y-junction longitudinal mixing region. In order to create the molds for the 3D trapezoidal structure with the 3D sharp edge tip angles of 30° and 0.3mm trapezoidal triangular sharp edge tip depth from PMMA glass (Polymethylmethacrylate) with advanced CNC machine and the channel manufactured using PDMS (Polydimethylsiloxane) which is grown up longitudinally on top surface of the Y-junction microchannel using soft lithography nanofabrication strategies. Flow visualization of 3D rolling steady acoustic streaming and mixing enhancement with high-viscosity miscible fluids with different trapezoidal, triangular structure longitudinal length, channel width, high volume flow rate, oscillation frequency, and amplitude using micro-particle image velocimetry (μPIV) techniques were used to study the 3D acoustic streaming flow patterns and mixing enhancement. The streaming velocity fields and vorticity flow fields show 16 times more high vorticity maps than in the absence of acoustic streaming, and mixing performance has been evaluated at various amplitudes, flow rates, and frequencies using the grayscale value of pixel intensity with MATLAB software. Mixing experiments were performed using fluorescent green dye solution with de-ionized water in one inlet side of the channel, and the de-ionized water-glycerol mixture on the other inlet side of the Y-channel and degree of mixing was found to have greatly improved from 67.42% without acoustic streaming to 0.96.83% with acoustic streaming. The results show that the creation of a new 3D steady streaming rolling motion with a high volume flowrate around the entrance was enhanced by the formation of a new, three-dimensional, intense streaming rolling motion with a high-volume flowrate around the entrance junction mixing zone with the two miscible high-viscous fluids which are influenced by laminar flow fluid transport phenomena.

Keywords: micro fabrication, 3d acoustic streaming flow visualization, micro-particle image velocimetry, mixing enhancement

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Authors: Sajana Suwal, Ganesh R. Nhemafuki

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Evaluation of ground response under earthquake shaking is crucial in geotechnical earthquake engineering. Damage due to seismic excitation is mainly correlated to local geological and geotechnical conditions. It is evident from the past earthquakes (e.g. 1906 San Francisco, USA, 1923 Kanto, Japan) that the local geology has strong influence on amplitude and duration of ground motions. Since then significant studies has been conducted on ground motion amplification revealing the importance of influence of local geology on ground. Observations from the damaging earthquakes (e.g. Nigata and San Francisco, 1964; Irpinia, 1980; Mexico, 1985; Kobe, 1995; L’Aquila, 2009) divulged that non-uniform damage pattern, particularly in soft fluvio-lacustrine deposit is due to the local amplification of seismic ground motion. Non-uniform damage patterns are also observed in Kathmandu Valley during 1934 Bihar Nepal earthquake and recent 2015 Gorkha earthquake seemingly due to the modification of earthquake ground motion parameters. In this study, site effects resulting from amplification of soft soil in Kathmandu are presented. A large amount of subsoil data was collected and used for defining the appropriate subsoil model for the Kathamandu valley. A comparative study of one-dimensional total-stress equivalent linear and non-linear site response is performed using four strong ground motions for six sites of Kathmandu valley. In general, one-dimensional (1D) site-response analysis involves the excitation of a soil profile using the horizontal component and calculating the response at individual soil layers. In the present study, both equivalent linear and non-linear site response analyses were conducted using the computer program DEEPSOIL. The results show that there is no significant deviation between equivalent linear and non-linear site response models until the maximum strain reaches to 0.06-0.1%. Overall, it is clearly observed from the results that non-linear site response model perform better as compared to equivalent linear model. However, the significant deviation between two models is resulted from other influencing factors such as assumptions made in 1D site response, lack of accurate values of shear wave velocity and nonlinear properties of the soil deposit. The results are also presented in terms of amplification factors which are predicted to be around four times more in case of non-linear analysis as compared to equivalent linear analysis. Hence, the nonlinear behavior of soil prevails the urgent need of study of dynamic characteristics of the soft soil deposit that can specifically represent the site-specific design spectra for the Kathmandu valley for building resilient structures from future damaging earthquakes.

Keywords: deep soil, equivalent linear analysis, non-linear analysis, site response

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Authors: Gökhan Polat, Dicle Kocaoğlu Yılmazer, Muhlis Nezihi Sarıdede

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Iron oxides are the main input to produce iron in integrated iron and steel plants. During production of iron from iron oxides, some wastes with high iron content occur. These main wastes can be classified as basic oxygen furnace (BOF) sludge, flue dust and rolling scale. Recycling of these wastes has a great importance for both environmental effects and reduction of production costs. In this study, recycling experiments were performed on basic oxygen furnace sludge, flue dust and rolling scale which contain 53.8%, 54.3% and 70.2% iron respectively. These wastes were mixed together with coke as reducer and these mixtures are pressed to obtain cylindrical briquettes. These briquettes were pressed under various compacting forces from 1 ton to 6 tons. Also, both stoichiometric and twice the stoichiometric cokes were added to investigate effect of coke amount on reduction properties of the waste mixtures. Then, these briquettes were reduced at 1000°C and 1100°C during 30, 60, 90, 120 and 150 min in a muffle furnace. According to the results of reduction experiments, the effect of compacting force, temperature and time on reduction ratio of the wastes were determined. It is found that 1 ton compacting force, 150 min reduction time and 1100°C are the optimum conditions to obtain reduction ratio higher than 75%.

Keywords: Coke, iron oxide wastes, recycling, reduction

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Authors: Sumit Roy, A. Uddin

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One of the significant reasons that increase the delay time in the intersections at heterogeneous traffic condition is a sudden reduction of the capacity of the roads. In this study, the delay for this sudden capacity reduction is estimated. Two intersections at Dhaka city were brought in to thestudy, i.e., Kakrail intersection, and SAARC Foara intersection. At Kakrail intersection, the sudden reduction of capacity in the roads is seen at three downstream legs of the intersection, which are because of slowing down or stopping of buses for loading and unloading of passengers. At SAARC Foara intersection, sudden reduction of capacity was seen at two downstream legs. At one leg, it was due to loading and unloading of buses, and at another leg, it was for both loading and unloading of buses and reduction of the number of lanes. With these considerations, the delay due to intentional stoppage or slowing down of buses and reduction of the number of lanes for these two intersections are estimated. Here the delay was calculated by two approaches. The first approach came from the concept of shock waves in traffic streams. Here the delay was calculated by determining the flow, density, and speed before and after the sudden capacity reduction. The second approach came from the deterministic analysis of queues. Here the delay is calculated by determining the volume, capacity and reduced capacity of the road. After determining the delay from these two approaches, the results were compared. For this study, the video of each of the two intersections was recorded for one hour at the evening peak. Necessary geometric data were also taken to determine speed, flow, and density, etc. parameters. The delay was calculated for one hour with one-hour data at both intersections. In case of Kakrail intersection, the per hour delay for Kakrail circle leg was 5.79, and 7.15 minutes, for Shantinagar cross intersection leg they were 13.02 and 15.65 minutes, and for Paltan T intersection leg, they were 3 and 1.3 minutes for 1st and 2nd approaches respectively. In the case of SAARC Foara intersection, the delay at Shahbag leg was only due to intentional stopping or slowing down of busses, which were 3.2 and 3 minutes respectively for both approaches. For the Karwan Bazar leg, the delays for buses by both approaches were 5 and 7.5 minutes respectively, and for reduction of the number of lanes, the delays for both approaches were 2 and 1.78 minutes respectively. Measuring the delay per hour for the Kakrail leg at Kakrail circle, it is seen that, with consideration of the first approach of delay estimation, the intentional stoppage and lowering of speed by buses contribute to 26.24% of total delay at Kakrail circle. If the loading and unloading of buses at intersection is made forbidden near intersection, and any other measures for loading and unloading of passengers are established far enough from the intersections, then the delay at intersections can be reduced at significant scale, and the performance of the intersections can be enhanced.

Keywords: delay, deterministic queue analysis, shock wave, passenger loading-unloading

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Authors: Sean Griffiths

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Introduction: This paper examines the expression of ‘objectivity’ in architecture in the context of the post-war rejection of this concept. It aims to re-examine the question in light of the assault on truth characterizing contemporary culture and of the unassailable truth of the climate emergency. The paper analyses the search for objective truth as it was prosecuted in the Modern Movement in the early 20th century, looking at the extent to which this quest was successful in contributing to the development of a radically new, politically-informed architecture and the extent to which its particular interpretation of objectivity, limited that development. The paper studies the influence of the Vienna Circle philosophers Rudolph Carnap and Otto Neurath on the pedagogy of the Bauhaus and the architecture of the Neue Sachlichkeit in Germany. Their logical positivism sought to determine objective truths through empirical analysis, expressed in an austere formal language as part of a ‘scientific world conception’ which would overcome metaphysics and unverifiable mystification. These ideas, and the concurrent prioritizing of measurement as the determinant of environmental quality, became key influences in the socially-driven architecture constructed in the 1920s and 30s by Bauhaus architects in numerous German Cities. Methodology: The paper reviews the history of the early Modern Movement and summarizes accounts of the relationship between the Vienna Circle and the Bauhaus. It looks at key differences in the approaches Neurath and Carnap took to the achievement of their shared philosophical and political aims. It analyses how the adoption of Carnap’s foundationalism influenced the architectural language of modern architecture and compares, through a close reading of the structure of Neurath’s ‘protocol sentences,’ the latter’s alternative approach, speculating on the possibility that its adoption offered a different direction of travel for Modern Architecture. Findings: The paper finds that the adoption of Carnap’s foundationalism, while helping Modern Architecture forge a new visual language, ultimately limited its development and is implicated in its failure to escape the very metaphysics against which it had set itself. It speculates that Neurath’s relational language-based approach to the issue of establishing objectivity has its architectural corollary in the process of revision and renovation that offers new ways an ‘objective’ language of architecture might be developed in a manner that is more responsive to our present-day crisis. Conclusion: The philosophical principles of the Vienna Circle and the architects of the Modern Movement had much in common. Both contributed to radical historical departures which sought to instantiate a world scientific conception in their respective fields, which would attempt to banish mystification and metaphysics and would align itself with socialism. However, in adopting Carnap’s foundationalism as the theoretical basis for the new architecture, Modern Architecture not only failed to escape metaphysics but arguably closed off new avenues of development to itself. The adoption of Neurath’s more open-ended and interactive approach to objectivity offers possibilities for new conceptions of the expression of objectivity in architecture that might be more tailored to the multiple crises we face today.

Keywords: Bauhaus, logical positivism, Neue Sachlichkeit, rationalism, Vienna Circle

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Authors: Abdul Ghaffar Memon, Xiao Hong Zhou, Yunpeng Xing, Ruoyu Wang, Miao He

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Due to deleterious environmental and health effects of the Hg²⁺ ions, various online, detection methods apart from the traditional analytical tools have been developed by researchers. Biosensors especially, label, label-free, colorimetric and optical sensors have advanced with sensitive detection. However, there remains a gap of ultrasensitive quantification as noise interact significantly especially in the AuNP based label-free colorimetry. This study reported an amplification strategy using Exo-III enzyme for target recycling of Hg²⁺ ions in a T-rich hairpin loop metallobase label-free colorimetric nanosensor with an improved sensitivity using unmodified gold nanoparticles (uGNPs) as an indicator. The two T-rich metallobase hairpin loop structures as 5’- CTT TCA TAC ATA GAA AAT GTA TGT TTG -3 (HgS1), and 5’- GGC TTT GAG CGC TAA GAA A TA GCG CTC TTT G -3’ (HgS2) were tested in the study. The thermodynamic properties of HgS1 and HgS2 were calculated using online tools (http://biophysics.idtdna.com/cgi-bin/meltCalculator.cgi). The lab scale synthesized uGNPs were utilized in the analysis. The DNA sequence had T-rich bases on both tails end, which in the presence of Hg²⁺ forms a T-Hg²⁺-T mismatch, promoting the formation of dsDNA. Later, the Exo-III incubation enable the enzyme to cleave stepwise mononucleotides from the 3’ end until the structure become single-stranded. These ssDNA fragments then adsorb on the surface of AuNPs in their presence and protect AuNPs from the induced salt aggregation. The visible change in color from blue (aggregation stage in the absence of Hg²⁺) and pink (dispersion state in the presence of Hg²⁺ and adsorption of ssDNA fragments) can be observed and analyzed through UV spectrometry. An ultrasensitive quantitative nanosensor employing Exo-III assisted target recycling of mercury ions through label-free colorimetry with nanomolar detection using uGNPs have been achieved and is further under the optimization to achieve picomolar range by avoiding the influence of the environmental matrix. The proposed strategy will supplement in the direction of uGNP based ultrasensitive, rapid, onsite, label-free colorimetric detection.

Keywords: colorimetric, Exo-III, gold nanoparticles, Hg²⁺ detection, label-free, signal amplification

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Authors: Arfan Ali, Idrees Ahmad Nasir

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Potato (Solanum tuberosum) is an important cash crop and popular vegetable in Pakistan and throughout the world. Cold storage of potatoes accelerates the conversion of starch into reduced sugars (glucose and fructose). This process causes dry mass and bitter taste in the potatoes that are not acceptable to end consumers. In the current study, the phosphofructokinase B gene was cloned into the pET-30 vector for protein expression and the pCambia-1301 vector for plant expression. Amplification of a 930bp product from an E. coli strain determined the successful isolation of the phosphofructokinase B gene. Restriction digestion using NcoI and BglII along with the amplification of the 930bp product using gene specific primers confirmed the successful cloning of the PfkB gene in both vectors. The protein was expressed as a His-PfkB fusion protein. Western blot analysis confirmed the presence of the 35 Kda PfkB protein when hybridized with anti-His antibodies. The construct Fani-01 was evaluated transiently using a histochemical gus assay. The appearance of blue color in the agroinfiltrated area of potato leaves confirmed the successful expression of construct Fani-01. Further, the area displaying gus expression was evaluated for PfkB expression using ELISA. Moreover, PfkB gene expression evaluated through transient expression determined successful gene expression and highlighted its potential utilization for stable expression in potato to reduce sweetening due to long-term storage.

Keywords: potato, Solanum tuberosum, transformation, PfkB, anti-sweetening

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Authors: Muhammad Sohail Sajid, Qurat-ul-Ain, Zafar Iqbal, Muhammad Nisar Khan, Asma Kausar, Adil Ejaz

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Rickettsiosis, caused by a Spotted Fever Group Rickettsiae (SFGR), is considered as an emerging infectious disease from public and veterinary perspective. The present study reports distribution of SFGR in the host (buffalo and cattle) and vector (ticks) population determined through gene specific amplification through PCR targeting outer membrane protein (ompA). Tick and blood samples were collected using standard protocols through convenient sampling from district Faisalabad. Ticks were dissected to extract salivary glands (SG). Blood and tick SG pools were subjected to DNA extraction and amplification of ompA using PCR. Overall prevalence of SFGR was reported as 21.5% and 33.6 % from blood and ticks, respectively. Hyalomma anatolicum was more prevalent tick associated with SFGR as compared to Rhipicephalus sp. Higher prevalence of SFGR was reported in cattle (25%) population as compared to that of buffalo (17.07%). On seasonal basis, high SFGR prevalence was recorded during spring season (48.1%, 26.32%, 17.76%) as compared to winter (27.9%, 21.43%, 15.38%) in vector and host (cattle and buffalo respectively) population. Sequencing analysis indicated that rickettsial endo-symbionts were associated with ticks of the study area. These results provided baseline information about the prevalence of SFGR in vector and host population.

Keywords: Rickettsia, livestock, polymerase chain reaction, sequencing, ticks, vectors

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Authors: Bernard Moeketsi Hlalele

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Drought is a complicated natural phenomenon that creates significant economic, social, and environmental problems. An analysis of paleoclimatic data indicates that severe and extended droughts are inevitable part of natural climatic circle. This study characterised drought in Lejweleputswa using both Standardised Precipitation Index (SPI) and neural networks (NN) to quantify and predict respectively. Monthly 37-year long time series precipitation data were obtained from online NASA database. Prior to the final analysis, this dataset was checked for outliers using SPSS. Outliers were removed and replaced by Expectation Maximum algorithm from SPSS. This was followed by both homogeneity and stationarity tests to ensure non-spurious results. A non-parametric Mann Kendall's test was used to detect monotonic trends present in the dataset. Two temporal scales SPI-3 and SPI-12 corresponding to agricultural and hydrological drought events showed statistically decreasing trends with p-value = 0.0006 and 4.9 x 10⁻⁷, respectively. The study area has been plagued with severe drought events on SPI-3, while on SPI-12, it showed approximately a 20-year circle. The concluded the analyses with a seasonal analysis that showed no significant trend patterns, and as such NN was used to predict possible SPI-3 for the last season of 2018/2019 and four seasons for 2020. The predicted drought intensities ranged from mild to extreme drought events to come. It is therefore recommended that farmers, agri-business owners, and other relevant stakeholders' resort to drought resistant crops as means of adaption.

Keywords: drought, risk, neural networks, agri-businesses, project, Lejweleputswa

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Authors: R. Ueda

Abstract:

Today global society is seeking resilient partnership in local organizations and individuals, which realizes multi-stakeholders relationship. Although it is proposed by modern global framework of sustainable development, it is conceivable that such affiliation can be found out in the traditional local community in Japan, and that traditional spirit is tacitly sustaining in modern context of disaster mitigation in society and economy. Then this research is aiming to clarify and analyze implication for the global world by actual case studies. Regional and urban resilience is the ability of multi-stakeholders to cooperate flexibly and to adapt in response to changes in the circumstances caused by disasters, but there are various conflicts affecting coordination of disaster relief measures. These conflicts arise not only from a lack of communication and an insufficient network, but also from the difficulty to jointly draw common context from fragmented information. This is because of the weakness of our modern engineering which focuses on maintenance and restoration of individual systems. Here local ‘circles’ holistically includes local community and interacts periodically. Focusing on examples of resilient organizations and wisdom created in communities, what can be seen throughout history is a virtuous cycle where the information and the knowledge are structured, the context to be adapted becomes clear, and an adaptation at a higher level is made possible, by which the collaboration between organizations is deepened and expanded. And the wisdom of a solid and autonomous disaster prevention formed by the historical community called’ Waju’ – an area surrounded by circle embankment to protect the settlement from flood – lives on in government efforts of the coastal industrial island of today. Industrial company there collaborates to create a circle including common evacuation space, road access improvement and infrastructure recovery. These days, people here adopts new interface technology. Large-scale AR- Augmented Reality for more than hundred people is expressing detailed hazard by tsunami and liquefaction. Common experiences of the major disaster space and circle of mutual discussion are enforcing resilience. Collaboration spirit lies in the center of circle. A consistent key point is a virtuous cycle where the information and the knowledge are structured, the context to be adapted becomes clear, and an adaptation at a higher level is made possible, by which the collaboration between organizations is deepened and expanded. This writer believes that both self-governing human organizations and the societal implementation of technical systems are necessary. Infrastructure should be autonomously instituted by associations of companies and other entities in industrial areas for working closely with local governments. To develop advanced disaster prevention and multi-stakeholder collaboration, partnerships among industry, government, academia and citizens are important.

Keywords: industrial recovery, multi-sakeholders, traditional culture, user experience, Waju

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Authors: Sanaz Ahmadzadeh Siyahrood, Arghavan Ebrahimi, Mohammadjavad Mahdavinejad

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Islamic culture was accountable for a plethora of development in astronomy and science in the medieval term, and in geometry likewise. Geometric patterns are reputable in a considerable number of cultures, but in the Islamic culture the patterns have specific features that connect the Islamic faith to mathematics. In Islamic art, three fundamental shapes are generated from the circle shape: triangle, square and hexagon. Originating from their quiddity, each of these geometric shapes has its own specific structure. Even though the geometric patterns were generated from such simple forms as the circle and the square, they can be combined, duplicated, interlaced, and arranged in intricate combinations. So in order to explain geometrical interaction principles between square and equal triangle, in the first definition step, all types of their linear forces individually and in the second step, between them, would be illustrated. In this analysis, some angles will be created from intersection of their directions. All angles are categorized to some groups and the mathematical expressions among them are analyzed. Since the most geometric patterns in Islamic art and architecture are based on the repetition of a single motif, the evaluation results which are obtained from a small portion, is attributable to a large-scale domain while the development of infinitely repeating patterns can represent the unchanging laws. Geometric ornamentation in Islamic art offers the possibility of infinite growth and can accommodate the incorporation of other types of architectural layout as well, so the logic and mathematical relationships which have been obtained from this analysis are applicable in designing some architecture layers and developing the plan design.

Keywords: angle, equal triangle, square, structural hierarchy

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Authors: F. Tahiri, F. Grajçevci

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The cities are coping with permanent demands to extend their residential and economical capacity. The new urban zones are sometimes induced to be developed in more vulnerable environments. This study is aimed to identify and mitigate the seismic hazards in the stage of urban planning for new settlements, including the existing urban environments which initially have not considered the seismic hazard. Seismic microzoning shall study the amplification/attenuation of seismic excitations from the bedrock to the ground surface. Modification of the seismic excitation is governed from the site specific ground conditions, presented on ground surface as mean values of the ratio of maximum accelerations at the surface versus acceleration of subsoil media – presented with dynamic amplification factors (DAF). The values shall be used to create the maps with isolines of DAF and then seismic microzoning with expected maximum mean surface acceleration as a product of DAF with maximum accelerations at bedrock. Development of resonant map shall conglomerate the information’s obtained from seismic microzoning in regard to expected predominant ground periods of seismic excitation and periods of vibrations of designed/built structures. These information’s shall be used as indispensible tool in early stages of urban planning to determine the most optimal zones for construction, the constructive materials, structural systems, range of buildings height, etc. so the resonance of soil media with built structures is avoided. The information’s could be used also for assessment of seismic risk and vulnerability-damageability of existing urban environments.

Keywords: vulnerable environment, mitigation, seismic microzoning, resonant map, urban planning

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Authors: Arūnas Gudinavičius

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The historiography of scholarly journals in Eastern Europe is fragmented, and so far, the development of scholarly journals in Eastern Europe has not been studied from a publishing point of view in the context of scientific communication. There are only a few general articles on the period before World War II; also, there is hardly any systematic and publicly available information about the Soviet period and the situation of scientific communication in Eastern Europe at the end of the XX century and the beginning of the XXI century. There is a lack of research data on scholarly journals in Lithuania. The existing researches focuses mostly on the specific needs of academic institutions. The publication of scientific journals and papers is analyzed as a part of the scientific communication circle. Formal science communication from the point of view that it is the results formed in the course of communication are examined, which are necessarily characterized by long-term access to a large circle of users. Improved model of scientific communication by supplementing the dissemination of research results with formal and informal communication channels is used, according to which the scientific communication system forms the essence of science, where the social, lasting value of science and the dissemination of scientific results to scientists and the public are the most important. The model covers the science communication process from research initiation to journal publication and citation. We are focusing on the publishing and dissemination stages of the model of scientific communication. The paper is to systematize and analyze the various types of scientific journal publishers from 1907 until 2020 as a means of formal documentary communication in the context of all scientific communication. The research analyses the case of a small European country and presents chronological and geographical characteristics of the publication of scientific periodicals, analyzes the publishers of scientific periodicals and their activities, publishing formats, and dissemination methods.

Keywords: scientific communication, scientific periodicals, scientific journals, publishing

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Authors: Rafael Martins Manzano Silva, Jean-Francois Tremong

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Electrification of railway lines allows to increase speed, power, capacity and energetic efficiency of rolling stocks. However, this process of electrification is complex and costly. An electrification project is not just about design of catenary. It also includes installation of structures around electrification, as substation installation, electrical isolation, signalling, telecommunication and civil engineering structures. France has more than 30,000 km of railways, whose only 53% are electrified. The others 47% of railways use diesel locomotive and represent only 10% of the circulation (tons.km). For this reason, a new type of electrification, less expensive than the usual, is requested to enable the modernization of these railways. One solution could be the use of hybrids trains. This technology opens up new opportunities for less expensive infrastructure development such as the partial electrification of railway lines. In a partially electrified railway, the power supply of theses hybrid trains could be made either by the catenary or by the on-board energy storage system (ESS). Thus, the on-board ESS would feed the energetic needs of the train along the non-electrified zones while in electrified zones, the catenary would feed the train and recharge the on-board ESS. This paper’s objective deals with the technical and economic potential identification of partial electrification of railway lines. This study provides different scenarios of electrification by replacing the most expensive places to electrify using on-board ESS. The target is to reduce the cost of new electrification projects, i.e. reduce the cost of electrification infrastructures while not increasing the cost of rolling stocks. In this study, scenarios are constructed in function of the electrification’s cost of each structure. The electrification’s cost varies considerably because of the installation of catenary support in tunnels, bridges and viaducts is much more expensive than in others zones of the railway. These scenarios will be used to describe the power supply system and to choose between the catenary and the on-board energy storage depending on the position of the train on the railway. To identify the influence of each partial electrification scenario in the sizing of the on-board ESS, a model of the railway line and of the rolling stock is developed for a real case. This real case concerns a railway line located in the south of France. The energy consumption and the power demanded at each point of the line for each power supply (catenary or on-board ESS) are provided at the end of the simulation. Finally, the cost of a partial electrification is obtained by adding the civil engineering costs of the zones to be electrified plus the cost of the on-board ESS. The study of the technical and economic potential ends with the identification of the most economically interesting scenario of electrification.

Keywords: electrification, hybrid, railway, storage

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Authors: Huazhen Lin, Ruihua Xu, Zhibin Jiang

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In this real-world case, timetabling the LRT network as a whole is rather challenging for the operator: they are supposed to create a timetable to avoid various route conflicts manually while satisfying a given interval and the number of rolling stocks, but the outcome is not satisfying. Therefore, the operator adopts a computerised timetabling tool, the Train Plan Maker (TPM), to cope with this problem. However, with various constraints in the dual-line network, it is still difficult to find an adequate pairing of turnback time, interval and rolling stocks’ number, which requires extra manual intervention. Aiming at current problems, a one-off model for timetabling is presented in this paper to simplify the procedure of timetabling. Before the timetabling procedure starts, this paper presents how the dual-line system with a ring and several branches is turned into a simpler structure. Then, a non-linear programming model is presented in two stages. In the first stage, the model sets a series of constraints aiming to calculate a proper timing for coordinating two lines by adjusting the turnback time at termini. Then, based on the result of the first stage, the model introduces a series of inequality constraints to avoid various route conflicts. With this model, an analysis is conducted to reveal the relation between the ratio of trains in different directions and the possible minimum interval, observing that the more imbalance the ratio is, the less possible to provide frequent service under such strict constraints.

Keywords: light rail transit (LRT), non-linear programming, railway timetabling, timetable coordination

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Authors: Muhammad SAFDAR, Mehmet Ozaslan, Musarrat Abbas Khan

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Babesiosis is a haemoparasitic disease due to the multiplication of protozoan’s parasite, Babesia ovis in the red blood cells of the host, and contributes numerous economical losses, including sheep and goat ruminants. The early identification and successful treatment of Babesia Ovis spp. belong to the key steps of control and health management of livestock resources. The objective of this study was to construct a polymerase chain reaction (PCR) based method for the detection of Babesia spp. in small ruminants and to determine the risk factors involved in the spreading of babesiosis infections. A total of 100 blood samples were collected from 50 sheep and 50 goats along with different areas of Muzaffargarh, Pakistan, from randomly selected herds. Data on the characteristics of sheep and goats were collected through questionnaires. Of 100 blood samples examined, 18 were positive for Babesia ovis upon microscopic studies, whereas 11 were positive for the presence of Babesia spp. by PCR assay. For the recognition of parasitic DNA, a set of 500bp oligonucleotide was designed by PCR amplification with sequence 18S rRNA gene for B. ovis. The prevalence of babesiosis in small ruminant’s sheep and goat detected by PCR was significantly higher in female animals (28%) than male herds (08%). PCR analysis of the reference samples showed that the detection limit of the PCR assay was 0.01%. Taken together, all data indicated that this PCR assay was a simple, fast, specific detection method for Babesia ovis species in small ruminants compared to other available methods.

Keywords: Babesia ovis, PCR amplification, 18S rRNA, sheep and goat

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Authors: Takamitsu Kodama, Eiji Kawamoto

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Introduction: Ultrasound in emergency room has advantages of safer, faster, repeatable and noninvasive. Especially focused Point-Of-Care Ultrasound (POCUS) is used daily for prompt and accurate diagnoses, for quickly identifying critical and life-threatening conditions. That is why ultrasound has demonstrated its usefulness in emergency medicine. The true value of ultrasound has been once again recognized in recent years. It is thought that all resident physicians working at emergency room should perform an ultrasound scan to interpret signs and symptoms of deteriorating patients in the emergency room. However, a practical education on ultrasound is still in development. To resolve this issue, we established a new educational program using high-fidelity simulators and evaluated the efficacy of this course. Methods: Educational program includes didactic lectures and skill stations in half-day course. Instructor gives a lecture on POCUS such as Rapid Ultrasound in Shock (RUSH) and/or Focused Assessment Transthoracic Echo (FATE) protocol at the beginning of the course. Then, attendees are provided for training of scanning with cooperation of normal simulated patients. In the end, attendees learn how to apply focused POCUS skills at clinical situation using high-fidelity simulators such as SonoSim® (SonoSim, Inc) and SimMan® 3G (Laerdal Medical). Evaluation was conducted through surveillance questionnaires to 19 attendees after two pilot courses. The questionnaires were focused on understanding course concept and satisfaction. Results: All attendees answered the questionnaires. With respect to the degree of understanding, 12 attendees (number of valid responses: 13) scored four or more points out of five points. High-fidelity simulators, especially SonoSim® was highly appreciated to enhance learning how to handle ultrasound at an actual practice site by 11 attendees (number of valid responses: 12). All attendees encouraged colleagues to take this course because the high level of satisfaction was achieved. Discussion: Newly introduced educational course using high-fidelity simulators realizes the circle of learning to deepen the understanding on focused POCUS by gradual stages. SonoSim® can faithfully reproduce scan images with pathologic findings of ultrasound and provide experimental learning for a growth number of beginners such as resident physicians. In addition, valuable education can be provided if it is used combined with SimMan® 3G. Conclusions: Newly introduced educational course using high-fidelity simulators is supposed to be effective and helps in providing better education compared with conventional courses for emergency physicians.

Keywords: point-of-care ultrasound, high-fidelity simulators, education, circle of learning

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Authors: Hanna Faron, Wojciech Marcinkowski, Daniel Prusak

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The aim of this article is to familiarize with the activity of AGH Racing scientific circle, pertaining to the international project -Formula Student, giving the opportunity to young engineers from all around the world to validate their talent and knowledge in the real world conditions, under the pressure of time, and the design requirements. Every year, the team begins the process of building a race car from the formation of human resources. In case of the public sector, to which public universities can be included, the scientific circles represent the structure uniting students with the common interests and level of determination. Due to the scientific nature of the project which simulates the market conditions, they have a chance to verify previously acquired knowledge in practice. High level of the innovation and competitiveness of participating in the project Formula Student teams, requires an intelligent organizational system, which is characterized by a high dynamics. It is connected with the necessity of separation of duties, setting priorities, selecting optimal solutions which is often a compromise between the available technology and a limited budget. Proper selection of the adequate guidelines in the design phase allows an efficient transition to the implementation stage, which is process-oriented implementation of the project. Four dynamic and three static competitions are the main verification and evaluation of year-round work and effort put into the process of building a race car. Acquired feedback flowing during the race is a very important part while monitoring the effectiveness of AGH Racing scientific circle, as well as the main criterion while determining long-term goals and all the necessary improvements in the team.

Keywords: SAE, formula student, race car, public sector, automotive industry

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Authors: Anjali Uday, Yuting Wang, Andres Alfonso Pena Olare

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The Discrete Element Method is a promising approach to modeling microscopic behaviors of granular materials. The quality of the simulations however depends on the model parameters utilized. The present study focuses on calibration and validation of the discrete element parameters for Cuxhaven sand based on the experimental data from triaxial and oedometer tests. A sensitivity analysis was conducted during the sample preparation stage and the shear stage of the triaxial tests. The influence of parameters like rolling resistance, inter-particle friction coefficient, confining pressure and effective modulus were investigated on the void ratio of the sample generated. During the shear stage, the effect of parameters like inter-particle friction coefficient, effective modulus, rolling resistance friction coefficient and normal-to-shear stiffness ratio are examined. The calibration of the parameters is carried out such that the simulations reproduce the macro mechanical characteristics like dilation angle, peak stress, and stiffness. The above-mentioned calibrated parameters are then validated by simulating an oedometer test on the sand. The oedometer test results are in good agreement with experiments, which proves the suitability of the calibrated parameters. In the next step, the calibrated and validated model parameters are applied to forecast the micromechanical behavior including the evolution of contact force chains, buckling of columns of particles, observation of non-coaxiality, and sample inhomogeneity during a simple shear test. The evolution of contact force chains vividly shows the distribution, and alignment of strong contact forces. The changes in coordination number are in good agreement with the volumetric strain exhibited during the simple shear test. The vertical inhomogeneity of void ratios is documented throughout the shearing phase, which shows looser structures in the top and bottom layers. Buckling of columns is not observed due to the small rolling resistance coefficient adopted for simulations. The non-coaxiality of principal stress and strain rate is also well captured. Thus the micromechanical behaviors are well described using the calibrated and validated material parameters.

Keywords: discrete element model, parameter calibration, triaxial test, oedometer test, simple shear test

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Authors: Talal S. Abdullah, Shahin Mehraban, Geraint Lodwig, Nicholas P. Lavery

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The defining property of Interstitial Free (IF) steels is formability, comprehensively measured using the Lankford coefficient (r-value) on uniaxial tensile test data. The contributing factors supporting this feature are grain size, orientation, and elemental additions. The processes that effectively modulate these factors are the casting procedure, hot rolling, and heat treatment. An existing methodology is well-practised in the steel Industry; however, large-scale production and experimentation consume significant proportions of time, money, and material. Introducing small-scale rapid alloy prototyping (RAP) as an alternative process would considerably reduce the drawbacks relative to standard practices. The aim is to finetune the existing fundamental procedures implemented in the industrial plant to adapt to the RAP route. IF material is remelted in the 80-gram coil induction melting (CIM) glovebox. To birth small grains, maximum deformation must be induced onto the cast material during the hot rolling process. The rolled strip must then satisfy the polycrystalline behaviour of the bulk material by displaying a resemblance in microstructure, hardness, and formability to that of the literature and actual plant steel. A successful outcome of this work is that small-scale RAP can achieve target compositions with similar microstructures and statistically consistent mechanical properties which complements and accelerates the development of novel steel grades.

Keywords: rapid alloy prototyping, plastic anisotropy, interstitial free, miniaturised tensile testing, formability

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Authors: Michela Quadrini

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Chord diagrams occur in mathematics, from the study of RNA to knot theory. They are widely used in theory of knots and links for studying the finite type invariants, whereas in molecular biology one important motivation to study chord diagrams is to deal with the problem of RNA structure prediction. An RNA molecule is a linear polymer, referred to as the backbone, that consists of four types of nucleotides. Each nucleotide is represented by a point, whereas each chord of the diagram stands for one interaction for Watson-Crick base pairs between two nonconsecutive nucleotides. A chord diagram is an oriented circle with a set of n pairs of distinct points, considered up to orientation preserving diffeomorphisms of the circle. A linear chord diagram (LCD) is a special kind of graph obtained cutting the oriented circle of a chord diagram. It consists of a line segment, called its backbone, to which are attached a number of chords with distinct endpoints. There is a natural fattening on any linear chord diagram; the backbone lies on the real axis, while all the chords are in the upper half-plane. Each linear chord diagram has a natural genus of its associated surface. To each chord diagram and linear chord diagram, it is possible to associate the intersection graph. It consists of a graph whose vertices correspond to the chords of the diagram, whereas the chord intersections are represented by a connection between the vertices. Such intersection graph carries a lot of information about the diagram. Our goal is to define an LCD equivalence class in terms of identity of intersection graphs, from which many chord diagram invariants depend. For studying these invariants, we introduce a new representation of Linear Chord Diagrams based on a set of appropriate topological operators that permits to model LCD in terms of the relations among chords. Such set is composed of: crossing, nesting, and concatenations. The crossing operator is able to generate the whole space of linear chord diagrams, and a multiple context free grammar able to uniquely generate each LDC starting from a linear chord diagram adding a chord for each production of the grammar is defined. In other words, it allows to associate a unique algebraic term to each linear chord diagram, while the remaining operators allow to rewrite the term throughout a set of appropriate rewriting rules. Such rules define an LCD equivalence class in terms of the identity of intersection graphs. Starting from a modelled RNA molecule and the linear chord, some authors proposed a topological classification and folding. Our LCD equivalence class could contribute to the RNA folding problem leading to the definition of an algorithm that calculates the free energy of the molecule more accurately respect to the existing ones. Such LCD equivalence class could be useful to obtain a more accurate estimate of link between the crossing number and the topological genus and to study the relation among other invariants.

Keywords: chord diagrams, linear chord diagram, equivalence class, topological language

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Authors: Matej Komanec, Tomas Nemecek, Dmytro Suslov, Petr Chvojka, Stanislav Zvanovec

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Nonlinear phenomena in the near- and mid-infrared region are attracting scientific attention mainly due to the supercontinuum generation possibilities and subsequent utilizations for ultra-wideband applications like e.g. absorption spectroscopy or optical coherence tomography. Thulium-based fiber lasers provide access to high-power ultrashort pump pulses in the vicinity of 2000 nm, which can be easily exploited for various nonlinear applications. The paper presents a simulation and experimental study of a pulsed thulium laser based for near-infrared (NIR) and mid-infrared (MIR) nonlinear applications in specialty optical fibers. In the first part of the paper the thulium laser is discussed. The thulium laser is based on a gain-switched seed-laser and a series of amplification stages for obtaining output peak powers in the order of kilowatts for pulses shorter than 200 ps in full-width at half-maximum. The pulsed thulium laser is first studied in a simulation software, focusing on seed-laser properties. Afterward, a pre-amplification thulium-based stage is discussed, with the focus of low-noise signal amplification, high signal gain and eliminating pulse distortions during pulse propagation in the gain medium. Following the pre-amplification stage a second gain stage is evaluated with incorporating a thulium-fiber of shorter length with increased rare-earth dopant ratio. Last a power-booster stage is analyzed, where the peak power of kilowatts should be achieved. Examples of analytical study are further validated by the experimental campaign. The simulation model is further corrected based on real components – parameters such as real insertion-losses, cross-talks, polarization dependencies, etc. are included. The second part of the paper evaluates the utilization of nonlinear phenomena, their specific features at the vicinity of 2000 nm, compared to e.g. 1550 nm, and presents supercontinuum modelling, based on the thulium laser pulsed output. Supercontinuum generation simulation is performed and provides reasonably accurate results, once fiber dispersion profile is precisely defined and fiber nonlinearity is known, furthermore input pulse shape and peak power must be known, which is assured thanks to the experimental measurement of the studied thulium pulsed laser. The supercontinuum simulation model is put in relation to designed and characterized specialty optical fibers, which are discussed in the third part of the paper. The focus is placed on silica and mainly on non-silica fibers (fluoride, chalcogenide, lead-silicate) in their conventional, microstructured or tapered variants. Parameters such as dispersion profile and nonlinearity of exploited fibers were characterized either with an accurate model, developed in COMSOL software or by direct experimental measurement to achieve even higher precision. The paper then combines all three studied topics and presents a possible application of such a thulium pulsed laser system working with specialty optical fibers.

Keywords: nonlinear phenomena, specialty optical fibers, supercontinuum generation, thulium laser

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