Search results for: laser-plasma interactions

Authors: Fadilah Aleanizy

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Colicins are a family of bacterial toxins that kill Escherichia coli and other closely related species. The mode of action of colicins involves binding to an outer membrane receptor and translocation across the cell envelope, leading to cytotoxicity through specific targets. The mechanism of colicin cytotoxicity includes a non-specific endonuclease activity or depolarization of the cytoplasmic membrane by pore-forming activity. For Group A colicins, translocation requires an interaction between the N-terminal domain of the colicin and a series of membrane- bound and periplasmic proteins known as the Tol system (TolB, TolR, TolA, TolQ, and Pal and the active domain must be translocated through the outer membranes. Protein-protein interactions are intrinsic to virtually every cellular process. The transient protein-protein interactions of the colicin include the interaction with much more complicated assemblies during colicin translocation across the cellular membrane to its target. The potassium release assay detects variation in the K+ content of bacterial cells (K+in). This assays is used to measure the effect of pore-forming colicins such as ColA on an indicator organism by measuring the changes of the K+ concentration in the external medium (K+out ) that are caused by cell killing with a K+ selective electrode. One of the goals of this work is to employ a quantifiable in-vivo method to spot which Tol protein are more implicated in the interaction with colicin A as it is translocated to its target.

Keywords: K+ efflux, Colicin A, Tol-proteins, E. coli

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Authors: Suelane Garcia Fontes, Silvio Luiz Stanzani, Pedro L. Pizzigatti Corrła Ronaldo G. Morato

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Environmental changes and major natural disasters are most prevalent in the world due to the damage that humanity has caused to nature and these damages directly affect the lives of animals. Thus, the study of animal behavior and their interactions with the environment can provide knowledge that guides researchers and public agencies in preservation and conservation actions. Exploratory analysis of animal movement can determine the patterns of animal behavior and with technological advances the ability of animals to be tracked and, consequently, behavioral studies have been expanded. There is a lot of research on animal movement and behavior, but we note that a proposal that combines resources and allows for exploratory analysis of animal movement and provide statistical measures on individual animal behavior and its interaction with the environment is missing. The contribution of this paper is to present the framework AniMoveMineR, a unified solution that aggregates trajectory analysis and data mining techniques to explore animal movement data and provide a first step in responding questions about the animal individual behavior and their interactions with other animals over time and space. We evaluated the framework through the use of monitored jaguar data in the city of Miranda Pantanal, Brazil, in order to verify if the use of AniMoveMineR allows to identify the interaction level between these jaguars. The results were positive and provided indications about the individual behavior of jaguars and about which jaguars have the highest or lowest correlation.

Keywords: data mining, data science, trajectory, animal behavior

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Authors: Niall J. English

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Under- and post-graduate training can benefit from a more active learning style, and most particularly so in engineering. Despite this, outreach to young children in primary and secondary schools is less-developed in terms of its documented effectiveness, especially given new emphasis placed within the third level and advanced research program’s on Education and Public Engagement (EPE). Bearing this in mind, outreach and school visits form the basis to ascertain how active learning, careers stimulus and EPE initiatives for young children can inform the university sector, helping to improve future engineering-teaching standards, and enhancing both quality and practicalities of the teaching-and-learning experience. Indeed, engineering-education EPE/outreach work has been demonstrated to lead to several tangible benefits and improved outcomes, such as greater engagement and interest with science/engineering for school-children, careers awareness, enabling teachers with strong contributions to technical knowledge of engineering subjects, and providing development of general professional skills for engineering, e.g., communication and teamwork. This intervention involved active learning in ‘buzz’ groups for young children of concepts in gas engineering, observing their peer interactions to develop university-level lessons on activity learning. In addition, at the secondary level, careers-outreach efforts have led to statistical determinations of motivations towards engineering education and training, which aids in the redesign of engineering curricula for more active learning.

Keywords: outreach, education and public engagement, careers, peer interactions

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Authors: Rachelle M. Johnson, Jenna E. Finch

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Motivation, persistence, and learning disability status are all associated with academic performance, but to the author's knowledge, little research has been done on how these variables interact with one another and how that interaction looks different within children with and without learning disabilities. The present study's goal was to examine the role motivation and persistence play in the academic success of children with learning disabilities and how these variables interact. Measurements were made using surveys and direct cognitive assessments on each child. Analyses were run on student's scores in motivation, persistence, and ability to learn compared to other fifth grade students. In this study, learning ability was intended as a proxy for learning disabilities (LDs). This study included a nationally representative sample of over 8,000 fifth-grade children from across the United States. Multiple interactions were found among these variables of motivation, persistence, and motivation as they relate to academic achievement. The major finding of the study was the significant role motivation played in academic achievement. This study shows the importance of measuring the within-group. One key finding was that motivation was associated with academic success and was moderated by the other variables. The interaction results were different for math and reading outcomes, suggesting that reading and math success are different and should be addressed differently. This study shows the importance of measuring the within-group differences in levels of motivation to better understand the academic success of children with and without learning disabilities. This study's findings call for further investigation into motivation and the possible need for motivational intervention for students, especially those with learning disabilities

Keywords: academic achievement, learning disabilities, motivation, persistence

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Authors: Mulaudzi Tshimbiluni Annah

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South African city centres depict dynamic urban spaces which reflect complex interactions between multiple actors: the state, formal businesses and informal street traders, with each competing for territorial claims and spatial dominance. The objective of the study is exploring how space is contested, negotiated and occupied between formal and informal sectors, while consequently trying to understand the implication that this has on spatial planning and spatial justice. Through a case-study analysis of the eThekwini city centre, this research examines spatial arrangement, coexistence and conflicts that shape the urban fabric. The study employs spatial justice as a theoretical lens to highlight the inequalities that are embedded within urban planning policies and how street traders are resilient to the harsh restrictive spatial frameworks. Limited evidence is known about how urban planning frameworks can integrate informal street traders in city centres and recognize them as legitimate stakeholders. The study investigates how spatial planning frameworks can be reimagined to promote spatial justice and further facilitate coexistence between formal and informal stakeholders in city centres. Primary data collection included interviews with key stakeholders, while NVivo software was used to analyse the interview data. Observations were conducted through transect walks, which allowed for insight into the spatial dynamics and daily interactions. Visual representations were depicted using GIS mapping to show areas of contestation as well as areas where formal and informal activities intersect. Furthermore, secondary data from literature enabled a comparative analysis of similar case studies through precedent studies. The study revealed continuous contestation by formal businesses and the state, who are for the most part often prioritized by planning frameworks while street traders are often marginalized regardless of their contribution towards economic development. This study therefore proposes strategies for spatial planning that supports an integrative urban framework which ensures equitable access and also a reduction of the marginalization of street traders within urban spaces. This study aims to contribute to understanding urban coexistence and further advocates for spatial planning approaches that integrates informal street traders as legitimate actors in the urban landscape while fostering spatial justice within city centres.

Keywords: coexistence, contestation, integration, spatial justice, spatial planning, street traders

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Authors: S. M. Jogdand, D. D. Jagtap, N. R. Dalal

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Sweet orange (Citrus sinensis Osbeck) is one of the most important commercially cultivated fruit crop in India. It stands on second position amongst citrus group after mandarin. Irrigation and fertigation are vital importance of sweet orange orchard and considered to be the most critical cultural operations. The soil acts as the reservoir of water and applied nutrients, the interaction between irrigation and fertigation leads to the ultimate quality and production of fruits. The increasing cost of fertilizers and scarcity of irrigation water forced the farmers for optimum use of irrigation and nutrients. The experiment was conducted with object to find out irrigation and nutrient interaction in sweet orange to optimize the use of both the factors. The experiment was conducted in medium to deep soil. The irrigation level I3,drip irrigation at 90% ER (effective rainfall) and fertigation level F3 80% RDF (recommended dose of fertilizer) recorded significantly maximum plant height, plant spread, canopy volume, number of fruits, weight of fruit, fruit yield kg/plant and t/ha followed by F2 , fertigation with 70% RDF. The interaction effect of irrigation and fertigation on growth was also significant and the maximum plant height, E-W spread, N-S spread, canopy volume, highest number of fruits, weight of fruit and yield kg/plant and t/ha was recorded in T9 i.e. I3F3 drip irrigation at 90% ER and fertigation with 80% of RDF followed by I3F2 drip irrigation at 90% ER and fertigation with 70% of RDF.

Keywords: sweet orange, fertigation, irrigation, interactions

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Authors: Isaac Owusu Asante, Yushi Jiang, Hailin Tao

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Live streaming marketing, the new electronic commerce element, became an optional marketing channel following the COVID-19 pandemic. Many sellers have leveraged the features presented by live streaming to increase sales. Studies on live streaming have focused on gaming and consumers’ loyalty to brands through live streaming, using interview questionnaires. This study, however, was conducted to measure real-time observable interactions between consumers and sellers. Based on the affordance theory, this study conceptualized constructs representing the interactive features and examined how they drive consumers’ purchase willingness during live streaming sessions using 1238 datasets from Amazon Live, following the manual observation of transaction records. Using structural equation modeling, the ordinary least square regression suggests that live viewers, new followers, live chats, and likes positively affect purchase willingness. The Sobel and Monte Carlo tests show that new followers, live chats, and likes significantly mediate the relationship between live viewers and purchase willingness. The study introduces a new way of measuring interactions in live streaming commerce and proposes a way to manually gather data on consumer behaviors in live streaming platforms when the application programming interface (API) of such platforms does not support data mining algorithms.

Keywords: livestreaming marketing, live chats, live viewers, likes, new followers, purchase willingness

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Authors: Omaimah Algohary

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Kaolin is one of the principle intestinal adsorbents, has traditionally been used internally in the treatment of various enteric disorders, colitis, enteritis, dysentery, and diarrhea associated with food and alkaloidal poisoning and in traveler’s diarrhea. It binds to and traps bacteria and its toxins and gases in the gut. It also binds to water in the gut, which helps to make the stools firmer, hence giving symptomatic relief. Metronidazole is a synthetic antibacterial agent that is used primarily in the treatment of various anaerobic infections such as intra-abdominal infections, antiprotozoal, and as amebicidal. The need for safe, therapeutically effective antidiarrheal combination continuously lead to effective treatment. Metronidazol used for treatment of anaerobic bacteria and kaolin , when administered simultaneously, Metronidazole–Kaolin interactions have been reported by FDA but not studied. This project is the first to study the effect of Metronidazole–Kaolin interactions on the antimicrobial activity of metronidazole. Agar diffusion method performed to test the antimicrobial activity of metronidazole–kaolin antidiarrheal combination from aqueous solutions at an in-vivo simulated pHs conditions that obtained at 37+0.5 °C on Helicobacter pylori as anaerobic bacteria and E.coli as aerobic bacteria and used as a control for the technique. The antimicrobial activity of metronidazole combination as 1:1 and 1:2 with kaolin was abolished in acidic media as no zones of inhibition shown compared to only metronidazole that used as a control. In alkaline media metronidazole combination as 1:1 and 1:2 with kaolin showed diminutive activity compared to the control. These results proved that the kaolin adsorb metronidazole and abolish its antimicrobial activity and such combination should be avoided.

Keywords: kaolin, metronidazole, interaction, Helicobacter pylori. E. coli, antimicrobial activity

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Authors: Friday Godwin Okibe, Elaoyi David Paul, Oladayo Thomas Ojekunle

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In this study, Nitrogen and Phosphorous co-doped Zinc Oxide (NPZ) was prepared through a solvent-free reaction. The NPZ was characterized by Scanning Electron Microscopy (SEM) and Fourier Transform Infrared (FTIR) spectroscopy. The photocatalytic activity of the catalyst was investigated by monitoring the degradation of para-nitrophenol (PNP) under visible light irradiation and the process was optimized using factorial design of experiment. The factors investigated were initial concentration of para-nitrophenol, catalyst loading, pH and irradiation time. The characterization results revealed a successful doping of ZnO by nitrogen and phosphorus and an improvement in the surface morphology of the catalyst. The photo-catalyst exhibited improved photocatalytic activity under visible light by 73.8%. The statistical analysis of the optimization result showed that the model terms were significant at 95% confidence level. Interactions plots revealed that irradiation time was the most significant factor affecting the degradation process. The cube plots of the interactions of the variables showed that an optimum degradation efficiency of 66.9% was achieved at 10mg/L initial PNP concentration, 0.5g catalyst loading, pH 7 and 150 minutes irradiation time.

Keywords: nitrogen and phosphorous co-doped Zno, p-nitrophenol, photocatalytic degradation, optimization, factorial design of experimental

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Authors: Rizwan Latif, Syed Adnan Qasim, Muzaffar Ali

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Fuel direct injection represents one of the key aspects in the development of the diesel engines, the idea of controlling the auto-ignition and the consequent combustion of a liquid spray injected in a reacting atmosphere during a time scale of few milliseconds has been a challenging task for the engine community and pushed forward to a massive research in this field. The quality of the air-fuel mixture defines the combustion efficiency, and therefore the engine efficiency. A droplet interaction in dense as well as thin portion of the spray receives equal importance as other parameters in spray structure. Usually, these are modeled along with breakup process and analyzed alike. In this paper, droplet interaction is modeled and simulated for high torque low speed scenario. Droplet interactions may further be subdivided into droplet collision and coalescence, spray wall impingement, droplets drag, etc. Droplet collisions may occur in almost all spray applications, but especially in diesel like conditions such as high pressure sprays as utilized in combustion engines. These collisions have a strong influence on the mean droplet size and its spatial distribution and can, therefore, affect sub-processes of spray combustion such as mass, momentum and energy transfer between gas and droplets. Similarly, for high-pressure injection systems spray wall impingement is an inherent sub-process of mixture formation. However, its influence on combustion is in-explicit.

Keywords: droplet collision, coalescence, low speed, diesel fuel

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Authors: Dani Sukkar, Ali Kanso, Philippe Laval-Gilly, Jairo Falla-Angel

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The honeybees' immune system is challenged by different risk factors that induce various responses. However, complex scenarios where bees are exposed to different pesticides simultaneously with immune activation are not well evaluated. The Toll pathway is one of the main signaling pathways studied in invertebrate immune responses, and it is a good indicator of the effect of such complex interactions in addition to key signaling elements of other pathways like Relish of the immune deficiency (IMD) pathway or Eater, the phagocytosis receptor or vitellogenin levels. Honeybee hemocytes extracted from 5th instar larvae were exposed to imidacloprid and/or amitraz with or without the presence of the zymosan a as an immune activator. The gene expression of multiple immune related genes were studied, including spaetzle, Toll, myD88, relish, eater and vitellogenin, by real-time polymerase chain reaction after RNA extraction. The results demonstrated that the Toll pathway is mainly affected by the pesticides; imidacloprid and amitraz, especially by their different combinations. Furthermore, immune activation by zymosan A, a fungal cell-wall component, acts to mitigate to some extent the effect of pesticides on the different levels of the Toll pathway. In addition, imidacloprid, amitraz, and zymosan A have complex and context-specific interactions depending on the levels of immune activation and the pathway evaluated affecting immune-gene expression differently.

Keywords: toll pathway, immune modulation, β-glucan, imidacloprid, amitraz, honeybees, immune genes

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Authors: Katherine Karayianis

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Children with Attention Deficit Hyperactivity Disorder (ADHD) have trouble learning in traditional classrooms. These children miss out on important developmental opportunities in school, which leads to challenges starting in early childhood, and these problems persist throughout their adult lives. Despite receiving supplemental support in school, children with ADHD still perform below their non-ADHD peers. Thus, there is a great need to find better ways of facilitating learning in children with ADHD. Evidence has shown that children with ADHD learn best through interactive engagement, but this is not always possible in schools, given classroom restraints and the large student-to-teacher ratio. Redesigning classrooms may not be feasible, so informal learning opportunities provide a possible alternative. One popular informal learning opportunity is educational TV shows like Sesame Street. These types of educational shows can teach children foundational skills taught in pre-K and early elementary school. One downside to these shows is the lack of interactive dialogue between the TV characters and the child viewers. Pseudo-interaction is often deployed, but the benefits are limited if the characters can neither understand nor contingently respond to the child. AI technology has become extremely advanced and is now popular in many electronic devices that both children and adults have access to. AI has been successfully used to create interactive dialogue in children’s educational TV shows, and results show that this enhances children’s learning and engagement, especially when children perceive the character as a reliable teacher. It is likely that children with ADHD, whose minds may otherwise wander, may especially benefit from this type of interactive technology, possibly to a greater extent depending on their perception of the animated dialogic agent. To investigate this issue, I have begun examining the moderating role of inattention among children’s learning from an educational TV show with different types of dialogic interactions. Preliminary results have shown that when character interactions are neither immediate nor accurate, children who are more easily distracted will have greater difficulty learning from the show, but contingent interactions with a TV character seem to buffer these negative effects of distractibility by keeping the child engaged. To extend this line of work, the moderating role of the child’s perception of the dialogic agent as a reliable teacher will be examined in the association between children’s attention and the type of dialogic interaction in the TV show. As such, the current study will investigate this moderated moderation.

Keywords: attention, dialogic TV, informal learning, educational TV, perception of teacher

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Authors: Kumbharkhane Ashok

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The time domain dielectric relaxation spectroscopy (TDRS) probes the interaction of a macroscopic sample with a time-dependent electrical field. The resulting complex permittivity spectrum, characterizes amplitude (voltage) and time scale of the charge-density fluctuations within the sample. These fluctuations may arise from the reorientation of the permanent dipole moments of individual molecules or from the rotation of dipolar moieties in flexible molecules, like polymers. The time scale of these fluctuations depends on the sample and its relative relaxation mechanism. Relaxation times range from some picoseconds in low viscosity liquids to hours in glasses, Therefore the DRS technique covers an extensive dynamical process, its corresponding frequency range from 10-4 Hz to 1012 Hz. This inherent ability to monitor the cooperative motion of molecular ensemble distinguishes dielectric relaxation from methods like NMR or Raman spectroscopy which yield information on the motions of individual molecules. An experimental set up for Time Domain Reflectometry (TDR) technique from 10 MHz to 30 GHz has been developed for the aqueous solutions. This technique has been very simple and covers a wide band of frequencies in the single measurement. Dielectric Relaxation Spectroscopy is especially sensitive to intermolecular interactions. The complex permittivity spectra of aqueous solutions have been fitted using Cole-Davidson (CD) model to determine static dielectric constants and relaxation times for entire concentrations. The heterogeneous molecular interactions in aqueous solutions have been discussed through Kirkwood correlation factor and excess properties.

Keywords: liquid, aqueous solutions, time domain reflectometry

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Authors: John Bankier

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Development of academic English occurs not only in communities of practice but also within wider social networks, referred to by Zappa-Hollman and Duff as individual networks of practice. Such networks may exist whether students are developing academic English in English-dominant contexts or in contexts in which English is not a majority language. As yet, little research has examined how newcomers to universities interact with a variety of social ties in such networks to receive academic and emotional support as they develop the academic English necessary to succeed in local and global academia. The one-year ethnographic study described in this presentation followed five Japanese university students enrolled on an academic English program in their home country. We graphically represent participants’ individual networks of practice related to academic English and display the role of interaction in these networks to socialization. Specific examples of academic practices will be linked to specific instances of social interaction. Interaction supportive of the development of academic practices often occurred during unplanned interactions outside the classroom and among small groups of close friends who were connected to each other in more than one way, such as those taking multiple classes together. These interactions occurred in study spaces, in hallways between class periods, at lunchtimes, and online. However, constraints such as differing accommodation arrangements, class scheduling and the hierarchical levelling of English classes by test scores discouraged some participants both from forming strong ties related to English and from interacting with existing ties. The presentation will briefly describe ways in which teachers in all contexts can maximise interaction outside the classroom.

Keywords: academic, english, practice, network

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Authors: Zakia Belhadj, Bing He, Hua Zhang, Xueqing Wang, Wenbing Dai, Qiang Zhang

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Mononuclear phagocyte system (MPS) forms an abominable obstacle hampering the tumor delivery efficiency of nanoparticles. Passively targeted nanocarriers have received clinical approval over the past 20 years. However, none of the actively targeted nanocarriers have entered clinical trials. Thus it is important to endue effective targeting ability to actively targeted approaches by overcoming biological barriers to nanoparticle drug delivery. Here, it presents that an Esomeprazole-based preconditioning strategy for regulating nanocarrier-MPS interaction to substantially prolong circulation time and enhance tumor targeting of nanoparticles. In vitro, the clinically approved proton pump inhibitor Esomeprazole “ESO” was demonstrated to reduce interactions between macrophages and subsequently injected targeted vesicles by interfering with their lysosomal trafficking. Of note, in vivo studies demonstrated that ESO pretreatment greatly decreased the liver and spleen uptake of c(RGDm7)-modified vesicles, highly enhanced their tumor accumulation, thereby provided superior therapeutic efficacy of c(RGDm7)-modified vesicles co-loaded with Doxorubicin (DOX) and Gefitinib (GE). This MPS-preconditioning strategy using ESO provides deeper insights into regulating nanoparticles interaction with the phagocytic system and enhancing their cancer cells' accessibility for anticancer therapy.

Keywords: esomeprazole (ESO), mononuclear phagocyte system (MPS), preconditioning strategy, targeted lipid vesicles

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Authors: Zeinab Yazdanfar, Dilan Robert, Daniel Lester, S. Setunge

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Scour has been identified as the most common threat to bridge stability worldwide. Traditionally, scour around bridge piers is calculated using the empirical approaches that have considerable limitations and are difficult to generalize. The multi-physic nature of scouring which involves turbulent flow, soil mechanics and solid-fluid interactions cannot be captured by simple empirical equations developed based on limited laboratory data. These limitations can be overcome by direct numerical modeling of coupled hydro-mechanical scour process that provides a robust prediction of bridge scour and valuable insights into the scour process. Several numerical models have been proposed in the literature for bridge scour estimation including Eulerian flow models and coupled Euler-Lagrange models incorporating an empirical sediment transport description. However, the contact forces between particles and the flow-particle interaction haven’t been taken into consideration. Incorporating collisional and frictional forces between soil particles as well as the effect of flow-driven forces on particles will facilitate accurate modeling of the complex nature of scour. In this study, a coupled Computational Fluid Dynamics and Discrete Element Model (CFD-DEM) has been developed to simulate the scour process that directly models the hydro-mechanical interactions between the sediment particles and the flowing water. This approach obviates the need for an empirical description as the fundamental fluid-particle, and particle-particle interactions are fully resolved. The sediment bed is simulated as a dense pack of particles and the frictional and collisional forces between particles are calculated, whilst the turbulent fluid flow is modeled using a Reynolds Averaged Navier Stocks (RANS) approach. The CFD-DEM model is validated against experimental data in order to assess the reliability of the CFD-DEM model. The modeling results reveal the criticality of particle impact on the assessment of scour depth which, to the authors’ best knowledge, hasn’t been considered in previous studies. The results of this study open new perspectives to the scour depth and time assessment which is the key to manage the failure risk of bridge infrastructures.

Keywords: bridge scour, discrete element method, CFD-DEM model, multi-phase model

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Authors: Keaghan Brown

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The prioritization of drug resistance mutations impacting protein folding or protein-drug and protein-DNA interactions within macromolecular systems is critical to the success of treatment regimens. With a continual increase in computational tools to assess these impacts, the need for scalability and reproducibility became an essential component of computational analysis and experimental research. Here it introduce a bioinformatics pipeline that combines several structural analysis tools in a simplified workflow, by optimizing the present computational hardware and software to automatically ease the flow of data transformations. Utilizing preestablished software tools, it was possible to develop a pipeline with a set of pre-defined functions that will automate mutation introduction into the HIV-1 Integrase protein structure, calculate the gain and loss of polar interactions and calculate the change in energy of protein fold. Additionally, an automated molecular dynamics analysis was implemented which reduces the constant need for user input and output management. The resulting pipeline, Automated Mutation Introduction and Analysis (AMIA) is an open source set of scripts designed to introduce and analyse the effects of mutations on the static protein structure as well as the results of the multi-conformational states from molecular dynamic simulations. The workflow allows the user to visualize all outputs in a user friendly manner thereby successfully enabling the prioritization of variant systems for experimental validation.

Keywords: automated workflow, variant prioritization, drug resistance, HIV Integrase

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Authors: Piotr J. Balwierz, Mikhail Pachkov, Phil Arnold, Andreas J. Gruber, Mihaela Zavolan, Erik van Nimwegen

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Understanding the key players and interactions in the regulatory networks that control gene expression and chromatin state across different cell types and tissues in metazoans remains one of the central challenges in systems biology. Our laboratory has pioneered a number of methods for automatically inferring core gene regulatory networks directly from high-throughput data by modeling gene expression (RNA-seq) and chromatin state (ChIP-seq) measurements in terms of genome-wide computational predictions of regulatory sites for hundreds of transcription factors and micro-RNAs. These methods have now been completely automated in an integrated webserver called ISMARA that allows researchers to analyze their own data by simply uploading RNA-seq or ChIP-seq data sets and provides results in an integrated web interface as well as in downloadable flat form. For any data set, ISMARA infers the key regulators in the system, their activities across the input samples, the genes and pathways they target, and the core interactions between the regulators. We believe that by empowering experimental researchers to apply cutting-edge computational systems biology tools to their data in a completely automated manner, ISMARA can play an important role in developing our understanding of regulatory networks across metazoans.

Keywords: gene expression analysis, high-throughput sequencing analysis, transcription factor activity, transcription regulation

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Authors: Agnieszka Krzemińska, Katarzyna Świderek, Vicente Molinier, Piotr Paneth

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In order to understand in details the interactions between ligands and the enzyme isotope effects were studied between clinically used drugs that bind in the active site of Human Immunodeficiency Virus Reverse Transcriptase, HIV-1 RT, as well as triazole-based inhibitor that binds in the allosteric pocket of this enzyme. The magnitudes and origins of the resulting binding isotope effects were analyzed. Subsequently, binding isotope effect of the same triazole-based inhibitor bound in the active site were analyzed and compared. Together, these results show differences in binding origins in two sites of the enzyme and allow to analyze binding mode and place of newly synthesized inhibitors. Typical protocol is described below on the example of triazole ligand in the allosteric pocket. Triazole was docked into allosteric cavity of HIV-1 RT with Glide using extra-precision mode as implemented in Schroedinger software. The structure of HIV-1 RT was obtained from Protein Data Bank as structure of PDB ID 2RKI. The pKa for titratable amino acids was calculated using PROPKA software, and in order to neutralize the system 15 Cl- were added using tLEaP package implemented in AMBERTools ver.1.5. Also N-terminals and C-terminals were build using tLEaP. The system was placed in 144x160x144Å3 orthorhombic box of water molecules using NAMD program. Missing parameters for triazole were obtained at the AM1 level using Antechamber software implemented in AMBERTools. The energy minimizations were carried out by means of a conjugate gradient algorithm using NAMD. Then system was heated from 0 to 300 K with temperature increment 0.001 K. Subsequently 2 ns Langevin−Verlet (NVT) MM MD simulation with AMBER force field implemented in NAMD was carried out. Periodic Boundary Conditions and cut-offs for the nonbonding interactions, range radius from 14.5 to 16 Å, are used. After 2 ns relaxation 200 ps of QM/MM MD at 300 K were simulated. The triazole was treated quantum mechanically at the AM1 level, protein was described using AMBER and water molecules were described using TIP3P, as implemented in fDynamo library. Molecules 20 Å apart from the triazole were kept frozen, with cut-offs established on range radius from 14.5 to 16 Å. In order to describe interactions between triazole and RT free energy of binding using Free Energy Perturbation method was done. The change in frequencies from ligand in solution to ligand bounded in enzyme was used to calculate binding isotope effects.

Keywords: binding isotope effects, molecular dynamics, HIV, reverse transcriptase

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Authors: Govinda Pathak

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In modern agriculture, the sustainable enhancement of crop productivity while minimizing environmental impacts remains a paramount challenge. Plant Growth Promoting Rhizobacteria (PGPR) have emerged as a promising solution to address this challenge. The rhizosphere, the dynamic interface between plant roots and soil, hosts intricate microbial interactions crucial for plant health and nutrient acquisition. PGPR, a subset of rhizospheric microorganisms, exhibit multifaceted beneficial effects on plants. Their abilities to stimulate growth, confer stress tolerance, enhance nutrient availability, and suppress pathogens make them invaluable contributors to sustainable agriculture. This work examines the pivotal role of free living nitrogen fixer in optimizing agricultural practices. We delve into the intricate mechanisms underlying PGPR-mediated plant-microbe interactions, encompassing quorum sensing, root exudate modulation, and signaling molecule exchange. Furthermore, we explore the diverse strategies employed by PGPR to enhance plant resilience against abiotic stresses such as drought, salinity, and metal toxicity. Additionally, we highlight the role of PGPR in augmenting nutrient acquisition and soil fertility through mechanisms such as nitrogen fixation, phosphorus solubilization, and mineral mobilization. Furthermore, we discuss the potential of PGPR in minimizing the reliance on chemical fertilizers and pesticides, thereby contributing to environmentally friendly agriculture. However, harnessing the full potential of PGPR requires a comprehensive understanding of their interactions with host plants and the surrounding microbial community. We also address challenges associated with PGPR application, including formulation, compatibility, and field efficacy. As the quest for sustainable agriculture intensifies, harnessing the remarkable attributes of PGPR offers a holistic approach to propel agricultural productivity while maintaining ecological balance. This work underscores the promising prospect of free living nitrogen fixer as a panacea for addressing critical agricultural challenges regarding chemical urea in an era of sustainable and resilient food production.

Keywords: PGPR, nitrogen fixer, quorum sensing, Rhizobacteria, pesticides

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Authors: Ömer Tamer, Davut Avcı, Yusuf Atalay

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Novel picolinate complex of manganese(II) ion, [Mn(pic)2] [pic: picolinate or 2-pyridinecarboxylate], was prepared and fully characterized by single crystal X-ray structure determination. The manganese(II) complex was characterized by FT-IR, FT-Raman and UV–Vis spectroscopic techniques. The C=O, C=N and C=C stretching vibrations were found to be strong and simultaneously active in IR and spectra. In order to support these experimental techniques, density functional theory (DFT) calculations were performed at Gaussian 09W. Although the supramolecular interactions have some influences on the molecular geometry in solid state phase, the calculated data show that the predicted geometries can reproduce the structural parameters. The molecular modeling and calculations of IR, Raman and UV-vis spectra were performed by using DFT levels. Nonlinear optical (NLO) properties of synthesized complex were evaluated by the determining of dipole moment (µ), polarizability (α) and hyperpolarizability (β). Obtained results demonstrated that the manganese(II) complex is a good candidate for NLO material. Stability of the molecule arising from hyperconjugative interactions and charge delocalization was analyzed using natural bond orbital (NBO) analysis. The highest occupied and the lowest unoccupied molecular orbitals (HOMO and LUMO) which is also known the frontier molecular orbitals were simulated, and obtained energy gap confirmed that charge transfer occurs within manganese(II) complex. Molecular electrostatic potential (MEP) for synthesized manganese(II) complex displays the electrophilic and nucleophilic regions. From MEP, the the most negative region is located over carboxyl O atoms while positive region is located over H atoms.

Keywords: DFT, picolinate, IR, Raman, nonlinear optic

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Authors: Szu-Hua Wang

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Urban areas contain abundant potential biochemical storages and renewable and non-renewable flows. Urban natural environments for breeding natural assets and urban economic development for maintaining urban functions can be analyzed form the concept of ecological economic system. Land use change and ecosystem services change are resulting from the interactions between human activities and environments factually. Land use change due to human activities is the major cause of climate change, leading to serious impacts on urban ecosystem services, including provisioning services, regulating services, cultural services and supporting services. However, it lacks discussion on the interactions among urban land use change, ecosystem services change, and extreme precipitation events. Energy synthesis can use the same measure standard unit, solar energy, for different energy resources (e.g. sunlight, water, fossil fuels, minerals, etc.) and analyze contributions of various natural environmental resources on human economic systems. Therefore, this research adopts the concept of ecological, economic systems and energy synthesis for analyzing dynamic spatial impacts of land use change on ecosystem services, using the Taipei area as a case study. The analysis results show that changes in land use in the Taipei area, especially the conversion of natural lands and agricultural lands to urban lands, affect the ecosystem services negatively. These negative effects become more significant during the extreme precipitation events.

Keywords: urban ecological economic system, extreme precipitation events, ecosystem services, energy

Procedia PDF Downloads 191

Authors: Laetitia Lemiere, Marie Gosme, Gerard Subsol, Marc Jaeger

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Agroforestry is recognized as a way of developing sustainable and resilient agriculture that can fight against climate change. However, the number of species combinations, spatial configurations, and management options for trees and crops is vast. These choices must be adapted to the pedoclimatic and socio-economic contexts and to the objectives of the farmer, who therefore needs support in designing his system. Participative design workshops are a good way to integrate the knowledge of several experts in order to design such complex systems. The design of agroforestry systems should take into account both spatial aspects (e.g., spacing of trees within the lines and between lines, tree line orientation, tree-crop distance, species spatial patterns) and temporal aspects (e.g., crop rotations, tree thinning and pruning, tree planting in the case of successional agroforestry). Furthermore, the interactions between trees and crops evolve as the trees grow. However, agroforestry design workshops generally emphasize the spatial aspect only through the use of static tokens to represent the different species when designing the spatial configuration of the system. Augmented reality (AR) may overcome this limitation, allowing to visualize dynamic representations of trees and crops, and also their interactions, while at the same time retaining the possibility to physically interact with the system being designed (i.e., move trees, add or remove species, etc.). We propose an ergonomic digital solution capable of assisting a group of agroforestry experts to design an agroforestry system and to represent it. We investigated the use of web-based marker-based AR that does not require specific hardware and does not require specific installation so that all users could use their own smartphones right out of the pocket. We developed a prototype mobilizing the AR.js, ArToolKit.js, and Three.js open source libraries. In our implementation, we gradually build a virtual agroforestry system pattern scene from the users' interactions. A specific set of markers initialize the scene properties, and the various plant species are added and located during the workshop design session. The full virtual scene, including the trees positions with their neighborhood, are saved for further uses, such as virtual, augmented instantiation in the farmer fields. The number of tree species available in the application is gradually increasing; we mobilize 3D digital models for walnut, poplar, wild cherry, and other popular species used in agroforestry systems. The prototype allows shadow computations and the representation of trees at various growth stages, as well as different tree generations, and is thus able to visualize the dynamics of the system over time. Future work will focus on i) the design of complex patterns mobilizing several tree/shrub organizations, not restricted to lines; ii) the design of interfaces related to cultural practices, such as clearing or pruning; iii) the representation of tree-crop interactions. Beside tree shade (light competition), our objective is to represent also below-ground competitions (water, nitrogen) or other variables of interest for the design of agroforestry systems (e.g., predicted crop yield).

Keywords: agroforestry system design, augmented reality, marker-based AR, participative design, web-based AR

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Authors: Huanhuan Qiang, Sijia Jin

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Population aging has become a global trend, and China has entered an aging society, implementing an active aging system focused on home and community-based care. However, most urban communities where elderly people live face issues such as monotonous planning, unappealing landscapes, and inadequate aging infrastructure, which do not meet the requirements for active aging. Intergenerational friendliness and mutual assistance are key components in China's active aging policy framework. Therefore, residential development should prioritize enhancing intergenerational friendliness. Residential and public spaces are central to community life and well-being, offering new and challenging venues to improve relationships among residents of different ages. They are crucial for developing intergenerational communities with diverse generations and non-blood relationships. This paper takes the Maigaoqiao community in Nanjing, China, as a case study, examining intergenerational interactions in public spaces. Based on Maslow's hierarchy of needs and using time geography analysis, it identifies the spatiotemporal behavior characteristics of intergenerational groups in outdoor activities. Then construct an intergenerational-friendly evaluation system and an IPA quadrant model for public spaces in residential areas. Lastly, it explores optimization strategies for public spaces to promote intergenerational friendly interactions, focusing on five aspects: accessibility, safety, functionality, a sense of belonging, and interactivity.

Keywords: intergenerational friendliness, demand theory, spatiotemporal behavior, IPA analysis, existing residential public space

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Authors: Smita Mathur

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Play is an innate, player-centric, joyful, fundamental activity of early childhood development that significantly contributes to social, emotional, and academic learning. Leveraging the power of play can enhance these domains by creating engaging, interactive, and developmentally appropriate learning experiences for young children. This research aimed to systematically examine young children’s play behaviors with a focus on four primary objectives: (1) the frequency and duration of on-task behaviors, (2) social interactions and emotional expressions during play, (3) the correlation between academic skills and play, and (4) identifying best practices for integrating play-based curricula. To achieve these objectives, a mixed-method study was conducted among young preschool-aged children in low socio-economic populations in the United States. The children were identified using purposive sampling. The children were observed during structured play in classrooms and unstructured play during outdoor playtime and in their home environments. The study sampled 97 preschool-aged children. A total of 3970 minutes of observations were coded to address the research questions. Thirty-seven percent of children lived in linguistically isolated families, and 76% lived in basic budget poverty. Children lived in overcrowded housing situations (67%), and most families had mixed citizenship status (66%). The observational study was conducted using the observation protocol during the Oxford Study Project. On-task behaviors were measured by tracking the frequency and duration of activities where children maintained focus and engagement. In examining social interactions and emotional expressions, the study recorded social interactions, emotional responses, and teacher involvement during play. The study aimed to identify best practices for integrating play-based curricula into early childhood education. By analyzing the effectiveness of different play-based strategies and their impact on on-task behaviors, social-emotional development, and academic skills, the research sought to provide actionable recommendations for educators and caregivers. The findings from study 1. Highlight play behaviors that increase on-task behaviors and academic, & social skills in young children. 2. Offers insights into teacher preparation and designing play-based curriculum 3. Research critiques observation as a data collection technique.

Keywords: play, early childhood education, social-emotional development, academic development

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Authors: Marietta Kékes Szabó

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The patterns of personality (mal)function and the individuals’ psychosocial environment influence the healthy status collectively and may lie in the background of psychosomatic disorders. Although the patients with their diversified symptoms usually do not have any organic problems, the experienced complaint, the fear of serious illness and the lack of social support often lead to increased anxiety and further enigmatic symptoms. The role of the family system and its atmosphere seem to be very important in this process. More studies explored the characteristics of dysfunctional family organization: inflexible family structure, hidden conflicts that are not spoken about by the family members during their daily interactions, undefined role boundaries, neglect or overprotection of the children by the parents and coalition between generations. However, questionnaires that are used to measure the properties of the family system are able to explore only its unit and cannot pay attention to the dyadic interactions, while the representation of the family structure by a figure placing test gives us a new perspective to better understand the organization of the (sub)system(s). Furthermore, its dynamic form opens new perspectives to explore the family members’ joint representations, which gives us the opportunity to know more about the flexibility of cohesion and hierarchy of the given family system. In this way, the communication among the family members can be also examined. The aim of my study was to collect a great number of information about the organization of psychosomatic families. In our research we used Gehring’s Family System Test (FAST) both in static and dynamic forms to mobilize the family members’ mental representations about their family and to get data in connection with their individual representations as well as cooperation. There were four families in our study, all of them with a young adult person. Two families with healthy participants and two families with asthmatic patient(s) were involved in our research. The family members’ behavior that could be observed during the dynamic situation was recorded on video for further data analysis with Noldus Observer XT 8.0 program software. In accordance with the previous studies, our results show that the family structure of the families with at least one psychosomatic patient is more rigid than it was found in the control group and the certain (typical, ideal, and conflict) dynamic representations reflected mainly the most dominant family member’s individual concept. The behavior analysis also confirmed the intensified role of the dominant person(s) in the family life, thereby influencing the family decisions, the place of the other family members, as well as the atmosphere of the interactions, which could also be grasped well by the applied methods. However, further research is needed to learn more about the phenomenon that can open the door for new therapeutic approaches.

Keywords: psychosomatic families, family structure, family system test (FAST), static and dynamic representations, behavior analysis

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Authors: Păcurar Diana Istina

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The indissoluble link between aesthetics and semiotics, the harmonization and semiotic understanding of the interactions between the viewer and the object being looked at, are the basis of the practical demonstration of the importance of aesthetic perception within the theater performance. The design of a theater performance includes several structures, some considered from the beginning, art forms (i.e., the text), others being represented by simple, common objects (e.g., scenographic elements), which, if reunited, can trigger a certain aesthetic perception. The audience is delivered, by the team involved in the performance, a series of auditory and visual signs with which they interact. It is necessary to explain some notions about the physiological support of the transformation of different types of stimuli at the level of the cerebral hemispheres. The cortex considered the superior integration center of extransecal and entanged stimuli, permanently processes the information received, but even if it is delivered at a constant rate, the generated response is individualized and is conditioned by a number of factors. Each changing situation represents a new opportunity for the viewer to cope with, developing feelings of different intensities that influence the generation of meanings and, therefore, the management of interactions. In this sense, aesthetic perception depends on the detection of the “correctness” of signs, the forms of which are associated with an aesthetic property. Fairness and aesthetic properties can have positive or negative values. Evaluating the emotions that generate judgment and implicitly aesthetic perception, whether we refer to visual emotions or auditory emotions, involves the integration of three areas of interest: Valence, arousal and context control. In this context, superior human cognitive processes, memory, interpretation, learning, attribution of meanings, etc., help trigger the mechanism of anticipation and, no less important, the identification of error. This ability to locate a short circuit produced in a series of successive events is fundamental in the process of forming an aesthetic perception. Our main purpose in this research is to investigate the possible conditions under which aesthetic perception and its minimum content are generated by all these structures and, in particular, by interactions with forms that are not commonly considered aesthetic forms. In order to demonstrate the quantitative and qualitative importance of the categories of signs used to construct a code for reading a certain message, but also to emphasize the importance of the order of using these indices, we have structured a mathematical analysis that has at its core the analysis of the percentage of signs used in a theater performance.

Keywords: semiology, aesthetics, theatre semiotics, theatre performance, structure, aesthetic perception

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Authors: Boda Sreenivas, Lyathakula Ravindranath, Kanugula Srishailam, Byru Venkatram Reddy

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Extensive research into the optimized structure and molecular properties of 3-Flouro-2-methylbenzoicacid(FMB), 3-Chloro-2-methoxybenzoicacid (CMB), and 3-Bromo-2-methylbenzoicacid (BMB) was carried out using FT-IR, FT-Raman and UV-Visible spectra, as well as theoretically using the DFT approach with B3LYPfunctional in conjunction with 6-311++G(d,p) basis set. The optimized structure was determined by evaluating torsional scans about free rotation bonds. Structure parameters, harmonic vibrational frequencies, potential energy distribution(PED), and infrared and Raman intensities were computed. The computational results from the DFT approach, such asFT-IR, FT-Raman, and UV-Visible spectra, were compared with the experimental results and found good agreement. Observed and calculated frequencies agreed with an rms error of 8.42, 6.60, and 6.95 cm-1 for FMB, CMB, and BMB, respectively. Unambiguous vibrational assignments were made for all fundamentals using PED and eigenvectors. The electronic HOMO-LUMO, H-bonding, and strong conjugative interactions across different molecular entities are discussed using experimental and simulated Ultraviolet-Visible spectra. The title molecules' molecular properties such as dipole moment, mean polarizability, and first-order hyperpolarizability, were calculated to study their non-linear optical (NLO) behavior. The chemical reactivity descriptors and mapped electrostatic surface potential (MESP) were also evaluated. Natural bond orbital (NBO) analysis was used to examine the stability of molecules resulting from hyperconjugative interactions and charge delocalization.

Keywords: ftir/raman spectra, DFT, NLO, homo-lumo, NBO, halogenated benzoic acids

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Authors: S. Chaudhuri, P. A. Bhobe

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Fe₂TiSn is a non-magnetic full Heusler alloy with a small gap (~ 0.07 eV) at the Fermi level. The electronic structure is highly symmetric in both the spin bands and a small percentage of substitution of holes or electrons can push the system towards spin polarization. A stable 100% spin polarization or half-metallicity is very desirable in the field of spintronics, making Fe₂TiSn a highly attractive material. However, this composition suffers from an inherent anti-site disorder between Fe and Ti sites. This paper reports on the method adopted to control the anti-site disorder and the realization of the half-metallic ground state in Fe₂TiSn, achieved by chemical substitution. Here, Sb was substituted at Sn site to obtain Fe₂TiSn₁₋ₓSbₓ compositions with x = 0, 0.1, 0.25, 0.5 and 0.6. All prepared compositions with x ≤ 0.6 exhibit long-range L2₁ ordering and a decrease in Fe – Ti anti-site disorder. The transport and magnetic properties of Fe₂TiSn₁₋ₓSbₓ compositions were investigated as a function of temperature in the range, 5 K to 400 K. Electrical resistivity, magnetization, and Hall voltage measurements were carried out. All the experimental results indicate the presence of the half-metallic ground state in x ≥ 0.25 compositions. However, the value of saturation magnetization is small, indicating the presence of compensated magnetic moments. The observed magnetic moments' values are in close agreement with the Slater–Pauling rule in half-metallic systems. Magnetic interactions in Fe₂TiSn₁₋ₓSbₓ are understood from the local crystal structural perspective using extended X-ray absorption fine structure (EXAFS) spectroscopy. The changes in bond distances extracted from EXAFS analysis can be correlated with the hybridization between constituent atoms and hence the RKKY type magnetic interactions that govern the magnetic ground state of these alloys. To complement the experimental findings, first principle electronic structure calculations were also undertaken. The spin-polarized DOS complies with the experimental results for Fe₂TiSn₁₋ₓSbₓ. Substitution of Sb (an electron excess element) at Sn–site shifts the majority spin band to the lower energy side of Fermi level, thus making the system 100% spin polarized and inducing long-range magnetic order in an otherwise non-magnetic Fe₂TiSn. The present study concludes that a stable half-metallic system can be realized in Fe₂TiSn with ≥ 50% Sb – substitution at Sn – site.

Keywords: antisite disorder, EXAFS, Full Heusler alloy, half metallic ferrimagnetism, RKKY interactions

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Authors: Mohammad R. Jalali

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Movement of liquid with a free surface in a container is known as slosh. For instance, slosh occurs when water in a closed tank is set in motion by a free surface displacement, or when liquid natural gas in a container is vibrated by an external driving force, such as an earthquake or movement induced by transport. Slosh is also derived from resonant switching of a natural basin. During sloshing, different types of motion are produced by energy exchange between the liquid and its container. In present study, a numerical model is developed to simulate the nonlinear even harmonic oscillations of free surface sloshing of an initial disturbance to the free surface of a liquid in a closed square basin. The response of the liquid free surface is affected by amplitude and motion frequencies of its container; therefore, sloshing involves complex fluid-structure interactions. In the present study, nonlinear interaction of free surface sloshing of an initial Gaussian hump with its uneven container is predicted numerically. For this purpose, Green-Naghdi (GN) equations are applied as governing equation of fluid field to produce nonlinear second-order and higher-order wave interactions. These equations reduce the dimensions from three to two, yielding equations that can be solved efficiently. The GN approach assumes a particular flow kinematic structure in the vertical direction for shallow and deep-water problems. The fluid velocity profile is finite sum of coefficients depending on space and time multiplied by a weighting function. It should be noted that in GN theory, the flow is rotational. In this study, GN numerical simulations of initial Gaussian hump are compared with Fourier series semi-analytical solutions of the linearized shallow water equations. The comparison reveals that satisfactory agreement exists between the numerical simulation and the analytical solution of the overall free surface sloshing patterns. The resonant free surface motions driven by an initial Gaussian disturbance are obtained by Fast Fourier Transform (FFT) of the free surface elevation time history components. Numerically predicted velocity vectors and magnitude contours for the free surface patterns indicate that interaction of Gaussian hump with its container has localized effect. The result of this sloshing is applicable to the design of stable liquefied oil containers in tankers and offshore platforms.

Keywords: fluid-structure interactions, free surface sloshing, Gaussian hump, Green-Naghdi equations, numerical predictions

Procedia PDF Downloads 400