Search results for: Computational Fluid Dynamics

Authors: R. O’Reilly Meehan, D. B. Murray

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In many practical situations, bubbles are dispersed in a liquid phase. Understanding these complex bubbly flows is therefore a key issue for applications such as shell and tube heat exchangers, mineral flotation and oxidation in water treatment. Although a large body of work exists for bubbles rising in an unbounded medium, that of bubbles rising in constricted geometries has received less attention. The particular case of a bubble sliding underneath an inclined surface is common to two-phase flow systems. The current study intends to expand this knowledge by performing experiments to quantify the streamwise flow structures associated with a single sliding air bubble under an inclined surface in quiescent water. This is achieved by means of two-dimensional, two-component particle image velocimetry (PIV), performed with a continuous wave laser and high-speed camera. PIV vorticity fields obtained in a plane perpendicular to the sliding surface show that there is significant bulk fluid motion away from the surface. The associated momentum of the bubble means that this wake motion persists for a significant time before viscous dissipation. The magnitude and direction of the flow structures in the streamwise measurement plane are found to depend on the point on its path through which the bubble enters the plane. This entry point, represented by a phase angle, affects the nature and strength of the vortical structures. This study reconstructs the vorticity field in the wake of the bubble, converting the field at different instances in time to slices of a large-scale wake structure. This is, in essence, Taylor’s ”frozen turbulence” hypothesis. Applying this to the vorticity fields provides a pseudo three-dimensional representation from 2-D data, allowing for a more intuitive understanding of the bubble wake. This study provides insights into the complex dynamics of a situation common to many engineering applications, particularly shell and tube heat exchangers in the nucleate boiling regime.

Keywords: bubbly flow, particle image velocimetry, two-phase flow, wake structures

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Authors: L. Achab, F. Iachachene

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In microvessels, red blood cells (RBCs) exhibit a tendency to migrate towards the vessel center, establishing a core-annular flow pattern. The core region, marked by a high concentration of RBCs, is governed by significantly non-Newtonian viscosity. Conversely, the annular layer, composed of cell-free plasma, is characterized by Newtonian low viscosity. This property enables the plasma layer to act as a lubricant for the vessel walls, efficiently reducing resistance to the movement of blood cells. In this study, we investigate the factors influencing blood flow in microvessels and the thickness of the annular plasma layer using a non-miscible fluids approach in a 2D axisymmetric geometry. The governing equations of an incompressible unsteady flow are solved numerically through the Volume of Fluid (VOF) method to track the interface between the two immiscible fluids. To model blood viscosity in the core region, we adopt the Quemada constitutive law which is accurately captures the shear-thinning blood rheology over a wide range of shear rates. Our results are then compared to an established theoretical approach under identical flow conditions, particularly concerning the radial velocity profile and the thickness of the annular plasma layer. The simulation findings for low Reynolds numbers, demonstrate a notable agreement with the theoretical solution, emphasizing the pivotal role of blood’s rheological properties in the core region in determining the thickness of the annular plasma layer.

Keywords: core-annular flows, microvessels, Quemada model, plasma layer thickness, volume of fluid method

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Authors: Amani Amamou, Sabra Habli, Nejla Mahjoub Saïd, Georges Le Palec

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Round jets have been widely studied due to their important application in industry. Many configurations of round jet were encountered in literature as free jet, co-flow jet, couterflowing jet and cross flow jet. In this paper, we are concerned with turbulent round jet in uniform counterflow stream which is known to enhance mixing and dispersion efficiency owing to flow reversal. This type of flow configuration is a typical application in environmental engineering such as the disposal of wastewater into seas or rivers. A computational study of a turbulent circular jet discharging into a uniform counterflow is conducted in order to investigate the characteristics of the diffusion field of the jet effluent. The investigation is carried out for three different cases of jet-to-current velocity ratios; low, medium and high velocity ratios. The Reynolds Stress Model (RSM) is used in the comparison with available experimental measurements. The decay of the center line velocity and the dynamic proprieties of the flow together with the centerline dilution of the passive scalar and the other characteristics of the concentration field are computationally analyzed in this paper.

Keywords: Counterflow stream, jet, velocity, concentration

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Authors: Priya Kulkarni, Soumya Koppikar, Narendrakumar Wagh, Dhanshri Ingle, Onkar Lande, Abhay Harsulkar

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Cartilage is an extracellular matrix composed of aggrecan, which imparts it with a great tensile strength, stiffness and resilience. Disruption in cartilage metabolism leading to progressive degeneration is a characteristic feature of Osteoarthritis (OA). The process involves enzymatic depolymerisation of cartilage specific proteoglycan, releasing free glycosaminoglycan (GAG). This released GAG in synovial fluid (SF) of knee joint serves as a direct measure of cartilage loss, however, limited due to its invasive nature. Western Ontario and McMaster Universities Arthritis Index (WOMAC) is widely used for assessing pain, stiffness and physical-functions in OA patients. The scale is comprised of three subscales namely, pain, stiffness and physical-function, intends to measure patient’s perspective of disease severity as well as efficacy of prescribed treatment. Twenty SF samples obtained from OA patients were analysed for their GAG values in SF using DMMB based assay. LK 1.0 vernacular version was used to attain WOMAC scale. The results were evaluated using SAS University software (Edition 1.0) for statistical significance. All OA patients revealed higher GAG values compared to the control value of 78.4±30.1µg/ml (obtained from our non-OA patients). Average WOMAC calculated was 51.3 while pain, stiffness and function estimated were 9.7, 3.9 and 37.7, respectively. Interestingly, a strong statistical correlation was established between WOMAC function subscale and GAG (p = 0.0102). This subscale is based on day-to-day activities like stair-use, bending, walking, getting in/out of car, rising from bed. However, pain and stiffness subscale did not show correlation with any of the studied markers and endorsed the atypical inflammation in OA pathology. On one side, where knee pain showed poor correlation with GAG, it is often noted that radiography is insensitive to cartilage degenerative changes; thus OA remains undiagnosed for long. Moreover, active cartilage degradation phase remains elusive to both, patient and clinician. Through analysis of large number of OA patients we have established a close association of Kellgren-Lawrence grades and increased cartilage loss. A direct attempt to correlate WOMAC and radiographic progression of OA with various biomarkers has not been attempted so far. We found a good correlation in GAG levels in SF and the function subscale.

Keywords: cartilage, Glycosaminoglycan, synovial fluid, western ontario and McMaster Universities Arthritis Index

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Authors: S. Raja, K. M. Parammasivam, V. Aghilesh

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Fluid-structure interaction is a crucial consideration in the design of many engineering systems such as flight vehicles and bridges. Aircraft lifting surfaces and turbine blades can fail due to oscillations caused by fluid-structure interaction. Hence, it is focussed to study the fluid-structure interaction in the present research. First, the effect of free vibration over the panel is studied. It is well known that the deformation of a panel and flow induced forces affects one another. The selected panel has a span 300mm, chord 300mm and thickness 2 mm. The project is to study, the effect of cross-sectional area and the stiffener location is carried out for the same panel. The stiffener spacing is varied along both the chordwise and span-wise direction. Then for that optimal location the ideal stiffener length is identified. The effect of stiffener cross-section shapes (T, I, Hat, Z) over flutter velocity has been conducted. The flutter velocities of the selected panel with two rectangular stiffeners of cantilever configuration are estimated using MSC NASTRAN software package. As the flow passes over the panel, deformation takes place which further changes the flow structure over it. With increasing velocity, the deformation goes on increasing, but the stiffness of the system tries to dampen the excitation and maintain equilibrium. But beyond a critical velocity, the system damping suddenly becomes ineffective, so it loses its equilibrium. This estimated in NASTRAN using PK method. The first 10 modal frequencies of a simple panel and stiffened panel are estimated numerically and are validated with open literature. A grid independence study is also carried out and the modal frequency values remain the same for element lengths less than 20 mm. The current investigation concludes that the span-wise stiffener placement is more effective than the chord-wise placement. The maximum flutter velocity achieved for chord-wise placement is 204 m/s while for a span-wise arrangement it is augmented to 963 m/s for the stiffeners location of ¼ and ¾ of the chord from the panel edge (50% of chord from either side of the mid-chord line). The flutter velocity is directly proportional to the stiffener cross-sectional area. A significant increment in flutter velocity from 218m/s to 1024m/s is observed for the stiffener lengths varying from 50% to 60% of the span. The maximum flutter velocity above Mach 3 is achieved. It is also observed that for a stiffened panel, the full effect of stiffener can be achieved only when the stiffener end is clamped. Stiffeners with Z cross section incremented the flutter velocity from 142m/s (Panel with no stiffener) to 328 m/s, which is 2.3 times that of simple panel.

Keywords: stiffener placement, stiffener cross-sectional area, stiffener length, stiffener cross sectional area shape

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Authors: Derick M. Rakgoale, Topside E. Mathonsi, Vusumuzi Malele

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Cloud computing offers distributed online and on-demand computational services from anywhere in the world. Cloud computing services have grown immensely over the past years, especially in the past year due to the Coronavirus pandemic. Cloud computing has changed the working environment and introduced work from work phenomenon, which enabled the adoption of technologies to fulfill the new workings, including cloud services offerings. The increased cloud computing adoption has come with new challenges regarding data privacy and its integrity in the cloud environment. Previously advanced encryption algorithms failed to reduce the memory space required for cloud computing performance, thus increasing the computational cost. This paper reviews the existing encryption algorithms used in cloud computing. In the future, artificial neural networks (ANN) algorithm design will be presented as a security solution to ensure data integrity, confidentiality, privacy, and availability of user data in cloud computing. Moreover, MATLAB will be used to evaluate the proposed solution, and simulation results will be presented.

Keywords: cloud computing, data integrity, confidentiality, privacy, availability

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Authors: C. Park, H. Lee, Y-J. Lee

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Aim: This study aims to present the Sustainability Innovation Capacity Building Framework (SICBF) to enable the wider public to achieve UN Sustainable Development Goals (UN SDGs) for a sustainable future. The intrinsically interwoven nature of sustainability requires systematic approaches to attain. However, there is a lack of an effective framework for capacity building that enables a systematic implementation approach for UN SDGs. The SICBF illustrates the six core components and their dynamics: 1. Momentum creation; 2. Exposure to diverse worldviews; 3. Serendipity/Eureka moment; 4. Creative problem solving; 5. Individual empowerment; 6. Systems thinking. Method: First, a structured literature review was used to synthesise existing sustainability competencies studies and generic innovation competencies. Secondly, the conceptual framework based on literature findings was tested with the participants' survey and interview data collected from four sets of MAKEathon events. The interview analysis and event observation data were used to further refine and validate the conceptual framework. Contributions: The scientific contribution of this study is to pave the way for SDGs specific capacity building framework that caters to the need for systematic approaches to allow the wider public aspiring to tackle the seemingly intractable sustainable development goals. The framework will aid sustainable development academics, educators, and practitioners in understanding the dynamics of how capacity building can be facilitated.

Keywords: capacity building, sustainability innovation, sustainable development, systems thinking, UN SDGs

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Authors: Ha T. T. Ly, Truc B. Truc, Hai N. Truong, Mai P. T. Nguyen, Ngoc D. Ngo, Khanh V. Tran, Hai T. Le

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Beta thalassemia is one of the most common inherited blood disorders, which is characterized by decreased or absent in beta globin expression. Patients with Beta thalassemia whose anemia is not so severe as to necessitate transfusions are said to have thalassemia intermedia. Objective: The goal of this study is prenatal diagnosis for pregnancy woman with Beta thalassemia intermedia and her husband with Beta thalassemia carrier at high risk of Beta thalassemia major in Northern of Vietnam. Material and method: The family has a 6 years-old compound heterozygous thalassemia major for CD71/72(+A) and Hbb:c. -78A>G/nt-28(A>G) male child. The father was heterozygous for CD71/72(+A) mutation which is Beta plus type and the mother was compound heterozygosity of two different variants, namely, Hbb: c. -78A>G/nt-28(A>G) and CD26(A-G) HbE. Prenatal Beta thalassemia mutation detection in fetal DNA was carried out using multiplex Amplification-refractory mutation system ARMS-PCR and confirmed by direct Sanger-sequencing Hbb gene. Prenatal diagnoses were perfomed by amniotic fluid sampling from pregnant woman in the 16-18th week of pregnancy after the genotypes of parents of the probands were identified. Result: When amniotic fluid sample was analyzed for Beta globin gene (Hbb), we found that the genotype is heterozygous for CD71/72(+A) and CD26(A-G) HbE. This genotype is different from the 1st child of this family. Conclusion: Prenatal diagnosis helps the parents to know the genotype and the thalassemia status of the fetus, so they can have early decision on their pregnancy. Genetic diagnosis provided a useful method in diagnosis for familial members in pedigree, genetic counseling and prenatal diagnosis.

Keywords: beta thalassemia intermedia, Hbb gene, pedigree, prenatal diagnosis

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Authors: Ramonika Sengupta, Stuti Kachhwaha, Asha Adhiya, K. Satya Raja Sekhar, Rajwinder Kaur

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Numerous efforts have been done in the past decade to develop the methods of secure communication that are free from interception and eavesdropping. In fiber optic communication, chaotic optical carrier signals are used for data encryption in secure data transmission. Mach-Zehnder Modulators (MZM) are the key components for generating the chaotic signals to be used as optical carriers. This paper presents the dynamics of a lithium niobate MZM modulator under various biasing conditions. The chaotic fluctuations of the intensity of a laser diode have been generated using the electro-optic MZM modulator operating in a highly nonlinear regime. The modulator is driven in closed loop by its own output at an earlier time. When used as an electro-optic oscillator employing delayed feedback, the MZM displays a wide range of output waveforms of varying complexity. The dynamical behavior of the system ranges from periodic to nonlinear oscillations. The nonlinearity displayed by the system is reproducible and is easily controllable. In this paper, we demonstrate a wide variety of optical signals generated by MZM using easily controllable device parameters in both open and close loop bias conditions.

Keywords: chaotic carrier, fiber optic communication, Mach-Zehnder modulator, secure data transmission

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Authors: Camilo Cerda Sarabia, Fernanda Bravo Cornejo, Diego Santibanez Oyarce, Hugo Osses Prado, Esteban Gómez Terán, Belén Diaz Diaz, Raúl Caulier-Cisterna, Jorge Vergara-Quezada, Ana Moya-Beltrán

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Antimicrobial resistance (AMR) represents a significant and rapidly escalating global health threat. Projections estimate that by 2050, AMR infections could claim up to 10 million lives annually. Respiratory infections, in particular, pose a severe risk not only to individual patients but also to the broader public health system. Despite the alarming rise in resistant respiratory infections, AMR within the lung microbiome (microbial community) remains underexplored and poorly characterized. The lungs, as a complex and dynamic microbial environment, host diverse communities of microorganisms whose interactions and resistance mechanisms are not fully understood. Unlike studies that focus on individual genomes, analyzing the entire microbiome provides a comprehensive perspective on microbial interactions, resistance gene transfer, and community dynamics, which are crucial for understanding AMR. However, this holistic approach introduces significant computational challenges and exposes the limitations of traditional analytical methods such as the difficulty of identifying the AMR. Machine learning has emerged as a powerful tool to overcome these challenges, offering the ability to analyze complex genomic data and uncover novel insights into AMR that might be overlooked by conventional approaches. This study investigates microbial resistance within the lung microbiome using unsupervised machine learning approaches to uncover resistance patterns and potential clinical associations. it downloaded and selected lung microbiome data from HumanMetagenomeDB based on metadata characteristics such as relevant clinical information, patient demographics, environmental factors, and sample collection methods. The metadata was further complemented by details on antibiotic usage, disease status, and other relevant descriptions. The sequencing data underwent stringent quality control, followed by a functional profiling focus on identifying resistance genes through specialized databases like Antibiotic Resistance Database (CARD) which contains sequences of AMR gene sequence and resistance profiles. Subsequent analyses employed unsupervised machine learning techniques to unravel the structure and diversity of resistomes in the microbial community. Some of the methods employed were clustering methods such as K-Means and Hierarchical Clustering enabled the identification of sample groups based on their resistance gene profiles. The work was implemented in python, leveraging a range of libraries such as biopython for biological sequence manipulation, NumPy for numerical operations, Scikit-learn for machine learning, Matplotlib for data visualization and Pandas for data manipulation. The findings from this study provide insights into the distribution and dynamics of antimicrobial resistance within the lung microbiome. By leveraging unsupervised machine learning, we identified novel resistance patterns and potential drivers within the microbial community.

Keywords: antibiotic resistance, microbial community, unsupervised machine learning., sequences of AMR gene

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Authors: Amir Reza Heydari, Yaser Jenab

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Coronary artery disease, a common cardiovascular disease, is attributed to the accumulation of cholesterol-based plaques in the coronary arteries, leading to atherosclerosis. This disease is associated with risk factors such as smoking, hypertension, diabetes, and elevated cholesterol levels, contributing to severe clinical consequences, including acute coronary syndromes and myocardial infarction. Treatment approaches such as from lifestyle interventions to surgical procedures like percutaneous coronary intervention and coronary artery bypass surgery. These interventions often employ stents, including bare-metal stents (BMS), drug-eluting stents (DES), and bioresorbable vascular scaffolds (BVS), each with its advantages and limitations. Computational tools have emerged as critical in optimizing stent designs and assessing their performance. The aim of this study is to provide an overview of the computational methods of studies based on the finite element (FE) method in the field of coronary stenting and discuss the potential for development and clinical application of stent devices. Additionally, the importance of assessing the ability of computational models is emphasized to represent real-world phenomena, supported by recent guidelines from the American Society of Mechanical Engineers (ASME). Validation processes proposed include comparing model performance with in vivo, ex-vivo, or in vitro data, alongside uncertainty quantification and sensitivity analysis. These methods can enhance the credibility and reliability of in silico simulations, ultimately aiding in the assessment of coronary stent designs in various clinical contexts.

Keywords: atherosclerosis, materials, restenosis, review, validation

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Authors: Markus Rütten, Olaf Wünsch

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Non-Newtonian fluid properties can change the flow behaviour significantly, its prediction is more difficult when thermal effects come into play. Hence, the focal point of this work is the wake flow behind a heated circular cylinder in the laminar vortex shedding regime for thermo-viscous shear thinning fluids. In the case of isothermal flows of Newtonian fluids the vortex shedding regime is characterised by a distinct Reynolds number and an associated Strouhal number. In the case of thermo-viscous shear thinning fluids the flow regime can significantly change in dependence of the temperature of the viscous wall of the cylinder. The Reynolds number alters locally and, consequentially, the Strouhal number globally. In the present CFD study the temperature dependence of the Reynolds and Strouhal number is investigated for the flow of a Carreau fluid around a heated cylinder. The temperature dependence of the fluid viscosity has been modelled by applying the standard Williams-Landel-Ferry (WLF) equation. In the present simulation campaign thermal boundary conditions have been varied over a wide range in order to derive a relation between dimensionless heat transfer, Reynolds and Strouhal number. Together with the shear thinning due to the high shear rates close to the cylinder wall this leads to a significant decrease of viscosity of three orders of magnitude in the nearfield of the cylinder and a reduction of two orders of magnitude in the wake field. Yet the shear thinning effect is able to change the flow topology: a complex K´arm´an vortex street occurs, also revealing distinct characteristic frequencies associated with the dominant and sub-dominant vortices. Heating up the cylinder wall leads to a delayed flow separation and narrower wake flow, giving lesser space for the sequence of counter-rotating vortices. This spatial limitation does not only reduce the amplitude of the oscillating wake flow it also shifts the dominant frequency to higher frequencies, furthermore it damps higher harmonics. Eventually the locally heated wake flow smears out. Eventually, the CFD simulation results of the systematically varied thermal flow parameter study have been used to describe a relation for the main characteristic order parameters.

Keywords: heat transfer, thermo-viscous fluids, shear thinning, vortex shedding

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Authors: Anna-Kaisa Sjolund

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The doctoral thesis examines interaction design and sensory ethnography as tools to create immersive education environments. In recent years, there has been increasing interest and discussions among researchers and educators on immersive education like augmented reality tools, virtual glasses and the possibilities to utilize them in education at all levels. Using virtual devices as learning environments it is possible to create multisensory learning environments. Sensory ethnography in this study refers to the way of the senses consider the impact on the information dynamics in immersive learning environments. The past decade has seen the rapid development of virtual world research and virtual ethnography. Christine Hine's Virtual Ethnography offers an anthropological explanation of net behavior and communication change. Despite her groundbreaking work, time has changed the users’ communication style and brought new solutions to do ethnographical research. The virtual reality with all its new potential has come to the fore and considering all the senses. Movie and image have played an important role in cultural research for centuries, only the focus has changed in different times and in a different field of research. According to Karin Becker, the role of image in our society is information flow and she found two meanings what the research of visual culture is. The images and pictures are the artifacts of visual culture. Images can be viewed as a symbolic language that allows digital storytelling. Combining the sense of sight, but also the other senses, such as hear, touch, taste, smell, balance, the use of a virtual learning environment offers students a way to more easily absorb large amounts of information. It offers also for teachers’ different ways to produce study material. In this article using sensory ethnography as research tool approaches the core question. Sensory ethnography is used to describe information dynamics in immersive environment through interaction design. Immersive education environment is understood as three-dimensional, interactive learning environment, where the audiovisual aspects are central, but all senses can be taken into consideration. When designing learning environments or any digital service, interaction design is always needed. The question what is interaction design is justified, because there is no simple or consistent idea of what is the interaction design or how it can be used as a research method or whether it is only a description of practical actions. When discussing immersive learning environments or their construction, consideration should be given to interaction design and sensory ethnography.

Keywords: immersive education, sensory ethnography, interaction design, information dynamics

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Authors: Daniel M. Barry

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Since more than half a century ago, attempts have been made to culture cells and embryos outside the body (in vitro or ex vivo). This was done with different culture media and in various “incubators”. In the present study two different culture media were used: a standard TCM-199 culture medium and first trimester amniotic fluid (BAF) collected sterilely from pregnant cows after slaughter. Two different culture conditions were also investigated, the standard laboratory CO2 incubator versus culturing bovine embryos in the vagina of a goat doe. Two experiments were done: Firstly the permeability of different receptacles to CO2 gas was analyzed for possible culture in the vagina. Four-well plates and straws were used to incubate TCM-199 and BAF for a period of 120 h in the presence or absence of 5% CO2 gas. The pH values were measured and recorded every 24 h. In the second experiment pre-compacted morula stage bovine embryos were cultured in the above culture media in sealed 0.25 mL straws in a standard laboratory incubator and in the vagina of a goat doe. Evaluation was done on (1) stage of development and (2) number of blastomeres after 96 h of culture. In the first experiment it was shown that the CO2 gas diffused out of the 4-well plate as well as through the wall of the straws in the absence of CO2 gas, while in the presence of CO2 the pH of both media stabilized between 7.3 and 7.5. This meant that the semen straws were permeable to CO2 gas and could therefore be used as receptacles for culturing early stage bovine embryos. In the second experiment no statistical differences (p>0.05) were found in the number of pre-compacted bovine embryos that developed to the blastocyst stage, or the hatched blastocyst stage, neither for the culture medium used, or the method of culturing in the two incubators. Neither was there any difference (p>0.05) in the number of blastomeres that developed at the blastocyst stage between the two types of incubators. The bovine embryos tended to develop more blastomeres when cultured in BAF than when cultured in TCM-199 in both the standard laboratory incubator and when using the vagina of a goat doe as an incubator.

Keywords: alternative culture, bovine embryos, vagina, bovine amniotic fluid, incubator

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Authors: Jake Gonzalez, Tommy Dang

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This paper proposes a temporal graph approach to visualize and analyze the evolution of gene relationships and nomenclature over time. An interactive web-based tool implements this temporal graph, enabling researchers to traverse a timeline and observe coupled dynamics in network topology and naming conventions. Analysis of a real human genomic dataset reveals the emergence of densely interconnected functional modules over time, representing groups of genes involved in key biological processes. For example, the antimicrobial peptide DEFA1A3 shows increased connections to related alpha-defensins involved in infection response. Tracking degree and betweenness centrality shifts over timeline iterations also quantitatively highlight the reprioritization of certain genes’ topological importance as knowledge advances. Examination of the CNR1 gene encoding the cannabinoid receptor CB1 demonstrates changing synonymous relationships and consolidating naming patterns over time, reflecting its unique functional role discovery. The integrated framework interconnecting these topological and nomenclature dynamics provides richer contextual insights compared to isolated analysis methods. Overall, this temporal graph approach enables a more holistic study of knowledge evolution to elucidate complex biology.

Keywords: temporal graph, gene relationships, nomenclature evolution, interactive visualization, biological insights

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Authors: Jiahui Song

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The application of an electric field can cause poration at cell membranes. This includes the outer plasma membrane, as well as the membranes of intracellular organelles. In order to analyze and predict such electroporation effects, it becomes necessary to first evaluate the electric fields and the transmembrane voltages. This information can then be used to assess changes in the pore formation energy that finally yields the pore distributions and their radii based on the Smolchowski equation. The dynamic pore model can be achieved by including a dynamic aspect and a dependence on the pore population density into the pore formation energy equation. These changes make the pore formation energy E(r) self-adjusting in response to pore formation without causing uncontrolled growth and expansion. By using dynamic membrane tension, membrane electroporation in response to a 180kV/cm trapezoidal pulse with a 10 ns on time and 1.5 ns rise- and fall-times is discussed. Poration is predicted to occur at times beyond the peak at around 9.2 ns. Modeling also yields time-dependent distributions of the membrane pore population after multiple pulses. It shows that the pore distribution shifts to larger values of the radius with multiple pulsing. Molecular dynamics (MD) simulations are also carried out for a fixed field of 0.5 V/nm to demonstrate nanopore formation from a microscopic point of view. The result shows that the pore is predicted to be about 0.9 nm in diameter and somewhat narrower at the central point.

Keywords: high-intensity, nanosecond, dynamics, electroporation

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Authors: Priya Arora, Ashutosh Mishra

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Gene identification, towards the pursuit of mutated genes, leading to Parkinson’s disease, puts forward a challenge towards proactive cure of the disorder itself. Computational analysis is an effective technique for exploring genes in the form of protein sequences, as the theoretical and manual analysis is infeasible. The limitations and effectiveness of a particular computational method are entirely dependent on the previous data that is available for disease identification. The article presents a sequence-based classification method for the identification of genes responsible for Parkinson’s disease. During the initiation phase, the physicochemical properties of amino acids transform protein sequences into a feature vector. The second phase of the method employs Jaccard distances to select negative genes from the candidate population. The third phase involves artificial neural networks for making final predictions. The proposed approach is compared with the state of art methods on the basis of F-measure. The results confirm and estimate the efficiency of the method.

Keywords: disease gene identification, Parkinson’s disease, physicochemical properties of amino acid, protein sequences

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Authors: Muhammad Qasim, Laura Minet

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Victoria (BC), Canada, is a major cruise ship destination, attracting over 600,000 tourists annually. Residents of the James Bay neighborhood, home to the Ogden Point cruise terminal, have expressed concerns about the impacts of cruise ship activity on local traffic, air pollution, and safety compliance. This study evaluates the effects of cruise ship-induced traffic in James Bay, focusing on traffic flow intensification, density surges, changes in traffic mix, and speeding violations. To achieve these objectives, traffic data was collected in James Bay during two key periods: May, before the peak cruise season, and August, during full cruise operations. Three Miovision cameras captured the vehicular traffic mix at strategic entry points, while nine traffic counters monitored traffic distribution and speeding violations across the network. Traffic data indicated an average volume of 308 vehicles per hour during peak cruise times in May, compared to 116 vehicles per hour when no ships were in port. Preliminary analyses revealed a significant intensification of traffic flow during cruise ship "hoteling hours," with a volume increase of approximately 10% per cruise ship arrival. A notable 86% surge in taxi presence was observed on days with three cruise ships in port, indicating a substantial shift in traffic composition, particularly near the cruise terminal. The number of tourist buses escalated from zero in May to 32 in August, significantly altering traffic dynamics within the neighborhood. The period between 8 pm and 11 pm saw the most significant increases in traffic volume, especially when three ships were docked. Higher vehicle volumes were associated with a rise in speed violations, although this pattern was inconsistent across all areas. Speeding violations were more frequent on roads with lower traffic density, while roads with higher traffic density experienced fewer violations, due to reduced opportunities for speeding in congested conditions. PTV VISUM software was utilized for fuzzy distribution analysis and to visualize traffic distribution across the study area, including an assessment of the Level of Service on major roads during periods before and during the cruise ship season. This analysis identified the areas most affected by cruise ship-induced traffic, providing a detailed understanding of the impact on specific parts of the transportation network. These findings underscore the significant influence of cruise ship activity on traffic dynamics in Victoria, BC, particularly during peak periods when multiple ships are in port. The study highlights the need for targeted traffic management strategies to mitigate the adverse effects of increased traffic flow, changes in traffic mix, and speed violations, thereby enhancing road safety in the James Bay neighborhood. Further research will focus on detailed emissions estimation to fully understand the environmental impacts of cruise ship activity in Victoria.

Keywords: cruise ship tourism, air quality, traffic violations, transport dynamics, pollution

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Authors: R. C. Tyagi

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Quasi-periodicity of frequency intervals observed in Shruti based Absolute Scale of Music has been used to graphically identify the Anchor notes ‘Vadi’ and ‘Samvadi’ which are nodal points for expansion, elaboration and iteration of the emotional theme represented by the characteristic tonic arrangement in Raga compositions. This analysis leads to defining the Tonic parameters in the octave including the key-note frequency, tonic intervals’ anchor notes and the on-set and range of quasi-periodicities as exponents of 2. Such uniformity of representation of characteristic data would facilitate computational analysis and synthesis of music compositions and also help develop noise suppression techniques. Criteria for tuning of strings for compatibility with placement of frets on finger boards is discussed. Natural Rhythmic cycles in music compositions are analytically shown to lie between 3 and 126 beats.

Keywords: absolute scale, anchor notes, computational analysis, frets, innovation, noise suppression, Quasi-periodicity, rhythmic cycle, tonic interval, Shruti

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Authors: Boris Melnikov, Ye Zhang, Dmitrii Chaikovskii

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We continue to consider one of the cybernetic methods in computational biology related to the study of DNA chains. Namely, we are considering the problem of reconstructing the not fully filled distance matrix of DNA chains. When applied in a programming context, it is revealed that with a modern computer of average capabilities, creating even a small-sized distance matrix for mitochondrial DNA sequences is quite time-consuming with standard algorithms. As the size of the matrix grows larger, the computational effort required increases significantly, potentially spanning several weeks to months of non-stop computer processing. Hence, calculating the distance matrix on conventional computers is hardly feasible, and supercomputers are usually not available. Therefore, we started publishing our variants of the algorithms for calculating the distance between two DNA chains; then, we published algorithms for restoring partially filled matrices, i.e., the inverse problem of matrix processing. In this paper, we propose an algorithm for restoring the distance matrix for DNA chains, and the primary focus is on enhancing the algorithms that shape the greedy function within the branches and boundaries method framework.

Keywords: DNA chains, distance matrix, optimization problem, restoring algorithm, greedy algorithm, heuristics

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Authors: Anirudh Lahiri

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Neuromorphic computing, inspired by the intricate operations of biological neural networks, offers a revolutionary approach to overcoming the limitations of traditional computing architectures. This research proposes the integration of spintronics with neuromorphic systems, aiming to enhance computational performance, scalability, and energy efficiency. Traditional computing systems, based on the Von Neumann architecture, struggle with scalability and efficiency due to the segregation of memory and processing functions. In contrast, the human brain exemplifies high efficiency and adaptability, processing vast amounts of information with minimal energy consumption. This project explores the use of spintronics, which utilizes the electron's spin rather than its charge, to create more energy-efficient computing systems. Spintronic devices, such as magnetic tunnel junctions (MTJs) manipulated through spin-transfer torque (STT) and spin-orbit torque (SOT), offer a promising pathway to reducing power consumption and enhancing the speed of data processing. The integration of these devices within a neuromorphic framework aims to replicate the efficiency and adaptability of biological systems. The research is structured into three phases: an exhaustive literature review to build a theoretical foundation, laboratory experiments to test and optimize the theoretical models, and iterative refinements based on experimental results to finalize the system. The initial phase focuses on understanding the current state of neuromorphic and spintronic technologies. The second phase involves practical experimentation with spintronic devices and the development of neuromorphic systems that mimic synaptic plasticity and other biological processes. The final phase focuses on refining the systems based on feedback from the testing phase and preparing the findings for publication. The expected contributions of this research are twofold. Firstly, it aims to significantly reduce the energy consumption of computational systems while maintaining or increasing processing speed, addressing a critical need in the field of computing. Secondly, it seeks to enhance the learning capabilities of neuromorphic systems, allowing them to adapt more dynamically to changing environmental inputs, thus better mimicking the human brain's functionality. The integration of spintronics with neuromorphic computing could revolutionize how computational systems are designed, making them more efficient, faster, and more adaptable. This research aligns with the ongoing pursuit of energy-efficient and scalable computing solutions, marking a significant step forward in the field of computational technology.

Keywords: material science, biological engineering, mechanical engineering, neuromorphic computing, spintronics, energy efficiency, computational scalability, synaptic plasticity.

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Authors: Jyotsna Gupta, S. Ghosh, S. Aravindan

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The requirement of artificial prostheses (such as hip and knee joints) has increased with time. Many researchers are working to develop new implants with improved properties such as excellent biocompatibility with no tissue reactions, corrosion resistance in body fluid, high yield strength and low elastic modulus. Further, the morphological properties of the artificial implants should also match with that of the human bone so that cell adhesion, proliferation and transportation of the minerals and nutrition through body fluid can be obtained. Present study attempts to make porous Ti6Al15Mo alloys through powder metallurgy route using space holder technique. The alloy consists of 6wt% of Al which was taken as α phase stabilizer and 15wt% Mo was taken as β phase stabilizer with theoretical density 4.708. Ammonium hydrogen carbonate is used as a space holder in order to generate the porosity. The porosity of these fabricated porous alloys was controlled by adding the 0, 50, 70 vol.% of the space holder content. Three phases were found in the microstructure: α, α_2 and β phase of titanium. Kirkendall pores are observed to be decreased with increase of holding time during sintering and parallelly compressive strength and elastic modulus value increased slightly. Compressive strength and elastic modulus of porous Ti-6Al-15Mo alloy (1.17 g/cm3 density) is found to be suitable for cancellous bone. Released ions from Ti-6Al-15Mo alloy are far below from the permissible limits in human body.

Keywords: bone implant, powder metallurgy, sintering time, Ti-6Al-15Mo

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Authors: Youjeong Hwang

Abstract:

Purpose: Insulin-like growth factor-I (IGF-I) promotes B-cell development, immunoglobulin formation, and interleukin-6 (IL-6) production, then regulate the immune response and inflammation. As IGF-I and their receptor also exist in the periodontal tissue, they may affect the immune response caused by periodontal pathogens in aggressive periodontitis (AgP) patients. The function of IGF is regulated by IGF binding proteins (IGFBPs), and IGFBP-3 is known to most abundant in plasma. The aim of the present study was to assess the concentration of IGF-I and IGFBP-3 in plasma and gingival crevicular fluid (GCF) in AgP patients and to find out their association. Methods: Nine patients with AgP (test group) and nine healthy subjects (control group) were included in this study. None of the subjects had a history of systemic disease, smoking or steroids medication. GCF samples were collected by microcapillary pipettes and plasma samples were obtained by venipuncture. Probing pocket depth (PD), clinical attachment level (CAL) and bleeding on probing (BOP) were recorded. Samples were assayed for IGF-I and IGFBP-3 levels using ELISA. Results: Mean IGF-I level in GCF was higher in the test group than control. Mean IGF-I level in plasma and IGFBP-3 level in GCF and plasma in control group were higher than that of the test group. However, there was no statistical significance (p > 0.05). The mean level of IGF-I and IGFBP-3 in GCF was lower than those in plasma. Mean IGF-I level in plasma showed a negative correlation with PD and CAL (p < 0.05) in both groups. The levels of IGF-I and IGFBP-3 in GCF seemed to be negatively correlated with BOP in the test group (p < 0.05). Conclusions: The difference in the level of IGF-I and IGFBP-3 between AgP and healthy subjects was not significant. Further studies that explain the mechanism of the protective role of IGF-I with more samples are needed.

Keywords: aggressive periodontitis, pathogenesis, insulin-like growth factor, insulin-like growth factor binding protein

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Authors: Taimur Khan, Zakirullah, Muhammad Shahab

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The SARS-CoV-2 variant BA.2.86 (Omicron) has emerged with unique mutations that may increase its transmission and infectivity. This study investigates how these mutations alter the Omicron receptor-binding domain's interaction network and dynamic properties (RBD) compared to the wild-type virus, focusing on its binding affinity to the human ACE2 (hACE2) receptor. Protein-protein docking and all-atom molecular dynamics simulations were used to analyze structural and dynamic differences. Despite the structural similarity to the wild-type virus, the Omicron variant exhibits a distinct interaction network involving new residues that enhance its binding capacity. The dynamic analysis reveals increased flexibility in the RBD, particularly in loop regions crucial for hACE2 interaction. Mutations significantly alter the secondary structure, leading to greater flexibility and conformational adaptability compared to the wild type. Binding free energy calculations confirm that the Omicron RBD has a higher binding affinity (-70.47 kcal/mol) to hACE2 than the wild-type RBD (-61.38 kcal/mol). These results suggest that the altered interaction network and enhanced dynamics of the Omicron variant contribute to its increased infectivity, providing insights for the development of targeted therapeutics and vaccines.

Keywords: SARS-CoV-2, molecular dynamic simulation, receptor binding domain, vaccine

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Authors: S. H. Nguyen, L. Li, R. S. Hegarty

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Two experiments were conducted assessing the effects of presence or absence of rumen protozoa and dietary nitrate addition on rumen fermentation characteristics and methane production in Brahman heifers. The first experiment assessed changes in rumen fermentation pattern and in-vitro methane production post-refaunation and the second experiment investigated whether addition of nitrate to the incubation would give rise to methane mitigation additional to that contributed by defaunation. Ten Brahman heifers were progressively adapted to a diet containing coconut oil distillate 4.5% (COD) for 18 d and then all heifers were defaunated using sodium 1-(2-sulfonatooxyethoxy) dodecane (Empicol). After 15 d, the heifers were given a second dose of Empicol. Fifteen days after the second dosing, all heifers were allocated to defaunated or refaunated groups by stratified randomisation. On d 48, an oral dose of rumen fluid collected from unrelated faunated cattle was used to inoculate 5 heifers and form a refaunated group so that the effects of re-establishment of protozoa on fermentation characteristics could be investigated. Samples of rumen fluid collected from each animal using oesophageal intubation before feeding on d 48, 55, 62 and 69 were incubated for 23h in-vitro (experiment 1). On day 82, 2% of NO3 (as NaNO3) was included in in-vitro incubations (experiment 2) to test for additivity of NO3 and absence of protozoa effects on fermentation and methane production. It was concluded that increasing protozoal numbers were associated with increased methane production, with methane production rate significantly higher from refaunated heifers than from defaunated heifers 7, 14 and 21 d after refaunation. Concentration and proportions of major VFA, however, were not affected by protozoal treatments. There is scope for further reducing methane output through combining defaunation and dietary nitrate as the addition of nitrate in the defaunated heifers resulted in 86% reduction in methane production in-vitro.

Keywords: defaunation, nitrate, fermentation, methane production

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Authors: Mennatallah M. Hussein, Olivier de Weck

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The advancement of space exploration demands a robust space launch services program capable of reliably propelling payloads into orbit. Despite rigorous testing and quality assurance, launch failures still occur, leading to significant financial losses and jeopardizing mission objectives. Traditional failure prediction methods often lack the sophistication to account for multi-mode failure scenarios, as well as the predictive capability in complex dynamic systems. Traditional approaches also rely on expert judgment, leading to variability in risk prioritization and mitigation strategies. Hence, there is a pressing need for robust approaches that enhance launch vehicle reliability from lift-off until it reaches its parking orbit through comprehensive simulation techniques. In this study, the developed model proposes a multi-mode launch vehicle simulation framework for predicting failure scenarios when incorporating new technologies, such as new propulsion systems or advanced staging separation mechanisms in the launch system. To this end, the model combined a 6-DOF system dynamics with comprehensive data analysis to simulate multiple failure modes impacting launch performance. The simulator utilizes high-fidelity physics-based simulations to capture the complex interactions between different subsystems and environmental conditions.

Keywords: launch vehicle, failure prediction, propulsion anomalies, rocket launch simulation, rocket dynamics

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Authors: Anurag Gaur Nidhi

Abstract:

Targeted drug delivery is a method of delivering medication to a patient in a manner that increases the concentration of the medication in some parts of the body relative to others. Targeted drug delivery seeks to concentrate the medication in the tissues of interest while reducing the relative concentration of the medication in the remaining tissues. This improves efficacy of the while reducing side effects. In the present work, we investigate the effect of magnetic field, flow rate and particle concentration on the capturing of magnetic particles transported in a stent implanted fluidic channel. Iron oxide magnetic nanoparticles (Fe3O4) nanoparticles were synthesized via co-precipitation method. The synthesized Fe3O4 nanoparticles were added in the de-ionized (DI) water to prepare the Fe3O4 magnetic particle suspended fluid. This fluid is transported in a cylindrical tube of diameter 8 mm with help of a peristaltic pump at different flow rate (25-40 ml/min). A ferromagnetic coil of SS 430 has been implanted inside the cylindrical tube to enhance the capturing of magnetic nanoparticles under magnetic field. The capturing of magnetic nanoparticles was observed at different magnetic magnetic field, flow rate and particle concentration. It is observed that capture efficiency increases from 47-67 % at magnetic field 2-5kG, respectively at particle concentration 0.6 mg/ml and at flow rate 30 ml/min. However, the capture efficiency decreases from 65 to 44 % by increasing the flow rate from 25 to 40 ml/min, respectively. Furthermore, it is observed that capture efficiency increases from 51 to 67 % by increasing the particle concentration from 0.3 to 0.6 mg/ml, respectively.

Keywords: capture efficiency, implant assisted-Magnetic drug targeting (IA-MDT), magnetic nanoparticles, In-vitro study

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Authors: Jonathan Galvan-Colin, Ariel Valladares, Renela Valladares, Alexander Valladares

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Both porous materials and bulk metallic glasses have been studied due to their potential applications and their exceptional physical and chemical properties. However, each material presents certain drawbacks which have been thought to be overcome by generating bulk metallic glass foams (BMGF). Although some experimental reports have been performed on multicomponent BMGF, still no ab initio works have been published, as far as we know. We present an approach based on the expanding lattice (EL) method to generate binary amorphous nanoporous Cu64Zr36. Starting from two different configurations: a 108-atom crystalline cubic supercell (cCu64Zr36) and a 108-atom amorphous supercell (aCu64Zr36), both with an initial density of 8.06 g/cm3, we applied EL method to halve the density and to get 50% of porosity. After the lattice expansion the supercells were subject to ab initio molecular dynamics for 500 steps at constant room temperature. Then, the samples were geometry-optimized and characterized with the pair and radial distribution functions, bond-angle distributions and a coordination number analysis. We found that pores appeared along specific spatial directions different from one to another and that they differed in size and form as well, which we think is related to the initial structure. Due to the lack of experimental counterparts our results should be considered predictive and further studies are needed in order to handle a larger number of atoms and its implication on pore topology.

Keywords: ab initio molecular dynamics, bulk mettalic glass, porous alloy

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Authors: Ismail Abubakar, Hamid Mehrabi, Reg Morton

Abstract:

Currently, extensive signal analysis is performed in order to evaluate structural health of turbomachinery blades. This approach is affected by constraints of time and the availability of qualified personnel. Thus, new approaches to blade dynamics identification that provide faster and more accurate results are sought after. Generally, modal analysis is employed in acquiring dynamic properties of a vibrating turbomachinery blade and is widely adopted in condition monitoring of blades. The analysis provides useful information on the different modes of vibration and natural frequencies by exploring different shapes that can be taken up during vibration since all mode shapes have their corresponding natural frequencies. Experimental modal testing and finite element analysis are the traditional methods used to evaluate mode shapes with limited application to real live scenario to facilitate a robust condition monitoring scheme. For a real time mode shape evaluation, rapid evaluation and low computational cost is required and traditional techniques are unsuitable. In this study, artificial neural network is developed to evaluate the mode shape of a lab scale rotating blade assembly by using result from finite element modal analysis as training data. The network performance evaluation shows that artificial neural network (ANN) is capable of mapping the correlation between natural frequencies and mode shapes. This is achieved without the need of extensive signal analysis. The approach offers advantage from the perspective that the network is able to classify mode shapes and can be employed in real time including simplicity in implementation and accuracy of the prediction. The work paves the way for further development of robust condition monitoring system that incorporates real time mode shape evaluation.

Keywords: modal analysis, artificial neural network, mode shape, natural frequencies, pattern recognition

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Authors: Richard Renou, Laurent Soulard

Abstract:

Lasers are widely used in glass material processing, from waveguide fabrication to channel drilling. The gradual damage of glass optics under UV lasers is also an important issue to be addressed. Glass materials (including metallic glasses) can undergo a permanent densification under laser-induced shock loading. Despite increased interest on interactions between laser and glass materials, little is known about the structural mechanisms involved under shock loading. For example, the densification process in silica glasses occurs between 8 GPa and 30 GPa. Above 30 GPa, the glass material returns to the original density after relaxation. Investigating these unusual mechanisms in silica glass will provide an overall better understanding in glass behaviour. Non-Equilibrium Molecular Dynamics simulations (NEMD) were carried out in order to gain insight on the silica glass microscopic structure under shock loading. The shock was generated by the use of a piston impacting the glass material at high velocity (from 100m/s up to 2km/s). Periodic boundary conditions were used in the directions perpendicular to the shock propagation to model an infinite system. One-dimensional shock propagations were therefore studied. Simulations were performed with the STAMP code developed by the CEA. A very specific structure is observed in a silica glass. Oxygen atoms around Silicon atoms are organized in tetrahedrons. Those tetrahedrons are linked and tend to form rings inside the structure. A significant amount of empty cavities is also observed in glass materials. In order to understand how a shock loading is impacting the overall structure, the tetrahedrons, the rings and the cavities were thoroughly analysed. An elastic behaviour was observed when the shock pressure is below 8 GPa. This is consistent with the Hugoniot Elastic Limit (HEL) of 8.8 GPa estimated experimentally for silica glasses. Behind the shock front, the ring structure and the cavity distribution are impacted. The ring volume is smaller, and most cavities disappear with increasing shock pressure. However, the tetrahedral structure is not affected. The elasticity of the glass structure is therefore related to a ring shrinking and a cavity closing. Above the HEL, the shock pressure is high enough to impact the tetrahedral structure. An increasing number of hexahedrons and octahedrons are formed with the pressure. The large rings break to form smaller ones. The cavities are however not impacted as most cavities are already closed under an elastic shock. After the material relaxation, a significant amount of hexahedrons and octahedrons is still observed, and most of the cavities remain closed. The overall ring distribution after relaxation is similar to the equilibrium distribution. The densification process is therefore related to two structural mechanisms: a change in the coordination of silicon atoms and a cavity closing. To sum up, non-equilibrium molecular dynamics were carried out to investigate silica behaviour under shock loading. Analysing the structure lead to interesting conclusions upon the elastic and the densification mechanisms in glass materials. This work will be completed with a detailed study of the mechanism occurring above 30 GPa, where no sign of densification is observed after the material relaxation.

Keywords: densification, molecular dynamics simulations, shock loading, silica glass

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