Search results for: computational biophysics

Authors: Subhankar Karmakar, Madhan Kumar Vasudevan, Manivannan Muniyandi

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Thermal Grill Illusion (TGI) elicits a strong and often painful sensation of burn when interlacing warm and cold stimuli that are individually non-painful, excites thermoreceptors beneath the skin. Among several theories of TGI, the “disinhibition” theory is the most widely accepted in the literature. According to this theory, TGI is the result of the disinhibition or unmasking of the pain-sensitive HPC (Heat-Pinch-Cold) nerve fibers due to the inhibition of cold-sensitive nerve fibers that are responsible for masking HPC nerve fibers. Although researchers focused on understanding TGI throughexperiments and models, none of them investigated the prediction of TGI pain intensity through a computational model. Furthermore, the comparison of psychophysically perceived TGI intensity with neurophysiological models has not yet been studied. The prediction of pain intensity through a computational model of TGI can help inoptimizing thermal displays and understanding pathological conditions related to temperature perception. The current studyfocuses on developing a computational model to predict the intensity of TGI pain and experimentally observe the perceived TGI pain. The computational model is developed based on the disinhibition theory and by utilizing the existing popular models of warm and cold receptors in the skin. The model aims to predict the neuronal activity of the HPC nerve fibers. With a temperature-controlled thermal grill setup, fifteen participants (ten males and five females) were presented with five temperature differences between warm and cold grills (each repeated three times). All the participants rated the perceived TGI pain sensation on a scale of one to ten. For the range of temperature differences, the experimentally observed perceived intensity of TGI is compared with the neuronal activity of pain-sensitive HPC nerve fibers. The simulation results show a monotonically increasing relationship between the temperature differences and the neuronal activity of the HPC nerve fibers. Moreover, a similar monotonically increasing relationship is experimentally observed between temperature differences and the perceived TGI intensity. This shows the potential comparison of TGI pain intensity observed through the experimental study with the neuronal activity predicted through the model. The proposed model intends to bridge the theoretical understanding of the TGI and the experimental results obtained through psychophysics. Further studies in pain perception are needed to develop a more accurate version of the current model.

Keywords: thermal grill Illusion, computational modelling, simulation, psychophysics, haptics

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Authors: Noah Odion, Honest Jimu, Blessing Atinuke Afuape

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Introduction: Motor control and gait abnormalities are commonly observed in individuals with autism spectrum disorder (ASD), affecting their mobility and coordination. Understanding the underlying neurological and biomechanical factors is essential for designing effective interventions. This study focuses on developing microchip-integrated wearable devices to capture real-time movement data from individuals with autism. By applying computational models to the collected data, we aim to analyze motor control patterns and gait abnormalities, bridging a crucial knowledge gap in autism-related motor dysfunction. Methods: We designed microchip-enabled wearable devices capable of capturing precise kinematic data, including joint angles, acceleration, and velocity during movement. A cross-sectional study was conducted on individuals with ASD and a control group to collect comparative data. Computational modelling was applied using machine learning algorithms to analyse motor control patterns, focusing on gait variability, balance, and coordination. Finite element models were also used to simulate muscle and joint dynamics. The study employed descriptive and analytical methods to interpret the motor data. Results: The wearable devices effectively captured detailed movement data, revealing significant gait variability in the ASD group. For example, gait cycle time was 25% longer, and stride length was reduced by 15% compared to the control group. Motor control analysis showed a 30% reduction in balance stability in individuals with autism. Computational models successfully predicted movement irregularities and helped identify motor control deficits, particularly in the lower limbs. Conclusions: The integration of microchip-based wearable devices with computational models offers a powerful tool for diagnosing and treating motor control deficits in autism. These results have significant implications for patient care, providing objective data to guide personalized therapeutic interventions. The findings also contribute to the broader field of neuroscience by improving our understanding of the motor dysfunctions associated with ASD and other neurodevelopmental disorders.

Keywords: motor control, gait abnormalities, autism, wearable devices, microchips, computational modeling, kinematic analysis, neurodevelopmental disorders

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Authors: Selma Bouasria, Mahi Abdelkader, Abbès Azzi, Herouz Keltoum

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This paper reports concept was used into the computational fluid dynamics (CFD) code cfx through user-defined functions to assess ventilation efficiency inside (forced-ventilation local). CFX is a simulation tool which uses powerful computer and applied mathematics, to model fluid flow situations for the prediction of heat, mass and momentum transfer and optimal design in various heat transfer and fluid flow processes to evaluate thermal comfort in a room ventilated (highly-glazed). The quality of the solutions obtained from CFD simulations is an effective tool for predicting the behavior and performance indoor thermo-aéraulique comfort.

Keywords: ventilation, thermal comfort, CFD, indoor environment, solar air heater

Procedia PDF Downloads 634

Authors: Abu Afree Andalib, Rafiur Rahman, Md Mezbah Uddin

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The main objective of this work is to anatomize on the various parameters of AGM 88 missile anatomized using FSI module in Ansys. Computational fluid dynamics is used for the study of fluid flow pattern and fluidic phenomenon such as drag, pressure force, energy dissipation and shockwave distribution in water. Using finite element analysis module of Ansys, structural parameters such as stress and stress density, localization point, deflection, force propagation is determined. Separate analysis on structural parameters is done on Abacus. State of the art coupling module is used for FSI analysis. Fine mesh is considered in every case for better result during simulation according to computational machine power. The result of the above-mentioned parameters is analyzed and compared for two phases using graphical representation. The result of Ansys and Abaqus are also showed. Computational Fluid Dynamics and Finite Element analyses and subsequently the Fluid-Structure Interaction (FSI) technique is being considered. Finite volume method and finite element method are being considered for modelling fluid flow and structural parameters analysis. Feasible boundary conditions are also utilized in the research. Significant change in the interaction and interference pattern while the impact was found. Theoretically as well as according to simulation angled condition was found with higher impact.

Keywords: FSI (Fluid Surface Interaction), impact, missile, high viscous fluid, CFD (Computational Fluid Dynamics), FEM (Finite Element Analysis), FVM (Finite Volume Method), fluid flow, fluid pattern, structural analysis, AGM-88, Ansys, Abaqus, meshing, k-omega, turbulence model

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Authors: Rofida Gamal, Mostafa Mohammed, Mariam Adel, Marwa Gamal, Marwa kamal, Ayat Saber, Maha Mamdouh, Amira Emad, Mai Ramadan

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Lynch Syndrome is an inherited genetic condition associated with an increased risk of colorectal and other cancers. Detecting Lynch Syndrome in individuals is crucial for early intervention and preventive measures. This study proposes a computational pipeline for Lynch Syndrome detection by integrating alignment, variant calling, and annotation. The pipeline leverages popular tools such as FastQC, Trimmomatic, BWA, bcftools, and ANNOVAR to process the input FASTQ file, perform quality trimming, align reads to the reference genome, call variants, and annotate them. It is believed that the computational pipeline was applied to a dataset of Lynch Syndrome cases, and its performance was evaluated. It is believed that the quality check step ensured the integrity of the sequencing data, while the trimming process is thought to have removed low-quality bases and adaptors. In the alignment step, it is believed that the reads were accurately mapped to the reference genome, and the subsequent variant calling step is believed to have identified potential genetic variants. The annotation step is believed to have provided functional insights into the detected variants, including their effects on known Lynch Syndrome-associated genes. The results obtained from the pipeline revealed Lynch Syndrome-related positions in the genome, providing valuable information for further investigation and clinical decision-making. The pipeline's effectiveness was demonstrated through its ability to streamline the analysis workflow and identify potential genetic markers associated with Lynch Syndrome. It is believed that the computational pipeline presents a comprehensive and efficient approach to Lynch Syndrome detection, contributing to early diagnosis and intervention. The modularity and flexibility of the pipeline are believed to enable customization and adaptation to various datasets and research settings. Further optimization and validation are believed to be necessary to enhance performance and applicability across diverse populations.

Keywords: Lynch Syndrome, computational pipeline, alignment, variant calling, annotation, genetic markers

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Authors: Wu Di, Yeo Khoon Seng, Lim Tee Tai

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The typical insects employ a flapping-wing mode of flight. The numerical simulations on free flight of a model fruit fly (Re=143) including hovering and are presented in this paper. Unsteady aerodynamics around a flapping insect is studied by solving the three-dimensional Newtonian dynamics of the flyer coupled with Navier-Stokes equations. A hybrid-grid scheme (Generalized Finite Difference Method) that combines great geometry flexibility and accuracy of moving boundary definition is employed for obtaining flow dynamics. The results show good points of agreement and consistency with the outcomes and analyses of other researchers, which validate the computational model and demonstrate the feasibility of this computational approach on analyzing fluid phenomena in insect flight. The present modeling approach also offers a promising route of investigation that could complement as well as overcome some of the limitations of physical experiments in the study of free flight aerodynamics of insects. The results are potentially useful for the design of biomimetic flapping-wing flyers.

Keywords: free hovering flight, flapping wings, fruit fly, insect aerodynamics, leading edge vortex (LEV), computational fluid dynamics (CFD), Navier-Stokes equations (N-S), fluid structure interaction (FSI), generalized finite-difference method (GFD)

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Authors: Hanik Park, Kyungsook Jeon, Suchul Shin, Youngchul Park

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The air vent head prevents the inflow of seawater into the cargo holds when it is used for the ballast tank on heavy weather. In this study, the flow characteristics and the grid size were created by the application of Computational Fluid Dynamics by taking into the consideration of comparison of test results. Then, the accuracy of the analysis was verified by comparing with experimental results. Based on this analysis, accurate turbulence model and grid size can be selected. Thus, the design characteristic of air vent head for bulk carrier contributes the reliability based on the research results.

Keywords: bulk carrier, FEM, SST, vent

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Authors: Remo Waser, Simon Maranda, Anastasia Stamatiou, Ludger J. Fischer, Joerg Worlitschek

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In latent heat storage, a phase change material (PCM) is used to store thermal energy. The heat transfer rate during solidification is limited and considered as a key challenge in the development of latent heat storages. Thus, finned heat exchangers (HEX) are often utilized to increase the heat transfer rate of the storage system. In this study, a new modeling approach to calculating the heat transfer rate in latent thermal energy storages with complex HEX geometries is presented. This model allows for an optimization of the HEX design in terms of costs and thermal performance of the system. Modeling solidification processes requires the calculation of time-dependent heat conduction with moving boundaries. Commonly used computational fluid dynamic (CFD) methods enable the analysis of the heat transfer in complex HEX geometries. If applied to the entire storage, the drawback of this approach is the high computational effort due to small time steps and fine computational grids required for accurate solutions. An alternative to describe the process of solidification is the so-called temperature-based approach. In order to minimize the computational effort, a quasi-stationary assumption can be applied. This approach provides highly accurate predictions for tube heat exchangers. However, it shows unsatisfactory results for more complex geometries such as finned tube heat exchangers. The presented simulation model uses a temporal and spatial discretization of heat exchanger tube. The spatial discretization is based on the smallest possible symmetric segment of the HEX. The heat flow in each segment is calculated using finite volume method. Since the heat transfer fluid temperature can be derived using energy conservation equations, the boundary conditions at the inner tube wall is dynamically updated for each time step and segment. The model allows a prediction of the thermal performance of latent thermal energy storage systems using complex HEX geometries with considerably low computational effort.

Keywords: modelling of solidification, finned tube heat exchanger, latent thermal energy storage

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Authors: Hamed K. Esfahani, Bithin Datta

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Transport of reactive chemical contaminant species in groundwater aquifers is a complex and highly non-linear physical and geochemical process especially for real life scenarios. Simulating this transport process involves solving complex nonlinear equations and generally requires huge computational time for a given aquifer study area. Development of optimal remediation strategies in aquifers may require repeated solution of such complex numerical simulation models. To overcome this computational limitation and improve the computational feasibility of large number of repeated simulations, Genetic Programming based trained surrogate models are developed to approximately simulate such complex transport processes. Transport process of acid mine drainage, a hazardous pollutant is first simulated using a numerical simulated model: HYDROGEOCHEM 5.0 for a contaminated aquifer in a historic mine site. Simulation model solution results for an illustrative contaminated aquifer site is then approximated by training and testing a Genetic Programming (GP) based surrogate model. Performance evaluation of the ensemble GP models as surrogate models for the reactive species transport in groundwater demonstrates the feasibility of its use and the associated computational advantages. The results show the efficiency and feasibility of using ensemble GP surrogate models as approximate simulators of complex hydrogeologic and geochemical processes in a contaminated groundwater aquifer incorporating uncertainties in historic mine site.

Keywords: geochemical transport simulation, acid mine drainage, surrogate models, ensemble genetic programming, contaminated aquifers, mine sites

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Authors: Olayiwola Moruf Oyedunsi

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This paper discusses the Modified Variational Iteration Method (MVIM) for the solution of nonlinear Burgers’ equation arising in longitudinal dispersion phenomena in fluid flow through porous media. The method is an elegant combination of Taylor’s series and the variational iteration method (VIM). Using Maple 18 for implementation, it is observed that the procedure provides rapidly convergent approximation with less computational efforts. The result shows that the concentration C(x,t) of the contaminated water decreases as distance x increases for the given time t.

Keywords: modified variational iteration method, Burger’s equation, porous media, partial differential equation

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Authors: Christopher Deekia Nwimae, Nigel Simms, Liyun Lao

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Erosion in pipe bends caused by particles is a major obstacle in the oil and gas fields and might cause the breakdown of production equipment. This work studied the effects imposed by flow velocity and impact of solid particles diameter in an elbow; erosion rate was verified with experimental data using the computational fluid dynamics (CFD) approach. Two-way coupled Euler-Lagrange and discrete phase model was employed to calculate the air/solid particle flow in an elbow. One erosion model and three-particle rebound models were used to predict the erosion rate on the 90° elbows. The generic erosion model was used in the CFD-based erosion model, and after comparing it with experimental data, results showed agreement with the CFD-based predictions as observed.

Keywords: erosion, prediction, elbow, computational fluid dynamics

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Authors: Raza Abdulla Saeed

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In this study, the three-dimensional cavitating turbulent flow in a complete Francis turbine is simulated using mixture model for cavity/liquid two-phase flows. Numerical analysis is carried out using ANSYS CFX software release 12, and standard k-ε turbulence model is adopted for this analysis. The computational fluid domain consist of spiral casing, stay vanes, guide vanes, runner and draft tube. The computational domain is discretized with a three-dimensional mesh system of unstructured tetrahedron mesh. The finite volume method (FVM) is used to solve the governing equations of the mixture model. Results of cavitation on the runner’s blades under three different boundary conditions are presented and discussed. From the numerical results it has been found that the numerical method was successfully applied to simulate the cavitating two-phase turbulent flow through a Francis turbine, and also cavitation is clearly predicted in the form of water vapor formation inside the turbine. By comparison the numerical prediction results with a real runner; it’s shown that the region of higher volume fraction obtained by simulation is consistent with the region of runner cavitation damage.

Keywords: computational fluid dynamics, hydraulic francis turbine, numerical simulation, two-phase mixture cavitation model

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Authors: Kalpana Dahiya

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This paper discusses a two-level hierarchical time minimization transportation problem, which is an important class of transportation problems arising in industries. This problem has been studied by various researchers, and a number of polynomial time iterative algorithms are available to find its solution. All the existing algorithms, though efficient, have some shortcomings. The current study proposes an alternate solution algorithm for the problem that is more efficient in terms of computational time than the existing algorithms. The results justifying the underlying theory of the proposed algorithm are given. Further, a detailed comparison of the computational behaviour of all the algorithms for randomly generated instances of this problem of different sizes validates the efficiency of the proposed algorithm.

Keywords: global optimization, hierarchical optimization, transportation problem, concave minimization

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Authors: Seyed Sadegh Naseralavi, Sadegh Balaghi, Ehsan Khojastehfar

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Time history dynamic analysis of structures is considered as an exact method while being computationally intensive. Filtration of earthquake strong ground motions applying wavelet transform is an approach towards reduction of computational efforts, particularly in optimization of structures against seismic effects. Wavelet transforms are categorized into continuum and discrete transforms. Since earthquake strong ground motion is a discrete function, the discrete wavelet transform is applied in the present paper. Wavelet transform reduces analysis time by filtration of non-effective frequencies of strong ground motion. Filtration process may be repeated several times while the approximation induces more errors. In this paper, strong ground motion of earthquake has been filtered once applying each wavelet. Strong ground motion of Northridge earthquake is filtered applying various wavelets and dynamic analysis of sampled shear and moment frames is implemented. The error, regarding application of each wavelet, is computed based on comparison of dynamic response of sampled structures with exact responses. Exact responses are computed by dynamic analysis of structures applying non-filtered strong ground motion.

Keywords: wavelet transform, computational error, computational duration, strong ground motion data

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Authors: Malo Pocheau-Lesteven, Olivier Le Maître

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Engineering and optimisation of complex systems is often achieved through multi-disciplinary analysis of the system, where each subsystem is modeled and interacts with other subsystems to model the complete system. The coherence of the output of the different sub-systems is achieved through the use of compatibility constraints, which enforce the coupling between the different subsystems. Due to the complexity of some sub-systems and the computational cost of evaluating their respective models, it is often necessary to build surrogate models of these subsystems to allow repeated evaluation these subsystems at a relatively low computational cost. In this paper, gaussian processes are used, as their probabilistic nature is leveraged to evaluate the likelihood of satisfying the compatibility constraints. This paper presents infilling strategies to build accurate surrogate models of the subsystems in areas where they are likely to meet the compatibility constraint. It is shown that these infilling strategies can reduce the computational cost of building surrogate models for a given level of accuracy. An application of these methods to velocity prediction programs used in offshore racing naval architecture further demonstrates these method's applicability in a real engineering context. Also, some examples of the application of uncertainty quantification to field of naval architecture are presented.

Keywords: infilling strategy, gaussian process, multi disciplinary analysis, velocity prediction program

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Authors: Mahendra Singh, Narasimhareddy Ravuru

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For the past decade, the production of biodiesel has significantly increased along with its by-product, glycerol. Biodiesel-derived glycerol massive entry into the glycerol market has caused its value to plummet. Newer ways to utilize the glycerol by-product must be implemented or the biodiesel industry will face serious economic problems. The biodiesel industry should consider steam reforming glycerol to produce hydrogen gas. Steam reforming is the most efficient way of producing hydrogen and there is a lot of demand for it in the petroleum and chemical industries. This study investigates the feasibility of glycerol steam reforming in an industrial sized fixed bed reactor. In this paper, using computational fluid dynamic (CFD) simulations, the extent of the transport resistances that would occur in an industrial sized reactor can be visualized. An important parameter in reactor design is the size of the catalyst particle. The size of the catalyst cannot be too large where transport resistances are too high, but also not too small where an extraordinary amount of pressure drop occurs. The goal of this paper is to find the best catalyst size under various flow rates that will result in the highest conversion. Computational fluid dynamics simulated the transport resistances and a pseudo-homogenous reactor model was used to evaluate the pressure drop and conversion. CFD simulations showed that glycerol steam reforming has strong internal diffusion resistances resulting in extremely low effectiveness factors. In the pseudo-homogenous reactor model, the highest conversion obtained with a Reynolds number of 100 (29.5 kg/h) was 9.14% using a 1/6 inch catalyst diameter. Due to the low effectiveness factors and high carbon deposition rates, a fluidized bed is recommended as the appropriate reactor to carry out glycerol steam reforming.

Keywords: computational fluid dynamic, fixed bed reactor, glycerol, steam reforming, biodiesel

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Authors: Indri Mahadiraka Rumamby, R. R. Dwinanti Rika Marthanty, Jessica Sjah

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Smoothed particle hydrodynamics (SPH) was originally created to simulate nonaxisymmetric phenomena in astrophysics. However, this method still has several shortcomings, namely the high computational cost required to model values with high resolution and problems with boundary conditions. The difficulty of modeling boundary conditions occurs because the SPH method is influenced by particle deficiency due to the integral of the kernel function being truncated by boundary conditions. This research aims to answer if SPH modeling with a focus on boundary layer interactions and continuous flow can produce quantifiably accurate values with low computational cost. This research will combine algorithms and coding in the main program of meandering river, continuous flow algorithm, and solid-fluid algorithm with the aim of obtaining quantitatively accurate results on solid-fluid interactions with the continuous flow on a meandering channel using the SPH method. This study uses the Fortran programming language for modeling the SPH (Smoothed Particle Hydrodynamics) numerical method; the model is conducted in the form of a U-shaped meandering open channel in 3D, where the channel walls are soil particles and uses a continuous flow with a limited number of particles.

Keywords: smoothed particle hydrodynamics, computational fluid dynamics, numerical simulation, fluid mechanics

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Authors: Aymen Laadhari, Gábor Székely

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In this work, the hemodynamics in the sinuses of Valsalva after Transcatheter Aortic Valve Implantation is numerically examined. We focus on the physical results in the two-dimensional case. We use a finite element methodology based on a Lagrange multiplier technique that enables to couple the dynamics of blood flow and the leaflets’ movement. A massively parallel implementation of a monolithic and fully implicit solver allows more accuracy and significant computational savings. The elastic properties of the aortic valve are disregarded, and the numerical computations are performed under physiologically correct pressure loads. Computational results depict that blood flow may be subject to stagnation in the lower domain of the sinuses of Valsalva after Transcatheter Aortic Valve Implantation.

Keywords: hemodynamics, simulations, stagnation, valve

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Authors: J. Joy, T. H. New, I. H. Ibrahim

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A computational study on bio-inspired NACA634-021 hydrofoils with leading-edge protuberances has been carried out to investigate their hydrodynamic flow control characteristics at a Reynolds number of 14,000 and different angles-of-attack. The numerical simulations were performed using ANSYS FLUENT and based on Reynolds-Averaged Navier-Stokes (RANS) solver mode incorporated with k-ω Shear Stress Transport (SST) turbulence model. The results obtained indicate varying flow phenomenon along the peaks and troughs over the span of the hydrofoils. Compared to the baseline hydrofoil with no leading-edge protuberances, the leading-edge modified hydrofoils tend to reduce flow separation extents along the peak regions. In contrast, there are increased flow separations in the trough regions of the hydrofoil with leading-edge protuberances. Interestingly, it was observed that dissimilar flow separation behaviour is produced along different peak- or trough-planes along the hydrofoil span, even though the troughs or peaks are physically similar at each interval for a particular hydrofoil. Significant interactions between adjacent flow structures produced by the leading-edge protuberances have also been observed. These flow interactions are believed to be responsible for the dissimilar flow separation behaviour along physically similar peak- or trough-planes.

Keywords: computational fluid dynamics, flow separation control, hydrofoils, leading-edge protuberances

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Authors: Imane Benghalia, Mohammed Zamoum, Rachid Boucetta

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Hydrodynamic cavitation is a complex physical phenomenon that appears in hydraulic systems (pumps, turbines, valves, Venturi tubes, etc.) when the fluid pressure decreases below the saturated vapor pressure. The works carried out in this study aimed to get a better understanding of the cavitating flow phenomena. For this, we have numerically studied a cavitating bubbly flow through a Venturi nozzle. The cavitation model is selected and solved using a commercial computational fluid dynamics (CFD) code. The obtained results show the effect of the inlet pressure (10, 7, 5, and 2 bars) of the Venturi on pressure, the velocity of the fluid flow, and the vapor fraction. We found that the inlet pressure of the Venturi strongly affects the evolution of the pressure, velocity, and vapor fraction formation in the cavitating flow.

Keywords: cavitating flow, CFD, phase change, venturi

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Authors: Norhashidah Hj. Mohd Ali, Teng Wai Ping

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In this paper, we present a high order group explicit method in solving the two dimensional Helmholtz equation. The presented method is derived from a nine-point fourth order finite difference approximation formula obtained from a 45-degree rotation of the standard grid which makes it possible for the construction of iterative procedure with reduced complexity. The developed method will be compared with the existing group iterative schemes available in literature in terms of computational time, iteration counts, and computational complexity. The comparative performances of the methods will be discussed and reported.

Keywords: explicit group method, finite difference, helmholtz equation, rotated grid, standard grid

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Authors: M. H. Alhajeri, Hamad M. Alhajeri, A. H. Alenezi

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This paper reports a Computational Fluid Dynamics (CFD) investigation for a high-temperature high-pressure filtration (ceramic candle filter). However, parallel flow to the filter is considered in this study. Different face (filtration) velocities are examined using the CFD code, FLUENT. Different sizes of particles are tracked through the domain to find the height at which the particles will impinge on the filter surface. Furthermore, particle distribution around the filter (or filter cake) is studied to design efficient cleaning mechanisms. Gravity effect to the particles with various inlet velocities and pressure drop are both considered. In the CFD study, it is found that the gravity influence should not be ignored if the particle sizes exceed 1 micron.

Keywords: fluid flow, CFD, filtration, HTHP

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Authors: Ashish Kumar Agrahari, Amit Kumar

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Paroxysmal nocturnal hemoglobinuria (PNH) is an acquired clonal blood disorder that manifests with hemolytic anemia, thrombosis, and peripheral blood cytopenias. The disease is caused by the deficiency of two glycosylphosphatidylinositols (GPI)-anchored proteins (CD55 and CD59) in the hemopoietic stem cells. The deficiency of GPI-anchored proteins has been associated with the somatic mutations in phosphatidylinositol glycan class A (PIGA). However, the mutations that do not cause PNH is associated with the multiple congenital anomalies-hypotonia-seizures syndrome 2 (MCAHS2). To best of our knowledge, no computational study has been performed to explore the atomistic level impact of PIGA mutations on the structure and dynamics of the protein. In the current work, we are mainly interested to get insights into the molecular mechanism of PIGA mutations. In the initial step, we screened the most pathogenic mutations from the pool of publicly available mutations. Further, to get a better understanding, pathogenic mutations were mapped to the modeled structure and subjected to 50ns molecular dynamics simulation. Our computational study suggests that four mutations are highly vulnerable to altering the structural conformation and stability of the PIGA protein, which illustrates its association with PNH and MCAHS2 phenotype.

Keywords: homology modeling, molecular dynamics simulation, missense mutations PNH, MCAHS2, PIGA

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Authors: Troy M. Houser

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The successor representation balances flexible and efficient reinforcement learning by learning to predict the future, given the present. As such, the successor representation models stimuli as what future states they lead to. Therefore, two stimuli that are perceptually dissimilar but lead to the same future state will come to be represented more similarly. This is very similar to an older behavioral paradigm -the acquired equivalence paradigm, which measures the generalization of learned associations. Here, we test via computational modeling the plausibility that the successor representation is the mechanism by which people generalize knowledge learned in the acquired equivalence paradigm. Computational evidence suggests that this is a plausible mechanism for acquired equivalence and thus can guide future empirical work on individual differences in associative-based generalization.

Keywords: acquired equivalence, successor representation, generalization, decision-making

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Authors: Nagaratna Rajur, J. D. Mallapur, Y. B. Kirankumar

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The security in mobile communication is very different from the internet or telecommunication, because of its poor user interface and limited processing capacity, as well as combination of complex network protocols. Hence, it poses a challenge for less memory usage and low computation speed based security system. Security involves all the activities that are undertaken to protect the value and on-going usability of assets and the integrity and continuity of operations. An effective network security strategies requires identifying threats and then choosing the most effective set of tools to combat them. Cryptography is a simple and efficient way to provide security in communication. RSA is an asymmetric key approach that is highly reliable and widely used in internet communication. However, it has not been efficiently implemented in mobile communication due its computational complexity and large memory utilization. The proposed algorithm modifies the current RSA to be useful in mobile communication by reducing its computational complexity and memory utilization.

Keywords: M-RSA, sensor networks, sensor applications, security

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Authors: P. Deepak Kumar, P. R. Maiti

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In recent years, sediment scour near bridge piers and abutment is a serious problem which causes nationwide concern because it has resulted in more bridge failures than other causes. Scour is the formation of scour hole around the structure mounted on and embedded in erodible channel bed due to the erosion of soil by flowing water. The formation of scour hole around the structures depends upon shape and size of the pier, depth of flow as well as angle of attack of flow and sediment characteristics. The flow characteristics around these structures change due to man-made obstruction in the natural flow path which changes the kinetic energy of the flow around these structures. Excessive scour affects the stability of the foundation of the structure by the removal of the bed material. The accurate estimation of scour depth around bridge pier is very difficult. The foundation of bridge piers have to be taken deeper and to provide sufficient anchorage length required for stability of the foundation. In this study, computational model simulations using a 3D Computational Fluid Dynamics (CFD) model were conducted to examine the mechanism of scour around a cylindrical pier. Subsequently, the flow characteristics around these structures are presented for different flow conditions. Mechanism of scouring phenomenon, the formation of vortex and its consequent effect is discussed for a straight channel. Effort was made towards estimation of scour depth around bridge piers under different flow conditions.

Keywords: bridge pier, computational fluid dynamics, multigrid, pier shape, scour

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Authors: Salvatore Luongo, Carlo Luongo

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This paper discusses the implementation solutions to reduce the computational load for the Traffic Situational Awareness with Alerts (TSAA) application, based on Automatic Dependent Surveillance-Broadcast (ADS-B) technology. In 2008, there were 23 total mid-air collisions involving general aviation fixed-wing aircraft, 6 of which were fatal leading to 21 fatalities. These collisions occurred during visual meteorological conditions, indicating the limitations of the see-and-avoid concept for mid-air collision avoidance as defined in the Federal Aviation Administration’s (FAA). The commercial aviation aircraft are already equipped with collision avoidance system called TCAS, which is based on classic transponder technology. This system dramatically reduced the number of mid-air collisions involving air transport aircraft. In general aviation, the same reduction in mid-air collisions has not occurred, so this reduction is the main objective of the TSAA application. The major difference between the original conflict detection application and the TSAA application is that the conflict detection is focused on preventing loss of separation in en-route environments. Instead TSAA is devoted to reducing the probability of mid-air collision in all phases of flight. The TSAA application increases the flight crew traffic situation awareness providing alerts of traffic that are detected in conflict with ownship in support of the see-and-avoid responsibility. The relevant effort has been spent in the design process and the code generation in order to maximize the efficiency and performances in terms of computational load and memory consumption reduction. The TSAA architecture is divided into two high-level systems: the “Threats database” and the “Conflict detector”. The first one receives the traffic data from ADS-B device and provides the memorization of the target’s data history. Conflict detector module estimates ownship and targets trajectories in order to perform the detection of possible future loss of separation between ownship and each target. Finally, the alerts are verified by additional conflict verification logic, in order to prevent possible undesirable behaviors of the alert flag. In order to reduce the computational load, a pre-check evaluation module is used. This pre-check is only a computational optimization, so the performances of the conflict detector system are not modified in terms of number of alerts detected. The pre-check module uses analytical trajectories propagation for both target and ownship. This allows major accuracy and avoids the step-by-step propagation, which requests major computational load. Furthermore, the pre-check permits to exclude the target that is certainly not a threat, using an analytical and efficient geometrical approach, in order to decrease the computational load for the following modules. This software improvement is not suggested by FAA documents, and so it is the main innovation of this work. The efficiency and efficacy of this enhancement are verified using fast-time and real-time simulations and by the execution on a real device in several FAA scenarios. The final implementation also permits the FAA software certification in compliance with DO-178B standard. The computational load reduction allows the installation of TSAA application also on devices with multiple applications and/or low capacity in terms of available memory and computational capabilities

Keywords: traffic situation awareness, general aviation, aircraft conflict detection, computational load reduction, implementation solutions, software certification

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Authors: Rajat Mittal, Jung Hee Seo, Jacob Turner, Harshal Raut

Abstract:

The perpetual advancement in computational capabilities, coupled with the continuous evolution of software tools and numerical algorithms, is creating novel avenues for research, exploration, and application at the nexus of computational fluid and structural mechanics. Fish leverage their remarkably flexible bodies and fins to harness energy from vortices, propelling themselves with an elegance and efficiency that captivates engineers. Bats fly with unparalleled agility and speed by using their flexible membrane wings. Wave-assisted propulsion (WAP) systems, utilizing elastically mounted hydrofoils, convert wave energy into thrust. Each of these problems involves a complex and elegant interplay between fluid dynamics and structural mechanics. Historically, investigations into such phenomena were constrained by available tools, but modern computational advancements now facilitate exploration of these multi-physics challenges with an unprecedented level of fidelity, precision, and realism. In this work, the author will discuss projects that harness the capabilities of high-fidelity sharp-interface immersed boundary methods to address a spectrum of engineering and biological challenges involving fluid-structure interaction.

Keywords: immersed boundary methods, CFD, bioflight, fluid structure interaction

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Authors: Emanuele Bonamente, Andrea Aquino, Franco Cotana

Abstract:

The exploitation of the low-temperature geothermal resource via ground-source heat pumps is often limited by the high investment cost mainly due to borehole drilling. From the monitoring of a prototypal system currently used by a commercial building, it was found that a simple upgrade of the conventional layout, obtained including a thermal storage between the ground-source heat exchangers and the heat pump, can optimize the ground energy exploitation requiring for shorter/fewer boreholes. For typical applications, a reduction of up to 66% with respect to the conventional layout can be easily achieved. Results from the monitoring campaign of the prototype are presented in this paper, and upgrades of the thermal storage using phase change materials (PCMs) are proposed using computational fluid dynamics simulations. The PCM thermal storage guarantees an improvement of the system coefficient of performance both for summer cooling and winter heating (up to 25%). A drastic reduction of the storage volume (approx. 1/10 of the original size) is also achieved, making it possible to easily place it within the technical room, avoiding extra costs for underground displacement. A preliminary optimization of the PCM geometry is finally proposed.

Keywords: computational fluid dynamics (CFD), geothermal energy, ground-source heat pumps, phase change materials (PCM)

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Authors: Janneth Gonzalez, Marco Avila, George Barreto

Abstract:

GRP78 participates in multiple functions in the cell during normal and pathological conditions, controlling calcium homeostasis, protein folding and unfolded protein response. GRP78 is located in the endoplasmic reticulum, but it can change its location under stress, hypoxic and apoptotic conditions. NF-κB represents the keystone of the inflammatory process and regulates the transcription of several genes related with apoptosis, differentiation, and cell growth. The possible relationship between GRP78-NF-κB could support and explain several mechanisms that may regulate a variety of cell functions, especially following brain injuries. Although several reports show interactions between NF-κB and heat shock proteins family members, there is a lack of information on how GRP78 may be interacting with NF-κB, and possibly regulating its downstream activation. Therefore, we assessed the computational predictions of the GRP78 (Chain A) and NF-κB complex (IkB alpha and p65) protein-protein interactions. The interaction interface of the docking model showed that the amino acids ASN 47, GLU 215, GLY 403 of GRP78 and THR 54, ASN 182 and HIS 184 of NF-κB are key residues involved in the docking. The electrostatic field between GRP78-NF-κB interfaces and molecular dynamic simulations support the possible interaction between the proteins. In conclusion, this work shed some light in the possible GRP78-NF-κB complex indicating key residues in this crosstalk, which may be used as an input for better drug design strategy targeting NF-κB downstream signaling as a new therapeutic approach following brain injuries.

Keywords: computational biology, protein interactions, Grp78, bioinformatics, molecular dynamics

Procedia PDF Downloads 343