Search results for: first-principle molecular dynamics simulation of multiscale shock technique

Authors: Asho Ali

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Tuberculosis is a disease of grave concern which infects one-third of the global population. The high incidence of tuberculosis is further compounded by the increasing emergence of drug resistant strains including multi drug resistant (MDR). Global incidence MDR-TB is ~4%. Molecular epidemiological studies, based on the assumption that patients infected with clustered strains are epidemiologically linked, have helped understand the transmission dynamics of disease. It has also helped to investigate the basis of variation in Mycobacterium tuberculosis (MTB) strains, differences in transmission, and severity of disease or drug resistance mechanisms from across the globe. This has helped in developing strategies for the treatment and prevention of the disease including MDR.

Keywords: Mycobcaterium tuberculosis, molecular epidemiology, drug resistance, disease

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Authors: Yansong Zhang, Xueyuan Li, Junjie Zhou, Xufeng Yin, Shihua Yuan, Shuxian Liu

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Aiming at the verification of control algorithms for skid-steering vehicles, a vehicle simulation model of 6×6 electric skid-steering unmanned vehicle was established based on Trucksim and Simulink. The original transmission and steering mechanism of Trucksim are removed, and the electric skid-steering model and a closed-loop controller for the vehicle speed and yaw rate are built in Simulink. The simulation results are compared with the ones got by theoretical formulas. The results show that the predicted tire mechanics and vehicle kinematics of Trucksim-Simulink simulation model are closed to the theoretical results. Therefore, it can be used as an effective approach to study the dynamic performance and control algorithm of skid-steering vehicle. In this paper, a method of motion control based on feed forward control is also designed. The simulation results show that the feed forward control strategy can make the vehicle follow the target yaw rate more quickly and accurately, which makes the vehicle have more maneuverability.

Keywords: skid-steering, Trucksim-Simulink, feedforward control, dynamics

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Authors: Ming-Yen Chang, Sheng-Hung Ke

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This research focuses on the development of a speed bump identification system for real-time control of adjustable shock absorbers in vehicular suspension systems. The study initially involved the collection of images of various speed bumps, and rubber speed bump profiles found on roadways. These images were utilized for training and recognition purposes through the deep learning object detection algorithm YOLOv5. Subsequently, the trained speed bump identification program was integrated with an in-vehicle camera system for live image capture during driving. These images were instantly transmitted to a computer for processing. Using the principles of monocular vision ranging, the distance between the vehicle and an approaching speed bump was determined. The appropriate control distance was established through both practical vehicle measurements and theoretical calculations. Collaboratively, with the electronically adjustable shock absorbers equipped in the vehicle, a shock absorber control system was devised to dynamically adapt the damping force just prior to encountering a speed bump. This system effectively mitigates passenger discomfort and enhances ride quality.

Keywords: adjustable shock absorbers, image recognition, monocular vision ranging, ride

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Authors: Sergio N. P. Laitón, Paulo G. P. Toro, João F. Martos

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A numerical study has been carried out to investigate the flow characteristics and performance of the 14-X B inlet with blunted cowl-lip. The Brazilian aerospace hypersonic vehicle 14-X B is a technology demonstrator of a hypersonic air-breathing propulsion system, based on supersonic combustion ramjet (scramjet). It is designed for Earth's atmospheric flight at Mach number of 6 and an altitude of 30 km. Currently, it is under development in the aerothermodynamics and hypersonic Professor Henry T. Nagamatsu laboratory at Advanced Studies Institute (IEAv). Numerical simulations were conducted at nominal freestream Mach number and altitude for two cowl-lip blunting radius and several angles of attack close to horizontal flight. The results show that the shock interference behavior on the blunted cowl-lip change with the angle of attack and blunted radius. The type VI or V together with III shock interferences are more likely to occur simultaneously at small negative angles of attack. When the inlet operates in positive angles of attack higher to 1, no shock interference occurs, only the bow shock conditions. The results indicate a high air pressure at beginning of the combustor and higher pressure recovery with 2 mm radius and positives angles of attack.

Keywords: blunted cowl-lip, hypersonic inlet, inlet unstart, shock interference

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Authors: Hiroyuki Aoki

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Polymeric materials are often used in a form of thin film such as food wrap and surface coating. In such the applications, polymer films thinner than 100 nm have been often used. The thickness of such the ultra-thin film is less than the unperturbed size of a polymer chain; therefore, the polymer chain in an ultra-thin film is strongly constrained. However, the details on the constrained dynamics of polymer molecules in ultra-thin films are still unclear. In the current study, the segmental dynamics of single polymer chain was directly investigated by fluorescence microscopy. The individual chains of poly(alkyl methacrylate) labeled by a perylenediimide dye molecule were observed by a highly sensitive fluorescence microscope in a defocus condition. The translational and rotational diffusion of the center segment in a single polymer chain was directly analyzed. The segmental motion in a thin film with a thickness of 10 nm was found to be suppressed compared to that in a bulk state. The detailed analysis of the molecular motion revealed that the diffusion rate of the in-plane rotation was similar to the thin film and the bulk; on the other hand, the out-of-plane motion was restricted in a thin film. This result indicates that the spatial restriction in an ultra-thin film thinner than the unperturbed chain dimension alters the dynamics of individual molecules in a polymer system.

Keywords: polymer materials, single molecule, molecular motion, fluorescence microscopy, super-resolution techniques

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Authors: Javier Varillas, Jorge Alcalá

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We investigate dislocation avalanche phenomena in face-centered cubic (FCC) and body-centered cubic (BCC) crystals using massive, large-scale molecular dynamics (MD) simulations. The analysis is focused on the intermittent development of dense dislocation arrangements subjected to uniaxial tensile straining under displacement control. We employ a novel computational scheme that allows us to inject an entangled dislocation structure in periodic MD domains. We assess the emission of plastic bursts (or dislocation avalanches) in terms of the sharp stress drops detected in the stress-strain curve. The plastic activity corresponds to the sporadic operation of specific dislocation glide processes exhibiting quiescent periods between successive avalanche events. We find that the plastic intermittences in our simulations do not overlap in time under sufficiently low strain rates as dissipation operates faster than driving, where the dense dislocation networks evolve through the emission of dislocation avalanche events whose carried slip adheres to self-organized power-law distributions. These findings enable the extension of the slip distributions obtained from strict displacement-controlled micropillar compression experiments towards smaller values of slip size. Our results furnish further understanding upon the development of entangled dislocation networks in metal plasticity, including specific mechanisms of dislocation propagation and annihilation, along with the evolution of specific dislocation populations through dislocation density analyses.

Keywords: dislocations, intermittent plasticity, molecular dynamics, slip distributions

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Authors: Geetanjali Yadav, Arpit Mishra, Parthsarathi Ghosh, Ramkrishna Sen

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The world is facing problems of increasing global CO2 emissions, climate change and fuel crisis. Therefore, several renewable and sustainable energy alternatives should be investigated to replace non-renewable fuels in future. Algae presents itself a versatile feedstock for the production of variety of fuels (biodiesel, bioethanol, bio-hydrogen etc.) and high value compounds for food, fodder, cosmetics and pharmaceuticals. Microalgae are simple microorganisms that require water, light, CO2 and nutrients for growth by the process of photosynthesis and can grow in extreme environments, utilize waste gas (flue gas) and waste waters. Mixing, however, is a crucial parameter within the culture system for the uniform distribution of light, nutrients and gaseous exchange in addition to preventing settling/sedimentation, creation of dark zones etc. The overarching goal of the present study is to improve photobioreactor (PBR) design for enhancing dissolution of CO2 from ambient air (0.039%, v/v), pure CO2 and coal-fired flue gas (10 ± 2%) into microalgal PBRs. Computational fluid dynamics (CFD), a state-of-the-art technique has been used to solve partial differential equations with turbulence closure which represents the dynamics of fluid in a photobioreactor. In this paper, the hydrodynamic performance of the PBR has been characterized and compared with that of the conventional bubble column PBR using CFD. Parameters such as flow rate (Q), mean velocity (u), mean turbulent kinetic energy (TKE) were characterized for each experiment that was tested across different aeration schemes. The results showed that the modified PBR design had superior liquid circulation properties and gas-liquid transfer that resulted in creation of uniform environment inside PBR as compared to conventional bubble column PBR. The CFD technique has shown to be promising to successfully design and paves path for a future research in order to develop PBRs which can be commercially available for scale-up microalgal production.

Keywords: computational fluid dynamics, microalgae, bubble column photbioreactor, flue gas, simulation

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Authors: Jayanthi Sivaraman

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Claudins are the important components of the tight junctions that play a key role in paracellular permeability. Among various members of Claudin family, Claudin 4 (CLDN4) is found to be overexpressed in ovarian, pancreatic carcinomas and other epithelial malignancies. Therefore, in this study, an attempt has been made to identify potent inhibitors for CLDN4 from the ZINC database using virtual screening, molecular docking and molecular dynamics simulations. A well refined molecular model of CLDN4 was built using Prime of Schrodinger v10.2(Template- PDB ID: 4P79). Approximately, 6 million compounds from ZINC database are subjected to high-throughput virtual screening (HTVS) against the active site of CLDN4. Molecular docking using GLIDE predicted ARG31, ASN142, ASP146 and ARG158 as critically important residues. Furthermore, three compounds from ZINC database (ZINC96331839, ZINC36533519 and ZINC75819394) showed highly promising ADME properties and binding affinity with stable conformation. The therapeutic efficiency of these lead compounds is evaluated and confirmed by in-vitro and in-vivo studies which leads to the development of novel anti-cancer drugs.

Keywords: ADME property, inhibitors, molecular docking, virtual screening

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Authors: Darma Putra Sitepu, Dewi Larasati, Yohanes Wolter Hendrik George

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Sepsis is a life-threatening medical emergency frequently observed in intensive care unit (ICU). Surviving Sepsis Campaign in 2018 has recommended the administration of early vasopressor in the first hour of sepsis or septic shock but has not yet included de-resuscitation protocol. De-resuscitation in acute management of septic shock is where patient received active removal of accumulated fluid. It has been proposed by some studies and ongoing clinical trials. Here we present a case with early vasopressor and de-resuscitation. Male, 27 years old presenting to the emergency room with shortness of breath, altered mental status, and widespread blisters on his body and lips started a few hours prior, after receiving non-steroidal anti-inflammatory drug through intravenous injection. Patient was hypotensive, tachycardic, and tachypneic at admission, diagnosed with Steven Johnson Syndrome with Septic Shock. Patient received fluid resuscitation, early vasopressor, and diuresis agent aimed to actively remove fluid after the initial phase of resuscitation. Patient was admitted to ICU and progressively recovering. At day-10, patient was stabilized and was transferred to general ward. Early vasopressor and de-resuscitation are beneficial for the patient.

Keywords: sepsis, shock, de-resuscitation, vasopressor, fluid, case report

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Authors: Neha Thakur, Pravin S. More

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The interaction of CO, H2 and LPG with Cu-dosed SnO2 catalysts was studied by means of Fourier transform infrared spectroscopy (FTIR). With increasing Cu loading, pronounced and progressive red shifts of the C–O stretching frequency associated with molecular CO adsorbed on the Cu/SnO2 component were observed. This decrease in n(CO) correlates with enhancement of CO dissociation at higher temperatures on Cu promoted SnO2 catalysts under conditions, where clean Cu is almost ineffective. In the conclusion, the capability of our technique is discussed, and a technique for enhancing the sensitivity in our technique is proposed.

Keywords: FTIR, spectroscopic, dissociation, n(CO)

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Authors: Sheng-Bo Zhang, Huan-Hao Zhang, Zhi-Hua Chen, Chun Zheng

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In this paper, the Richtmyer-Meshkov instability has been studied numerically by using the high-resolution Roe scheme based on the two-dimensional unsteady Euler equation, which was caused by the interaction between shock wave and the helium circular light gas cylinder with different component distributions. The numerical results further discuss the deformation process of the gas cylinder, the wave structure of the flow field and quantitatively analyze the characteristic dimensions (length, height, and central axial width) of the gas cylinder, the volume compression ratio of the cylinder over time. In addition, the flow mechanism of shock-driven interface gas mixing is analyzed from multiple perspectives by combining it with the flow field pressure, velocity, circulation, and gas mixing rate. Then the effects of different initial component distribution conditions on interface instability are investigated. The results show when the diffusion interface transit to the sharp interface, the reflection coefficient gradually increases on both sides of the interface. When the incident shock wave interacts with the cylinder, the transmission of the shock wave will transit from conventional transmission to unconventional transmission. At the same time, the reflected shock wave is gradually strengthened, and the transmitted shock wave is gradually weakened, which leads to an increase in the Richtmyer-Meshkov instability. Moreover, the Atwood number on both sides of the interface also increases as the diffusion interface transit to the sharp interface, which leads to an increase in the Rayleigh-Taylor instability and the Kelvin-Helmholtz instability. Therefore, the increase in instability will lead to an increase the circulation, resulting in an increase in the growth rate of gas mixing rate.

Keywords: shock wave, He light cylinder, Richtmyer-Meshkov instability, Gaussian distribution

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Authors: Mohamed Moussaoui, Mouna Baassi, Soukayna Baammi, Hatim Soufi, Mohammed Salah, Rachid Daoud, Achraf EL Allali, Mohammed Elalaoui Belghiti, Said Belaaouad

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The present study aims to investigate the quantitative structure-activity relationship (QSAR) of a series of Thiazole derivatives reported as anticancer agents (hepatocellular carcinoma), using principally the electronic descriptors calculated by the density functional theory (DFT) method and by applying the multiple linear regression method. The developed model showed good statistical parameters (R²= 0.725, R²ₐ𝒹ⱼ= 0.653, MSE = 0.060, R²ₜₑₛₜ= 0.827, Q²𝒸ᵥ = 0.536). The energy of the highest occupied molecular orbital (EHOMO) orbital, electronic energy (TE), shape coefficient (I), number of rotatable bonds (NROT), and index of refraction (n) were revealed to be the main descriptors influencing the anti-cancer activity. Additional Thiazole derivatives were then designed and their activities and pharmacokinetic properties were predicted using the validated QSAR model. These designed molecules underwent evaluation through molecular docking (MD) and molecular dynamic (MD) simulations, with binding affinity calculated using the MMPBSA script according to a 100 ns simulation trajectory. This process aimed to study both their affinity and stability towards Cyclin-Dependent Kinase 2 (CDK2), a target protein for cancer disease treatment. The research concluded by identifying four CDK2 inhibitors - A1, A3, A5, and A6 - displaying satisfactory pharmacokinetic properties. MDs results indicated that the designed compound A5 remained stable in the active center of the CDK2 protein, suggesting its potential as an effective inhibitor for the treatment of hepatocellular carcinoma. The findings of this study could contribute significantly to the development of effective CDK2 inhibitors.

Keywords: QSAR, ADMET, Thiazole, anticancer, molecular docking, molecular dynamic simulations, MMPBSA calculation

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Authors: Keltoum Chahour, Mickael Binois

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Due to a lack of standardization during the invasive fractional flow reserve (FFR) procedure, the index is subject to many sources of uncertainties. In this paper, we investigate -through simulation- the effect of the (FFR) device position and configuration on the obtained value of the (FFR) fraction. For this purpose, we use computational fluid dynamics (CFD) in a 3D domain corresponding to a diseased arterial portion. The (FFR) pressure captor is introduced inside it with a given length and coefficient of bending to capture the (FFR) value. To get over the computational limitations, basically, the time of the simulation is about 2h 15min for one (FFR) value; we generate a Gaussian Process (GP) model for (FFR) prediction. The (GP) model indicates good accuracy and demonstrates the effective error in the measurement created by the random configuration of the pressure captor.

Keywords: fractional flow reserve, Gaussian processes, computational fluid dynamics, drift

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Authors: Luong A. Nguyen, Elihu Deneke, Thomas L. Harman

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This paper describes a multibody dynamics algorithm formulated for parallel implementation on multiprocessor computing platforms using the divide-and-conquer approach. The system of interest is a general topology of rigid and elastic articulated bodies with or without loops. The algorithm is an extension of Featherstone’s divide and conquer approach to include the flexible-body dynamics formulation. The equations of motion, configured for the International Space Station (ISS) with its robotic manipulator arm as a system of articulated flexible bodies, are implemented in separate computer processors. The performance of this divide-and-conquer algorithm implementation in multiple processors is compared with an existing method implemented on a single processor.

Keywords: multibody dynamics, multiple processors, multithreading, divide-and-conquer algorithm, computational efficiency, flexible body dynamics

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Authors: Timo Avikainen, Tuukka Verho

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The use of natural fibers as reinforcements is growing increasingly in polymers which are involved in e.g. structural, vibration, and acoustic applications. The use of bio composites is being investigated as lightweight materials with specific properties like the ability to dissipate vibration energy and positive environmental profile and are thus considered as potential replacements for synthetic composites. The macro-level mechanical properties of the biocomposite material depend on several parameters in the detailed architecture and morphology of the reinforcing fiber structure. The polymer matrix phase is often applied to remain the fiber structure in touch. A big role in the packaging details of the fibers is related to the used manufacturing processes like extrusion, injection molding and treatments. There are typically big variances in the detailed parameters of the microstructure fibers. The study addressed the question of how the multiscale simulation methodology works in bio composites with short pulp fibers. The target is to see how the vibro – acoustic performance of thin–walled panels can be controlled by the detailed characteristics of the fiber material. Panels can be used in sound-producing speakers or sound insulation applications. The multiscale analysis chain is tested starting from the microstructural level and continuing via macrostructural material parameters to the product component part/assembly levels. Another application is the dynamic impact type of loading, exposing the material to the crack type damages that is in this study modeled as the Charpy impact tests.

Keywords: bio composite, pulp fiber, vibration, acoustics, impact, FEM

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Authors: Giacomo Rossi, Bernardo Favini, Eugenio Giacomazzi, Franca Rita Picchia, Nunzio Maria Salvatore Arcidiacono

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A numerical technique for mesh refinement in the HeaRT (Heat Release and Transfer) numerical code is presented. In the CFD framework, Large Eddy Simulation (LES) approach is gaining in importance as a tool for simulating turbulent combustion processes, also if this approach has an high computational cost due to the complexity of the turbulent modeling and the high number of grid points necessary to obtain a good numerical solution. In particular, when a numerical simulation of a big domain is performed with a structured grid, the number of grid points can increase so much that the simulation becomes impossible: this problem can be overcame with a mesh refinement technique. Mesh refinement technique developed for HeaRT numerical code (a staggered finite difference code) is based on an high order reconstruction of the variables at the grid interfaces by means of a least square quasi-ENO interpolation: numerical code is written in modern Fortran (2003 standard of newer) and is parallelized using domain decomposition and message passing interface (MPI) standard.

Keywords: LES, multi-resolution, ENO, fortran

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Authors: Changgil Lee, Seunghee Park

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Although vehicle driving test for the development of BWIM system is necessary, but it needs much cost and time in addition application of various driving condition. Thus, we need the numerical-simulation method resolving the cost and time problems of vehicle driving test and the way of measuring response of bridge according to the various driving condition. Using the precision analysis model reflecting the dynamic characteristic is contributed to increase accuracy in numerical simulation. In this paper, we conduct a numerical simulation to apply precision analysis model, which reflects the dynamic characteristic of bridge using Bridge Weigh-in-Motion technique and suggest overload vehicle enforcement technology using precision analysis model.

Keywords: bridge weigh-in-motion(BWIM) system, precision analysis model, dynamic characteristic of bridge, numerical simulation

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Authors: Sundaram Arulmozhiraja, Kanade Shimizu, Yuta Yamamoto, Satoshi Ichikawa, Maenaka Katsumi, Hiroaki Tokiwa

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Drug discovery is shifting from small molecule based drugs targeting local active site to middle molecules (MM) targeting large, flat, and groove-shaped binding sites, for example, protein-protein interface because at least half of all targets assumed to be involved in human disease have been classified as “difficult to drug” with traditional small molecules. Hence, MMs such as peptides, natural products, glycans, nucleic acids with various high potent bioactivities become important targets for drug discovery programs in the recent years as they could be used for ‘undruggable” intracellular targets. Cell membrane permeability is one of the key properties of pharmacodynamically active MM drug compounds and so evaluating this property for the potential MMs is crucial. Computational prediction for cell membrane permeability of molecules is very challenging; however, recent advancement in the molecular dynamics simulations help to solve this issue partially. It is expected that MMs with high membrane permeability will enable drug discovery research to expand its borders towards intracellular targets. Further to understand the chemistry behind the permeability of MMs, it is necessary to investigate their conformational changes during the permeation through membrane and for that their interactions with the membrane field should be studied reliably because these interactions involve various non-bonding interactions such as hydrogen bonding, -stacking, charge-transfer, polarization dispersion, and non-classical weak hydrogen bonding. Therefore, parameters-based classical mechanics calculations are hardly sufficient to investigate these interactions rather, quantum mechanical (QM) calculations are essential. Fragment molecular orbital (FMO) method could be used for such purpose as it performs ab initio QM calculations by dividing the system into fragments. The present work is aimed to study the cell permeability of middle molecules using molecular dynamics simulations and FMO-QM calculations. For this purpose, a natural compound syringolin and its analogues were considered in this study. Molecular simulations were performed using NAMD and Gromacs programs with CHARMM force field. FMO calculations were performed using the PAICS program at the correlated Resolution-of-Identity second-order Moller Plesset (RI-MP2) level with the cc-pVDZ basis set. The simulations clearly show that while syringolin could not permeate the membrane, its selected analogues go through the medium in nano second scale. These correlates well with the existing experimental evidences that these syringolin analogues are membrane-permeable compounds. Further analyses indicate that intramolecular -stacking interactions in the syringolin analogues influenced their permeability positively. These intramolecular interactions reduce the polarity of these analogues so that they could permeate the lipophilic cell membrane. Conclusively, the cell membrane permeability of various middle molecules with potent bioactivities is efficiently studied using molecular dynamics simulations. Insight of this behavior is thoroughly investigated using FMO-QM calculations. Results obtained in the present study indicate that non-bonding intramolecular interactions such as hydrogen-bonding and -stacking along with the conformational flexibility of MMs are essential for amicable membrane permeation. These results are interesting and are nice example for this theoretical calculation approach that could be used to study the permeability of other middle molecules. This work was supported by Japan Agency for Medical Research and Development (AMED) under Grant Number 18ae0101047.

Keywords: fragment molecular orbital theory, membrane permeability, middle molecules, molecular dynamics simulation

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Authors: Jingde Li, Hong Hao

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Recent oil and gas accidents have reminded us the severe consequences of gas explosion on structure damage and financial loss. In order to protect the structures and personnel, engineers and researchers have been working on numerous different explosion mitigation methods. Amongst, venting is the most economical approach to mitigate gas explosion overpressure. In this paper, venting is used as the overpressure alleviation method. A theoretical method and a numerical technique are presented to predict the internal and external pressure from vented gas explosion in a large enclosure. Under idealized conditions, a number of experiments are used to calibrate the accuracy of the theoretically calculated data. A good agreement between the theoretical results and experimental data is seen. However, for realistic scenarios, the theoretical method over-estimates internal pressures and is incapable of predicting external pressures. Therefore, a CFD simulation procedure is proposed in this study to estimate both the internal and external overpressure from a large-scale vented explosion. Satisfactory agreement between CFD simulation results and experimental data is achieved.

Keywords: vented gas explosion, internal pressure, external pressure, CFD simulation, FLACS, ANSYS Fluent

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Authors: Amira M. Attia, Karim H. Youssef, Nabil H. Abbasy

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Energy consumption schedule (ECS) technique shifts usage of loads from on peak hours and redistributes them throughout the day according to residents’ operating time preferences. This technique is used as form of indirect control from utility to improve the load curve and hence its load factor and reduce customer’s total electric bill as well. Similarly, load shifting technique achieves ECS purposes but as direct control form applied from utility. In this paper, ECS is simulated twice as optimal constrained mathematical formula, solved by using CVX program in MATLAB^® R2013b. First, it is utilized for single residential building with ten apartments to determine max allowable energy consumption per hour for each residential apartment. Then, it is used for single apartment with number of shiftable domestic devices, where operating schedule is deduced using previous simulation output results as constraints. The paper ends by giving differences between ECS technique and load shifting technique via literature and simulation. Based on results assessment, it will be shown whether using ECS or load shifting is more beneficial to both customer and utility.

Keywords: energy consumption schedule, load shifting, comparison, demand side mangement

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Authors: D. Šedivý, S. Fialová

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The main purpose of this study is to show differences between the numerical solution of the flow through the artificial heart valve using Newtonian or non-Newtonian fluid. The simulation was carried out by a commercial computational fluid dynamics (CFD) package based on finite-volume method. An aortic bileaflet heart valve (Sorin Bicarbon) was used as a pattern for model of real heart valve replacement. Computed tomography (CT) was used to gain the accurate parameters of the valve. Data from CT were transferred in the commercial 3D designer, where the model for CFD was made. Carreau rheology model was applied as non-Newtonian fluid. Physiological data of cardiac cycle were used as boundary conditions. Outputs were taken the leaflets excursion from opening to closure and the fluid dynamics through the valve. This study also includes experimental measurement of pressure fields in ambience of valve for verification numerical outputs. Results put in evidence a favorable comparison between the computational solutions of flow through the mechanical heart valve using Newtonian and non-Newtonian fluid.

Keywords: computational modeling, dynamic mesh, mechanical heart valve, non-Newtonian fluid

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Authors: Jing Zhao, Yongqing Bai, Qiaofang Shi, Huaihao Zhang

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Advances in software technology enable computational chemistry to be commonly applied in various research fields, especially in pedagogy. Thus, in order to expand and improve experimental instructions of computational chemistry for undergraduates, we designed an introductory experiment—research on acrylamide molecular structure and physicochemical properties. Initially, students construct molecular models of acrylamide and polyacrylamide in Gaussian and Materials Studio software respectively. Then, the infrared spectral data, atomic charge and molecular orbitals of acrylamide as well as solvation effect of polyacrylamide are calculated to predict their physicochemical performance. At last, rheological experiments are used to validate these predictions. Through the combination of molecular simulation (performed on Gaussian, Materials Studio) with experimental verification (rheology experiment), learners have deeply comprehended the chemical nature of acrylamide and polyacrylamide, achieving good learning outcomes.

Keywords: upper-division undergraduate, computer-based learning, laboratory instruction, molecular modeling

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Authors: K. Jagannath, Akhilesh Kotian, S. S. Sharma, Achutha Kini U., P. R. Prabhu

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Boiling process is characterized by the rapid formation of vapour bubbles at the solid–liquid interface (nucleate boiling) with pre-existing vapour or gas pockets. Computational fluid dynamics (CFD) is an important tool to study bubble dynamics. In the present study, CFD simulation has been carried out to determine the bubble detachment diameter and its terminal velocity. Volume of fluid method is used to model the bubble and the surrounding by solving single set of momentum equations and tracking the volume fraction of each of the fluids throughout the domain. In the simulation, bubble is generated by allowing water-vapour to enter a cylinder filled with liquid water through an inlet at the bottom. After the bubble is fully formed, the bubble detaches from the surface and rises up during which the bubble accelerates due to the net balance between buoyancy force and viscous drag. Finally when these forces exactly balance each other, it attains a constant terminal velocity. The bubble detachment diameter and the terminal velocity of the bubble are captured by the monitor function provided in FLUENT. The detachment diameter and the terminal velocity obtained is compared with the established results based on the shape of the bubble. A good agreement is obtained between the results obtained from simulation and the equations in comparison with the established results.

Keywords: bubble growth, computational fluid dynamics, detachment diameter, terminal velocity

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Authors: Hyung T. Kwak, Jun Gao, Yao An, Alfred Kleinhammes, Yue Wu

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Surface wettability is a crucial factor in oil recovery. In oil industry, the rock wettability involves the interplay between water, oil, and solid surface. Therefore, studying the interplay between adsorptions of water and hydrocarbon molecules on solid surface would be very informative for understanding rock wettability. Here we use the in-situ Nuclear Magnetic Resonance (NMR) gas isotherm technique to study competitive adsorptions of water and isopropanol, an intermediate step from hydrocarbons. This in-situ NMR technique obtains information on thermodynamic properties such as the isotherm, molecular dynamics via spin relaxation measurements, and adsorption kinetics such as how fast the system can reach thermal equilibrium after changes of vapor pressures. Using surfaces of silica glass beads, which can be modified from hydrophilic to hydrophobic, we obtained information on the influence of surface hydrophilicity on the state of surface water via obtained thermodynamic and dynamic properties.

Keywords: Wettability, NMR, Gas Isotherm, Hydrophilicity, adsorption

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Authors: Murali Aarthy, Sanjeev Kumar Singh

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High risk human papillomaviruses are highly associated with the carcinoma of the cervix and the other genital tumors. Cervical cancer develops through the multistep process in which increasingly severe premalignant dysplastic lesions called cervical intraepithelial neoplastic progress to invasive cancer. The oncoprotein E7 of human papillomavirus expressed in the lower epithelial layers drives the cells into S-phase creating an environment conducive for viral genome replication and cell proliferation. The replication of the virus occurs in the terminally differentiating epithelium and requires the activation of cellular DNA replication proteins. To date, no suitable drug molecule is available to treat HPV infection whereas identification of potential drug targets and development of novel anti-HPV chemotherapies with unique mode of actions are expected. Hence, our present study aimed to identify the potential inhibitors analogous to EGCG, a green tea molecule which is considered to be safe to use for mammalian systems. A 3D similarity search on the natural small molecule library from natural product database using EGCG identified 11 potential hits based on their similarity score. The structure based docking strategies were implemented in the potential hits and the key interacting residues of protein with compounds were identified through simulation studies and binding free energy calculations. The conformational changes between the apoprotein and the complex were analyzed with the simulation and the results demonstrated that the dynamical and structural effects observed in the protein were induced by the compounds and indicated the dominance to the oncoprotein. Overall, our study provides the basis for the structural insights of the identified potential hits and EGCG and hence, the analogous compounds identified can be potent inhibitors against the HPV 16 E7 oncoprotein.

Keywords: EGCG, oncoprotein, molecular dynamics simulation, analogues

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Authors: A. Ferasat, S. Rostampour Yasouri

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Seasonal flu is a highly contagious infection caused by influenza viruses. These viruses undergo genetic changes that result in new epidemics across the globe. Medical attention is crucial in severe cases, particularly for the elderly, frail, and those with chronic illnesses, as their immune systems are often weaker. The purpose of this study was to detect new subtypes of the influenza A virus rapidly using a specific RT-PCR method based on the HA gene (hemagglutinin). In the winter and spring of 2022_2023, 120 embryonated egg samples were cultured, suspected of seasonal influenza. RNA synthesis, followed by cDNA synthesis, was performed. Finally, the PCR technique was applied using a pair of specific primers designed based on the HA gene. The PCR product was identified after purification, and the nucleotide sequence of purified PCR products was compared with the sequences in the gene bank. The results showed a high similarity between the sequence of the positive samples isolated from the patients and the sequence of the new strains isolated in recent years. This RT-PCR technique is entirely specific in this study, enabling the detection and multiplication of influenza and its subspecies from clinical samples. The RT-PCR technique based on the HA gene, along with sequencing, is a fast, specific, and sensitive diagnostic method for those infected with influenza viruses and its new subtypes. Rapid molecular diagnosis of influenza is essential for suspected people to control and prevent the spread of the disease to others. It also prevents the occurrence of secondary (sometimes fatal) pneumonia that results from influenza and pathogenic bacteria. The critical role of rapid diagnosis of new strains of influenza is to prepare a drug vaccine against the latest viruses that did not exist in the community last year and are entirely new viruses.

Keywords: influenza, molecular diagnosis, patients, RT-PCR technique

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Authors: Jae Kyung Lee, Joon Young Park

Abstract:

Maintenance on power transmission lines requires a lot of works. Sometimes they should be maintained on live-line environment with high altitude. Therefore, there always exist risks of falling from height and electric shock. To decline those risks, drones are recently applying on the electric power industry. This paper presents new operational technology while inspecting power transmission line. This paper also describes a technique for creating a flight path of a drone for transmission line inspection and a technique for controlling the drones of different types. Its technical and economical feasibilities have confirmed through experiments.

Keywords: drones, transmission line, inspection, control system

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Authors: Lei Zhang, Wen-jun Ruan, Hao Wang, Peng-Xin Wang

Abstract:

The source of the jet noise is generated by rocket exhaust plume during rocket engine testing. A domain decomposition approach is applied to the jet noise prediction in this paper. The aerodynamic noise coupling is based on the splitting into acoustic sources generation and sound propagation in separate physical domains. Large Eddy Simulation (LES) is used to simulate the supersonic jet flow. Based on the simulation results of the flow-fields, the jet noise distribution of the sound pressure level is obtained by applying the Ffowcs Williams-Hawkings (FW-H) acoustics equation and Fourier transform. The calculation results show that the complex structures of expansion waves, compression waves and the turbulent boundary layer could occur due to the strong interaction between the gas jet and the ambient air. In addition, the jet core region, the shock cell and the sound pressure level of the gas jet increase with the nozzle size increasing. Importantly, the numerical simulation results of the far-field sound are in good agreement with the experimental measurements in directivity.

Keywords: supersonic gas jet, Large Eddy Simulation(LES), acoustic noise, Ffowcs Williams-Hawkings(FW-H) equations, nozzle size

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

Abstract:

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: Lukasz Grabowski, Konrad Pietrykowski, Michal Bialy

Abstract:

This paper presents the results of the research to verify the combustion in aircraft piston engine Asz62-IR. This engine was modernized and a type of ignition system was developed. Due to the high costs of experiments of a nine-cylinder 1,000 hp aircraft engine, a simulation technique should be applied. Therefore, computational fluid dynamics to simulate the combustion process is a reasonable solution. Accordingly, the tests for varied ignition advance angles were carried out and the optimal value to be tested on a real engine was specified. The CFD model was created with the AVL Fire software. The engine in the research had two spark plugs for each cylinder and ignition advance angles had to be set up separately for each spark. The results of the simulation were verified by comparing the pressure in the cylinder. The courses of the indicated pressure of the engine mounted on a test stand were compared. The real course of pressure was measured with an optical sensor, mounted in a specially drilled hole between the valves. It was the OPTRAND pressure sensor, which was designed especially to engine combustion process research. The indicated pressure was measured in cylinder no 3. The engine was running at take-off power. The engine was loaded by a propeller at a special test bench. The verification of the CFD simulation results was based on the results of the test bench studies. The course of the simulated pressure obtained is within the measurement error of the optical sensor. This error is 1% and reflects the hysteresis and nonlinearity of the sensor. The real indicated pressure measured in the cylinder and the pressure taken from the simulation were compared. It can be claimed that the verification of CFD simulations based on the pressure is a success. The next step was to research on the impact of changing the ignition advance timing of spark plugs 1 and 2 on a combustion process. Moving ignition timing between 1 and 2 spark plug results in a longer and uneven firing of a mixture. The most optimal point in terms of indicated power occurs when ignition is simultaneous for both spark plugs, but so severely separated ignitions are assured that ignition will occur at all speeds and loads of engine. It should be confirmed by a bench experiment of the engine. However, this simulation research enabled us to determine the optimal ignition advance angle to be implemented into the ignition control system. This knowledge allows us to set up the ignition point with two spark plugs to achieve as large power as possible.

Keywords: CFD model, combustion, engine, simulation

Procedia PDF Downloads 331