Search results for: molecular dynamics simulation

Authors: Nouf Alharbi

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The electrospray deposition technique became an important method that enables fragile, nonvolatile molecules to be deposited in situ in high vacuum environments. Furthermore, it is considered one of the ways to close the gap between basic surface science and molecular engineering, which represents a gradual change in the range of scientist research. Also, this paper talked about one of the most important techniques that have been developed and aimed for helping to further develop and characterize the electrospray by providing data collected using an image charge detection instrument. Image charge detection mass spectrometry (CDMS) is used to measure speed and charge distributions of the molecular ions. As well as, some data has been included using SIMION simulation to simulate the energies and masses of the molecular ions through the system in order to refine the mass-selection process.

Keywords: charge, deposition, electrospray, image, ions, molecules, SIMION

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Authors: Phinyo Mueangmeesap

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This paper describes about pure sinusoidal inverter simulation and implementation from high voltage DC (156 Vdc). This simulation is to study and improve the efficiency of the inverter. By reducing the loss of power from boost converter in current inverter. The simulation is done by using the H-bridge circuit with pulse width modulate (PWM) signal and low-pass filter circuit. To convert the DC into AC. This paper used the PSCad for simulation. The result of simulation can be used to create prototype inverter by converting 156 Vdc to 110Vac. The inverter gives the output signal similar to the output from a simulation.

Keywords: inverter simulation, PWM signal, single-phase inverter, sinusoidal inverter

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Authors: Opeyemi Fadipe, Seong Lee, Guangming Chen, Steve Efe

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In comparison to conventional combustion technologies, fluidized bed combustion has several advantages, such as superior heat transfer characteristics due to homogeneous particle mixing, lower temperature needs, nearly isothermal process conditions, and the ability to operate continuously. Computational fluid dynamics (CFD) can help anticipate the intricate combustion process and the hydrodynamics of a fluidized bed thoroughly by using CFD techniques. Bubbling Fluidized bed was model using the Eulerian-Eulerian model, including the kinetic theory of the flow. The model was validated by comparing it with other simulation of the fluidized bed. The effects of operational gas velocity, volume fraction, and feed rate were also investigated numerically. A higher gas velocity and feed rate cause an increase in fluidization of the bed.

Keywords: fluidized bed, operational gas velocity, volume fraction, computational fluid dynamics

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Authors: Mahmoud A. Abdulhamid

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Poly(ether-ether-ketone) (PEEK) has received increased attention due to its outstanding performance in different membrane applications including gas and liquid separation. However, it suffers from a semi-crystalline morphology, bad solubility and low porosity. To fabricate membranes from PEEK, the usage of harsh acid such as sulfuric acid is essential, regardless its hazardous properties. In this work, we report the molecular design of poly(ether-ether-ketones) (iPEEKs) with intrinsic porosity character, by incorporating kinked units into PEEK backbone such as spirobisindane, Tröger's base, and triptycene. The porous polymers were used to fabricate stable membranes for organic solvent nanofiltration application. To better understand the mechanism, we conducted molecular dynamics simulations to evaluate the possible interactions between the polymers and the solvents. Notable enhancement in separation performance was observed confirming the importance of molecular engineering of high-performance polymers. The iPEEKs demonstrated good solubility in polar aprotic solvents, a high surface area of 205–250 m² g⁻¹, and excellent thermal stability. Mechanically flexible nanofiltration membranes were prepared from N-methyl-2-pyrrolidone dope solution at iPEEK concentrations of 19–35 wt%. The molecular weight cutoff of the membranes was fine-tuned in the range of 450–845 g mol⁻¹ displaying 2–6 fold higher permeance (3.57–11.09 L m⁻² h⁻¹ bar⁻¹) than previous reports. The long-term stabilities were demonstrated by a 7 day continuous cross-flow filtration.

Keywords: molecular engineering, polymer synthesis, membrane fabrication, liquid separation

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Authors: Neslihan Demirci, Serdar Durdağı

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Mycobacterium tuberculosis is still a worldwide disease-causing agent that, according to WHO, led to the death of 1.5 million people from tuberculosis (TB) in 2020. The bacteria reside in macrophages located specifically in the lung. There is a known quadruple drug therapy regimen for TB consisting of isoniazid (INH), rifampin (RIF), pyrazinamide (PZA), and ethambutol (EMB). Over the past 60 years, there have been great contributions to treatment options, such as recently approved delamanid (OPC67683) and bedaquiline (TMC207/R207910), targeting mycolic acid and ATP synthesis, respectively. Also, there are natural compounds that can block the tryptophanyl-tRNA synthetase (TrpRS) enzyme, chuangxinmycin, and indolmycin. Yet, already the drug resistance is reported for those agents. In this study, the newly released TrpRS enzyme structure is investigated for potential inhibitor drugs from already synthesized molecules to help the treatment of resistant cases and to propose an alternative drug for the quadruple drug therapy of tuberculosis. Maestro, Schrodinger is used for docking and molecular dynamic simulations. In-house library containing ~8000 compounds among FDA-approved indole-containing compounds, a total of 57 obtained from the ChemBL were used for both ATP and tryptophan binding pocket docking. Best of indole-containing 57 compounds were subjected to hit expansion and compared later with virtual screening workflow (VSW) results. After docking, VSW was done. Glide-XP docking algorithm was chosen. When compared, VSW alone performed better than the hit expansion module. Best scored compounds were kept for ten ns molecular dynamic simulations by Desmond. Further, 100 ns molecular dynamic simulation was performed for elected molecules according to Z-score. The top three MMGBSA-scored compounds were subjected to steered molecular dynamic (SMD) simulations by Gromacs. While SMD simulations are still being conducted, ponesimod (for multiple sclerosis), vilanterol (β₂ adrenoreceptor agonist), and silodosin (for benign prostatic hyperplasia) were found to have a significant affinity for tuberculosis TrpRS, which is the propulsive force for the urge to expand the research with in vitro studies. Interestingly, top-scored ponesimod has been reported to have a side effect that makes the patient prone to upper respiratory tract infections.

Keywords: drug repurposing, molecular dynamics, tryptophanyl-tRNA synthetase, tuberculosis

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Authors: M. R. Ghasemi, R. Ghiasi, H. Varaee

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Surrogate model has received increasing attention for use in detecting damage of structures based on vibration modal parameters. However, uncertainties existing in the measured vibration data may lead to false or unreliable output result from such model. In this study, an efficient approach based on Monte Carlo simulation is proposed to take into account the effect of uncertainties in developing a surrogate model. The probability of damage existence (PDE) is calculated based on the probability density function of the existence of undamaged and damaged states. The kriging technique allows one to genuinely quantify the surrogate error, therefore it is chosen as metamodeling technique. Enhanced version of ideal gas molecular movement (EIGMM) algorithm is used as main algorithm for model updating. The developed approach is applied to detect simulated damage in numerical models of 72-bar space truss and 120-bar dome truss. The simulation results show the proposed method can perform well in probability-based damage detection of structures with less computational effort compared to direct finite element model.

Keywords: probability-based damage detection (PBDD), Kriging, surrogate modeling, uncertainty quantification, artificial intelligence, enhanced ideal gas molecular movement (EIGMM)

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Authors: Alok Khaware, Vinay Kumar Gupta, Jean Noel Pederzani

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Lifeboat launching from marine vessel or offshore platform is one of the important areas of research in offshore applications. With the advancement of computational fluid dynamic simulation (CFD) technology to solve fluid induced motions coupled with Six Degree of Freedom (6DOF), rigid body dynamics solver, it is now possible to predict the motion of the lifeboat precisely in different challenging conditions. Traditionally dynamic remeshing approach is used to solve this kind of problems, but remeshing approach has some bottlenecks to control good quality mesh in transient moving mesh cases. In the present study, an overset method with higher-order interpolation is used to simulate a lifeboat launched from an offshore platform into calm water, and volume of fluid (VOF) method is used to track free surface. Overset mesh consists of a set of overlapping component meshes, which allows complex geometries to be meshed with lesser effort. Good quality mesh with local refinement is generated at the beginning of the simulation and stay unchanged throughout the simulation. Overset mesh accuracy depends on the precise interpolation technique; the present study includes a robust and accurate least square interpolation method and results obtained with overset mesh shows good agreement with experiment.

Keywords: computational fluid dynamics, free surface flow, lifeboat launching, overset mesh, volume of fluid

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Authors: Oleg Oborin

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This paper is dedicated to the development of the model, which can be used to evaluate the effectiveness of long-term corporate strategies and identify the best strategies. The theoretical model of the relatively homogenous product market (such as iron and steel industry, mobile services or road transport) has been developed. In the model, the market consists of a large number of companies with different internal characteristics and objectives. The companies can perform mergers and acquisitions in order to increase their market share. The model allows the simulation of long-time dynamics of the market (for a period longer than 20 years). Therefore, a large number of simulations on random input data was conducted in the framework of the model. After that, the results of the model were compared with the dynamics of real markets, such as the US steel industry from the beginning of the XX century to the present day, and the market of mobile services in Germany for the period between 1990 and 2015.

Keywords: Economic Modelling, Long-Time Strategy, Mergers and Acquisitions, Simulation

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Authors: Adel Belayadi, Ahmed Mougari, Boualem Bourahla

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Molecular junctions are currently considered a promising style in the miniaturization of electronic devices. In this contribution, we provide a tight-binding model to investigate the quantum transport properties across-molecular junctions sandwiched between 2D-graphene nanoribbons in the zigzag direction. We investigate, in particular, the effect of embedded atoms such as Gold and Silicon across the molecular junction. The results exhibit a resonance behavior in terms of incident Fermi levels, depending on the molecular junction type. Additionally, the transport properties under a perpendicular magnetic field exhibit an oscillation for the transmittance versus the magnetic field strength.

Keywords: molecular junction, 2D-graphene nanoribbons, quantum transport properties, magnetic field

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Authors: Beata Jackowska-Zduniak

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We formulate and analyze a mathematical model describing dynamics of cancer growth under the influence of radiation therapy. The effect of this type of therapy is considered as an additional equation of discussed model. Numerical simulations show that delay, which is added to ordinary differential equations and represent time needed for transformation from one type of cells to the other one, affects the behavior of the system. The validation and verification of proposed model is based on medical data. Analytical results are illustrated by numerical examples of the model dynamics. The model is able to reconstruct dynamics of treatment of cancer and may be used to determine the most effective treatment regimen based on the study of the behavior of individual treatment protocols.

Keywords: mathematical modeling, numerical simulation, ordinary differential equations, radiation therapy

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Authors: C. E. Madubueze, S. C. Madubueze, S. Ajama

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Cholera is a disease that is predominately common in developing countries due to poor sanitation and overcrowding population. In this paper, a deterministic model for the dynamics of cholera is developed and control measures such as health educational message, therapeutic treatment, and vaccination are incorporated in the model. The effective reproduction number is computed in terms of the model parameters. The existence and stability of the equilibrium states, disease free and endemic equilibrium states are established and showed to be locally and globally asymptotically stable when R0 < 1 and R0 > 1 respectively. The existence of backward bifurcation of the model is investigated. Furthermore, numerical simulation of the model developed is carried out to show the impact of the control measures and the result indicates that combined control measures will help to reduce the spread of cholera in the population

Keywords: backward bifurcation, cholera, equilibrium, dynamics, stability

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Authors: Marianna Maiaru, Gregory M. Odegard

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During the processing of high-performance thermoset polymer matrix composites, chemical reactions occur during elevated pressure and temperature cycles, causing the constituent monomers to crosslink and form a molecular network that gradually can sustain stress. As the crosslinking process progresses, the material naturally experiences a gradual shrinkage due to the increase in covalent bonds in the network. Once the cured composite completes the cure cycle and is brought to room temperature, the thermal expansion mismatch of the fibers and matrix cause additional residual stresses to form. These compounded residual stresses can compromise the reliability of the composite material and affect the composite strength. Composite process modeling is greatly complicated by the multiscale nature of the composite architecture. At the molecular level, the degree of cure controls the local shrinkage and thermal-mechanical properties of the thermoset. At the microscopic level, the local fiber architecture and packing affect the magnitudes and locations of residual stress concentrations. At the macroscopic level, the layup sequence controls the nature of crack initiation and propagation due to residual stresses. The goal of this research is use molecular dynamics (MD) and finite element analysis (FEA) to predict the residual stresses in composite laminates and the corresponding effect on composite failure. MD is used to predict the polymer shrinkage and thermomechanical properties as a function of degree of cure. This information is used as input into FEA to predict the residual stresses on the microscopic level resulting from the complete cure process. Virtual testing is subsequently conducted to predict strength allowables. Experimental characterization is used to validate the modeling.

Keywords: molecular dynamics, finite element analysis, processing modeling, multiscale modeling

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Authors: Iftekhar Hassan, Sayedil Morsalin, Easir A Khan

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Accidents involving fire occur frequently in recent times and their causes showing a great deal of variety which require intervention methods and risk assessment strategies are unique in each case. On September 4, 2020, a fire and explosion occurred in a confined space caused by a methane gas leak from an underground pipeline in Baitus Salat Jame mosque during Night (Esha) prayer in Narayanganj District, Bangladesh that killed 34 people. In this research, this incident is simulated using Fire Dynamics Simulator (FDS) software to analyze and understand the nature of the accident and associated consequences. FDS is an advanced computational fluid dynamics (CFD) system of fire-driven fluid flow which solves numerically a large eddy simulation form of the Navier–Stokes’s equations for simulation of the fire and smoke spread and prediction of thermal radiation, toxic substances concentrations and other relevant parameters of fire. This study focuses on understanding the nature of the fire and consequence evaluation due to thermal radiation caused by vapor cloud explosion. An evacuation modeling was constructed to visualize the effect of evacuation time and fractional effective dose (FED) for different types of agents. The results were presented by 3D animation, sliced pictures and graphical representation to understand fire hazards caused by thermal radiation or smoke due to vapor cloud explosion. This study will help to design and develop appropriate respond strategy for preventing similar accidents.

Keywords: consequence modeling, fire and explosion, fire dynamics simulation (FDS), thermal radiation

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Authors: Nicola G. G. Cecca

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In Italian IPSSEOAs, high schools that give a vocational education to students that will work in the field of Enogastronomy and Hotel Management, the course of Food Science allows the students to start and see food as a mixture of substances that they will transform during their profession. These substances are characterized not only by a chemical composition but also by a molecular structure that makes them nutritionally active. But the increasing number of new products proposed by Food Industry, the modern techniques of production and transformation, the innovative preparations required by customers have made many information reported in the most wide spread Food Science textbooks not up-to-date or too poor for the people who will work in catering sector. Often Authors offer information aged to Bohr’s Atomic Model and to the ‘Octet Rule’ proposed by G.N. Lewis to describe the Chemical Bond, without giving any reference to new as Orbital Atomic Model and Molecular Orbital Theory that, in the meantime, start to be old themselves. Furthermore, this antiquated information precludes an easy understanding of a wide range of properties of nutritive substances and many reactions in which the food constituents are involved. In this paper, our attention is pointed out to use GEOMAG™ to represent the dynamics with which the chemical bond is formed during the synthesis of the molecules. GEOMAG™ is a toy, produced by the Swiss Company Geomagword S.A., pointed to stimulate in children, aged between 6-10 years, their fantasy and their handling ability and constituted by metallic spheres and metallic magnetic bars coated by coloured plastic materials. The simulation carried out with GEOMAG™ is based on the similitude existing between the Coulomb’s force and the magnetic attraction’s force and in particular between the formulae with which they are calculated. The electrostatic force (F in Newton) that allows the formation of the chemical bond can be calculated by mean Fc = kc q1 q2/d2 where: q1 e q2 are the charge of particles [in Coulomb], d is the distance between the particles [in meters] and kc is the Coulomb’s constant. It is surprising to observe that the attraction’s force (Fm) acting between the magnetic extremities of GEOMAG™ used to simulate the chemical bond can be calculated in the same way by using the formula Fm = km m1 m2/d2 where: m1 e m2 represent the strength of the poles [A•m], d is the distance between the particles [m], km = μ/4π in which μ is the magnetic permeability of medium [N•A-2]. The magnetic attraction can be tested by students by trying to keep the magnetic elements of GEOMAG™ separate by hands or trying to measure by mean an appropriate dynamometric system. Furthermore, by using a dynamometric system to measure the magnetic attraction between the GEOMAG™ elements is possible draw a graphic F=f(d) to verify that the curve obtained during the simulation is very similar to that one hypnotized, around the 1920’s by Linus Pauling to describe the formation of H2+ in according with Molecular Orbital Theory.

Keywords: chemical bond, molecular orbital theory, magnetic attraction force, GEOMAG™

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Authors: Saeed Khandan Siar, Stefan Tenbohlen, Christian Breuer, Raphael Lebreton

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The goal of this article is to investigate the detailed temperature distribution and the fluid flow of an oil cooled winding of a power transformer by means of computational fluid dynamics (CFD). The experimental setup consists of three passes of a zig-zag cooled disc type winding, in which losses are modeled by heating cartridges in each winding segment. A precise temperature sensor measures the temperature of each turn. The laboratory setup allows the exact control of the boundary conditions, e.g. the oil flow rate and the inlet temperature. Furthermore, a simulation model is solved using the open source computational fluid dynamics solver OpenFOAM and validated with the experimental results. The model utilizes the laminar and turbulent flow for the different mass flow rate of the oil. The good agreement of the simulation results with experimental measurements validates the model.

Keywords: CFD, conjugated heat transfer, power transformers, temperature distribution

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Authors: Hiroyuki Aoki

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The physical properties of polymer materials are dependent on the conformation and molecular motion of a polymer chain. Therefore, the structure and dynamic behavior of the single polymer chain have been the most important concerns in the field of polymer physics. However, it has been impossible to directly observe the conformation of the single polymer chain in a bulk medium. In the current work, the novel techniques to study the conformation and dynamics of a single polymer chain are proposed. Since a fluorescence method is extremely sensitive, the fluorescence microscopy enables the direct detection of a single molecule. However, the structure of the polymer chain as large as 100 nm cannot be resolved by conventional fluorescence methods because of the diffraction limit of light. In order to observe the single chains, we developed the labeling method of polymer materials with a photo-switchable dye and the super-resolution microscopy. The real-space conformational analysis of single polymer chains with the spatial resolution of 15-20 nm was achieved. The super-resolution microscopy enables us to obtain the three-dimensional coordinates; therefore, we succeeded the conformational analysis in three dimensions. The direct observation by the nanometric optical microscopy would reveal the detailed information on the molecular processes in the various polymer systems.

Keywords: polymer materials, single molecule, super-resolution techniques, conformation

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Authors: M. Ekiert, T. Uhl, A. Mlyniec

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Tendons are the biological soft tissue structures composed of collagen, proteoglycan, glycoproteins, water and cells of extracellular matrix (ECM). Tendons, which primary function is to transfer force generated by the muscles to the bones causing joints movement, are exposed to many micro and macro damages. In fact, tendons and ligaments trauma are one of the most numerous injuries of human musculoskeletal system, causing for many people (particularly for athletes and physically active people), recurring disorders, chronic pain or even inability of movement. The number of tendons reconstruction and transplantation procedures is increasing every year. Therefore, studies on soft tissues storage conditions (influencing i.e. tissue aging) seem to be an extremely important issue. In this study, an atomic-scale investigation on the kinetics of decomposition of two selected tendon components – collagen type I (which forms a 60-85% of a tendon dry mass) and elastin protein (which combine with ECM creates elastic fibers of connective tissues) is presented. A molecular model of collagen and elastin was developed based on crystal structure of triple-helical collagen-like 1QSU peptide and P15502 human elastin protein, respectively. Each model employed 4 linear strands collagen/elastin strands per unit cell, distributed in 2x2 matrix arrangement, placed in simulation box filled with water molecules. A decomposition phenomena was simulated with molecular dynamics (MD) method using ReaxFF force field and periodic boundary conditions. A set of NVT-MD runs was performed for 1000K temperature range in order to obtained temperature-depended rate of production of decomposition by-products. Based on calculated reaction rates activation energies and pre-exponential factors, required to formulate Arrhenius equations describing kinetics of decomposition of tested soft tissue components, were calculated. Moreover, by adjusting a model developed for collagen, system scalability and correct implementation of the periodic boundary conditions were evaluated. An obtained results provide a deeper insight into decomposition of selected tendon components. A developed methodology may also be easily transferred to other connective tissue elements and therefore might be used for further studies on soft tissues aging.

Keywords: decomposition, molecular dynamics, soft tissue, tendons

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Authors: Quy Dang Nguyen, Reza Nakhaie Jazar

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The paper investigates vibration dynamics of tire-road separation for a quarter-car model; this separation model is developed to be close to the real situation considering the tire is able to separate from the ground plane. A set of piecewise linear mathematical models is developed and matches the in-contact and no-contact states to be considered as mother models for further investigations. The bound dynamics are numerically simulated in the time response and phase portraits. The separation analysis may determine which values of suspension parameters can delay and avoid the no-contact phenomenon, which results in improving ride comfort and eliminating the potentially dangerous oscillation. Finally, model verification is carried out in the MSC-ADAMS environment.

Keywords: quarter-car vibrations, tire-road separation, separation analysis, separation dynamics, ride comfort, ADAMS validation

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Authors: Mojtaba Zabihi, Stephen Munro, Jonathan Little, Ri Li, Joshua Brinkerhoff, Sina Kheirkhah

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Occupational Safety and Health Administration (OSHA) identified dental workers at the highest risk of contracting COVID-19. This is because aerosol-generating procedures (AGP) during dental practices generate aerosols ( < 5µm) and droplets. These particles travel at varying speeds, in varying directions, and for varying durations. If these particles bear infectious viruses, their spreading causes airborne transmission of the virus in the dental room, exposing dentists, hygienists, dental assistants, and even other dental clinic clients to the infection risk. Computational fluid dynamics (CFD) simulation of two-phase flows based on a discrete phase model (DPM) is carried out to study the spreading of aerosol and droplets in a dental room. The simulation includes momentum, heat, and mass transfers between the particles and the airflow. Two simulations are conducted and compared. One simulation focuses on the effects of room ventilation in winter and summer on the particles' travel. The other simulation focuses on the control of aerosol and droplets' spreading. A suction collector is added near the source of aerosol and droplets, creating a flow sink in order to remove the particles. The effects of the suction flow on the aerosol and droplet travel are studied. The suction flow can remove aerosols and also reduce the spreading of droplets.

Keywords: aerosols, computational fluid dynamics, COVID-19, dental, discrete phase model, droplets, two-phase flow

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Authors: Audrey Ngambia, Ondrej Masek, Valentina Erastova

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Biochar is an amorphous carbon-rich material generated from the pyrolysis of biomass with multifarious properties and functionality. Biochar has shown proven applications in the treatment of flue gas and organic and inorganic pollutants in soil and water/wastewater as a result of its multiple surface functional groups and porous structures. These properties have also shown potential in energy storage and carbon capture. The availability of diverse sources of biomass to produce biochar has increased interest in it as a sustainable and environmentally friendly material. The properties and porous structures of biochar vary depending on the type of biomass and high heat treatment temperature (HHT). Biochars produced at HHT between 400°C – 800°C generally have lower H/C and O/C ratios, higher porosities, larger pore sizes and higher surface areas with temperature. While all is known experimentally, there is little knowledge on the porous role structure and functional groups play on processes occurring at the atomistic scale, which are extremely important for the optimization of biochar for application, especially in the adsorption of gases. Atomistic simulations methods have shown the potential to generate such amorphous materials; however, most of the models available are composed of only carbon atoms or graphitic sheets, which are very dense or with simple slit pores, all of which ignore the important role of heteroatoms such as O, N, S and pore morphologies. Hence, developing realistic models that integrate these parameters are important to understand their role in governing adsorption mechanisms that will aid in guiding the design and optimization of biochar materials for target applications. In this work, molecular dynamics simulations in the isobaric ensemble are used to generate realistic biochar models taking into account experimentally determined H/C, O/C, N/C, aromaticity, micropore size range, micropore volumes and true densities of biochars. A pore generation approach was developed using virtual atoms, which is a Lennard-Jones sphere of varying van der Waals radius and softness. Its interaction via a soft-core potential with the biochar matrix allows the creation of pores with rough surfaces while varying the van der Waals radius parameters gives control to the pore-size distribution. We focused on microporosity, creating average pore sizes of 0.5 - 2 nm in diameter and pore volumes in the range of 0.05 – 1 cm3/g, which corresponds to experimental gas adsorption micropore sizes of amorphous porous biochars. Realistic biochar models with surface functionalities, micropore size distribution and pore morphologies were developed, and they could aid in the study of adsorption processes in confined micropores.

Keywords: biochar, heteroatoms, micropore size, molecular dynamics simulations, surface functional groups, virtual atoms

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Authors: Wolfram Jahn, Jose Manuel Munita

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While computational fluid dynamics (CFD) simulations of fire scenarios are commonly used in the design of buildings, less attention has been given to the use of CFD simulations as an operational tool for the fire services. The reason of this lack of attention lies mainly in the fact that CFD simulations typically take large periods of time to complete, and their results would thus not be available in time to be of use during an emergency. Firefighters often face uncertain conditions when entering a building to attack a fire. They would greatly benefit from a technology based on predictive fire simulations, able to assist their decision-making process. The principal constraint to faster CFD simulations is the fine grid necessary to solve accurately the physical processes that govern a fire. This paper explores the possibility of overcoming this constraint and using coarse grid CFD simulations for fire scenarios, and proposes a methodology to use the simulation results in a meaningful way that can be used by the fire fighters during an emergency. Data from real scale compartment fire tests were used to compare CFD fire models with different grid arrangements, and empirical correlations were obtained to interpolate data points into the grids. The results show that the strongly predominant effect of the heat release rate of the fire on the fluid dynamics allows for the use of coarse grids with relatively low overall impact of simulation results. Simulations with an acceptable level of accuracy could be run in real time, thus making them useful as a forecasting tool for emergency response purposes.

Keywords: CFD, fire simulations, emergency response, forecast

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Authors: Athmane Bakhta, Sebastien Leclaire, David Vidal, Francois Bertrand, Mohamed Cheriet

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This work presents a new three-dimensional variational model proposed for the simulation of ink seepage into paper sheets at the fiber level. The model, inspired by the Hising model, takes into account a finite volume of ink and describes the system state through gravity, cohesion, and adhesion force interactions. At the mesoscopic scale, the paper substrate is modeled using a discretized fiber structure generated using a numerical deposition procedure. A modified Monte Carlo method is introduced for the simulation of the ink dynamics. Besides, a multiphase lattice Boltzmann method is suggested to fine-tune the mesoscopic variational model parameters, and it is shown that the ink seepage behaviors predicted by the proposed model can resemble those predicted by a method relying on first principles.

Keywords: fibrous media, lattice Boltzmann, modelling and simulation, Monte Carlo, variational model

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Authors: Khizir Mohd Ismail, Yu Jun Lim, Tshun Howe Yong

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The study of flow behavior in an enclosed volume using Computational Fluid Dynamics (CFD) has been around for decades. However, due to the knowledge limitation of adaptive grid methods, the flow in an enclosed volume near the moving wall using CFD is less explored. A CFD simulation of flow in an enclosed volume near a moving wall was demonstrated and studied by introducing a moving mesh method and was modeled with Unsteady Reynolds-Averaged Navier-Stokes (URANS) approach. A static enclosed volume with controlled opening size in the bottom was positioned against a moving, translational wall with sliding mesh features. Controlled variables such as smoothed, crevices and corrugated wall characteristics, the distance between the enclosed volume to the wall and the moving wall speed against the enclosed chamber were varied to understand how the flow behaves and reacts in between these two geometries. These model simulations were validated against experimental results and provided result confidence when the simulation had shown good agreement with the experimental data. This study had provided better insight into the flow behaving in an enclosed volume when various wall types in motion were introduced within the various distance between each other and create a potential opportunity of application which involves adaptive grid methods in CFD.

Keywords: moving wall, adaptive grid methods, CFD, moving mesh method

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Authors: Ankur Chaudhuri, Sibani Sen Chakraborty

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In human, glutaminyl cyclase activity is highly abundant in neuronal and secretory tissues and is preferentially restricted to hypothalamus and pituitary. The N-terminal modification of β-amyloids (Aβs) peptides by the generation of a pyro-glutamyl (pGlu) modified Aβs (pE-Aβs) is an important process in the initiation of the formation of neurotoxic plaques in Alzheimer’s disease (AD). This process is catalyzed by glutaminyl cyclase (QC). The expression of QC is characteristically up-regulated in the early stage of AD, and the hallmark of the inhibition of QC is the prevention of the formation of pE-Aβs and plaques. A computer-aided drug design (CADD) process was employed to give an idea for the designing of potentially active compounds to understand the inhibitory potency against human glutaminyl cyclase (QC). This work elaborates the ligand-based and structure-based pharmacophore exploration of glutaminyl cyclase (QC) by using the known inhibitors. Three dimensional (3D) quantitative structure-activity relationship (QSAR) methods were applied to 154 compounds with known IC50 values. All the inhibitors were divided into two sets, training-set, and test-sets. Generally, training-set was used to build the quantitative pharmacophore model based on the principle of structural diversity, whereas the test-set was employed to evaluate the predictive ability of the pharmacophore hypotheses. A chemical feature-based pharmacophore model was generated from the known 92 training-set compounds by HypoGen module implemented in Discovery Studio 2017 R2 software package. The best hypothesis was selected (Hypo1) based upon the highest correlation coefficient (0.8906), lowest total cost (463.72), and the lowest root mean square deviation (2.24Å) values. The highest correlation coefficient value indicates greater predictive activity of the hypothesis, whereas the lower root mean square deviation signifies a small deviation of experimental activity from the predicted one. The best pharmacophore model (Hypo1) of the candidate inhibitors predicted comprised four features: two hydrogen bond acceptor, one hydrogen bond donor, and one hydrophobic feature. The Hypo1 was validated by several parameters such as test set activity prediction, cost analysis, Fischer's randomization test, leave-one-out method, and heat map of ligand profiler. The predicted features were then used for virtual screening of potential compounds from NCI, ASINEX, Maybridge and Chembridge databases. More than seven million compounds were used for this purpose. The hit compounds were filtered by drug-likeness and pharmacokinetics properties. The selective hits were docked to the high-resolution three-dimensional structure of the target protein glutaminyl cyclase (PDB ID: 2AFU/2AFW) to filter these hits further. To validate the molecular docking results, the most active compound from the dataset was selected as a reference molecule. From the density functional theory (DFT) study, ten molecules were selected based on their highest HOMO (highest occupied molecular orbitals) energy and the lowest bandgap values. Molecular dynamics simulations with explicit solvation systems of the final ten hit compounds revealed that a large number of non-covalent interactions were formed with the binding site of the human glutaminyl cyclase. It was suggested that the hit compounds reported in this study could help in future designing of potent inhibitors as leads against human glutaminyl cyclase.

Keywords: glutaminyl cyclase, hit lead, pharmacophore model, simulation

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Authors: Sung-Pill Kim, Dae-Gyu Sung, Hee-Sung Shin, Jong-Chun Park

Abstract:

When a sloshing tank filled partially with liquid is excited with the motion of platform, it can be observed that the center of mass inside the tank is changed and impact loads is instantaneously applied to the wall, which causes dynamic loads additionally to the supporting links of platform. In this case, therefore, the dynamic behavior of platform associated with fluid motion should be considered in the early stage of design for safety and economics of the system. In this paper, the dynamic loads due to liquid sloshing motion in a rectangular tank which is loaded up on the upper deck of a Stewart platform are simulated using a coupled analysis of Moving Particle Simulation (MPS) and Flexible Multi-Body Dynamics (FMBD). The co-simulation is performed using two commercial softwares, Recurdyn for solving FMBD and Particleworks for analyzing fluid motion based on MPS method. For validating the present coupled system, a rectangular sloshing tank being enforced with inline sway motion by 1-DOF motion platform is assumed, and time-varied free-surface elevation and reaction force at a fixed joint are compared with experiments.

Keywords: dynamic loads, liquid sloshing tank, Stewart platform, moving particle semi-implicit (MPS) method, flexible multi-body dynamics (FMBD)

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Authors: Francesco Rizzuto, Matthew Stickland, Stephan Hannot

Abstract:

The simulation of a positive displacement pump system with commercial software for Computer Fluid Dynamics (CFD), will result in an enormous computational effort due to the complexity of the pump system. This drawback restricts the use of it to a specific part of the pump in one simulation. This research focuses on developing an algorithm that provides a suitable result in agreement with experiment data, without that computational effort. The compressible equations are solved with an explicit algorithm. A comparison is presented between the FV method with Monotonic Upwind scheme for Conservative Laws (MUSCL) with slope limiter and experimental results. The source term for cavitation and friction is introduced into the algorithm with a slipping strategy and solved with a 4th order Runge-Kutta scheme (RK4). Different pumps are modeled and analyzed to evaluate the flexibility of the code. The simulation required minimal computation time and resources without compromising the accuracy of the simulation results. Therefore, this algorithm highlights the feasibility of pressure pulsation simulation as a design tool for an industrial purpose.

Keywords: cavitation, diaphragm, DVCM, finite volume, MUSCL, positive displacement pump

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Authors: Ting Ye, Nhan Phan-Thien, Chwee Teck Lim, Lina Peng, Huixin Shi

Abstract:

In biofluid flow systems, often the flow problems of fluids of complex structures, such as the flow of red blood cells (RBCs) through complex capillary vessels, need to be considered. In this paper, we aim to apply a particle-based method, Smoothed Dissipative Particle Dynamics (SDPD), to simulate the motion and deformation of RBCs in complex micro-tubes. We first present the theoretical models, including SDPD model, RBC-fluid interaction model, RBC deformation model, RBC aggregation model, and boundary treatment model. After that, we show the verification and validation of these models, by comparing our numerical results with the theoretical, experimental and previously-published numerical results. Finally, we provide some simulation cases, such as the motion and deformation of RBCs in rectangular, cylinder, curved, bifurcated, and constricted micro-tubes, respectively.

Keywords: aggregation, deformation, red blood cell, smoothed dissipative particle dynamics

Procedia PDF Downloads 141

Authors: Muhammad Zaman Shakir, Mingfa Yao, Zohaib Iqbal

Abstract:

This study proposed four Jet fuel surrogate (S1, S2 S3, and 4) with careful selection of seven large hydrocarbon fuel components, ranging from C₉-C₁₆ of higher molecular weight and higher boiling point, adapting the standard molecular distribution size of the actual jet fuel. The surrogate was composed of seven components, including n-propyl cyclohexane (C₉H₁₈), n- propylbenzene (C₉H₁₂), n-undecane (C₁₁H₂₄), n- dodecane (C₁₂H₂₆), n-tetradecane (C₁₄H₃₀), n-hexadecane (C₁₆H₃₄) and iso-cetane (iC₁₆H₃₄). The skeletal jet fuel surrogate reaction mechanism was developed by two approaches, firstly based on a decoupling methodology by describing the C₄ -C₁₆ skeletal mechanism for the oxidation of heavy hydrocarbons and a detailed H₂ /CO/C₁ mechanism for prediction of oxidation of small hydrocarbons. The combined skeletal jet fuel surrogate mechanism was compressed into 128 species, and 355 reactions and thereby can be used in computational fluid dynamics (CFD) simulation. The extensive validation was performed for individual single-component including ignition delay time, species concentrations profile and laminar flame speed based on various fundamental experiments under wide operating conditions, and for their blended mixture, among all the surrogate, S1 has been extensively validated against the experimental data in a shock tube, rapid compression machine, jet-stirred reactor, counterflow flame, and premixed laminar flame over wide ranges of temperature (700-1700 K), pressure (8-50 atm), and equivalence ratio (0.5-2.0) to capture the properties target fuel Jet-A, while the rest of three surrogate S2, S3 and S4 has been validated for Shock Tube ignition delay time only to capture the ignition characteristic of target fuel S-8 & GTL, IPK and RP-3 respectively. Based on the newly proposed HyChem model, another four surrogate with similar components and composition, was developed and parallel validations data was used as followed for previously developed surrogate but at high-temperature condition only. After testing the mechanism prediction performance of surrogates developed by the decoupling methodology, the comparison was done with the results of surrogates developed by the HyChem model. It was observed that all of four proposed surrogates in this study showed good agreement with the experimental measurements and the study comes to this conclusion that like the decoupling methodology HyChem model also has a great potential for the development of oxidation mechanism for heavy alkanes because of applicability, simplicity, and compactness.

Keywords: computational fluid dynamics, decoupling methodology Hychem, jet fuel, surrogate, skeletal mechanism

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Authors: Zdravko Eškinja, Lovre Miljanić, Ognjen Kuljača

Abstract:

This paper is an overview of simulation tools used to model specific thermal dynamics that occurs while controlling double skin façade. Research has been conducted on simplified construction with single zone where one side is glazed. Heat flow and temperature responses are simulated in three different simulation tools: IDA-ICE, EnergyPlus and HAMBASE. The excitation of observed system, used in all simulations, was a temperature step of exterior environment. Air infiltration, insulation and other disturbances are excluded from this research. Although such isolated behaviour is not possible in reality, experiments are carried out to gain novel information about heat flow transients which are not observable under regular conditions. Results revealed new possibilities for adapting the parameters of the neural network regulator. Along numerical simulations, the same set-up has been also tested in a real-time experiment with a 1:18 scaled model and thermal chamber. The comparison analysis brings out interesting conclusion about simulation accuracy in this particular case.

Keywords: double skin façade, experimental tests, heat control, heat flow, simulated tests, simulation tools

Procedia PDF Downloads 204

Authors: Ishtiaq A. Chaudhry, Zia R. Tahir, F. A. Siddiqui, F. Noor, M. J. Rashid

Abstract:

It has experimentally been proved that the performance of compression ignition (CI) engine is spray characteristics related. In modern diesel engine the spray formation and the eventual combustion process are the vital processes that offer more challenges towards enhancing the engine performance. In the present work, the numerical simulation has been carried out for evaporating diesel sprays using Fluent software. For computational fluid dynamics simulation “Meshing” is done using Gambit software before transmitting it into fluent. The simulation is carried out using hot bomb conditions under varying chamber conditions such as gas pressure, nozzle diameter and fuel injection pressure. For comparison purpose, the numerical simulations the chamber conditions were kept the same as that of the experimental data. At varying chamber conditions the spray penetration rates are compared with the existing experimental results.

Keywords: evaporating diesel sprays, penetration rates, hot bomb conditions

Procedia PDF Downloads 332