Search results for: reactive molecular dynamics simulation

Authors: Ahmed Al-Saadi, Ali Hassanpour, Tariq Mahmud

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The main objective of this study is to investigate ways to reduce the aerodynamic drag coefficient and to increase the stability of the full-size Sport Utility Vehicle using three-dimensional Computational Fluid Dynamics (CFD) simulation. The baseline model in the simulation was the Land Rover Discovery 4. Many aerodynamic devices and external design modifications were used in this study. These reduction aerodynamic techniques were tested individually or in combination to get the best design. All new models have the same capacity and comfort of the baseline model. Uniform freestream velocity of the air at inlet ranging from 28 m/s to 40 m/s was used. ANSYS Fluent software (version 16.0) was used to simulate all models. The drag coefficient obtained from the ANSYS Fluent for the baseline model was validated with experimental data. It is found that the use of modern aerodynamic add-on devices and modifications has a significant effect in reducing the aerodynamic drag coefficient.

Keywords: aerodynamics, RANS, sport utility vehicle, turbulent flow

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Authors: Malik I. Al-Amayreh, Mohammad I. Kilani, Ahmed S. Al-Salaymeh

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This works presents a Computational Fluid Dynamics (CFD) simulation of a butterfly valve used to control the flow of combustible gas mixture in an industrial process setting. The work uses CFD simulation to analyze the flow characteristics in the vicinity of the valve, including the velocity distributions, streamlines and path lines. Frequency spectrum of the pressure pulsations downstream the valves, and the vortex shedding allow predicting the torque fluctuations acting on the valve shaft and the possibility of generating mechanical vibration and resonance. These fluctuations are due to aerodynamic torque resulting from fluid turbulence and vortex shedding in the valve vicinity. The valve analyzed is located in a pipeline between two opposing 90o elbows, which exposes the valve and the surrounding structure to the turbulence generated upstream and downstream the elbows at either end of the pipe. CFD simulations show that the best location for the valve from a vibration point of view is in the middle of the pipe joining the elbows.

Keywords: butterfly valve vibration analysis, computational fluid dynamics, fluid flow circuit design, fluctuation

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Authors: Ali Afaghi, Sehraneh Ghaemi

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The coordination of the multi-agent systems has been one of the interesting topic in recent years, because of its potential applications in many branches of science and engineering such as sensor networks, flocking, underwater vehicles and etc. In the most of the related studies, it is assumed that the dynamics of the multi-agent systems are integer-order and linear and the multi-agent systems with the fractional-order nonlinear dynamics are rarely considered. However many phenomena in nature cannot be described within integer-order and linear characteristics. This paper investigates the leader-following consensus problem for a class of nonlinear fractional-order multi-agent systems based on observer-based cooperative control. In the system, the dynamics of each follower and leader are nonlinear. For a multi-agent system with fixed directed topology firstly, an observer-based consensus protocol is proposed based on the relative observer states of neighboring agents. Secondly, based on the property of the stability theory of fractional-order system, some sufficient conditions are presented for the asymptotical stability of the observer-based fractional-order control systems. The proposed method is applied on a five-agent system with the fractional-order nonlinear dynamics and unavailable states. The simulation example shows that the proposed scenario results in the good performance and can be used in many practical applications.

Keywords: fractional-order multi-agent systems, leader-following consensus, nonlinear dynamics, directed graphs

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Authors: Michal Biały, Konrad Pietrykowski, Rafal Sochaczewski

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The kinematics and dynamics analysis of crank-piston system of aircraft engine. The object of the study was the high power aircraft engine ASz 62-IR. This engine is produced by a Polish company WSK "PZL-KALISZ" S.A.". All analyzes were performed numerically using CAD and CAE environment. Three-dimensional model of the crank-piston system was developed based on real engine located in the Laboratory of Centre of Innovation and Advanced Technologies of Lublin University of Technology. During the development of the model, the technique of reverse engineering - 3D scanning was used. ASz 62-IR engine is characterized by a radial type of crank-piston system. In this system the cylinders are arranged radially around the circle. This crank-piston system consists of a main connecting rod and eight additional connecting rods. In addition, three-dimensional model consists of a piston pins, pistons and piston rings. As a result of the specific engine design, characteristics of the piston individual movement are slightly different from each other. But the model assumes that they are the same during the analysis. Three-dimensional model of the engine was implemented into the MSC Adams software. The environment of MSC Adams allows for multibody simulation of the dynamic phenomena. This determines the state parameters of the moving elements, among which the load or force distribution on each kinematic node can be distinguished. Materials and characteristic materials parameters were adopted on the basis of commonly used materials for engine parts. The mass values of individual elements were adopted on the basis of real engine parts. The piston gas forces were replaced by calculation of pressure variations recorded during engine tests on the engine test bench. The research the changes of forces acting in the individual kinematic pairs of crank-piston system. The model allows to determine the load on the crankshaft main bearings. This gives the possibility for the main supports forces analysis The model allows for testing and simulation of kinematics and dynamics of a radial aircraft engine. This is the first stage of the work, which aims to numerical simulation of vibration of multi-cylinder aircraft engine. This work has been financed by the Polish National Centre for Research and Development, INNOLOT, under Grant Agreement No. INNOLOT/I/1/NCBR/2013.

Keywords: aircraft engine, CAD, CAE, dynamics, kinematics, MSC Adams, numerical simulation

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Authors: Alexandra C. Blaga, Dan Caşcaval, Alexandra Tucaliuc, Madalina Poştaru, Anca I. Galaction

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Amino acids are valuable chemical products used in in human foods, in animal feed additives and in the pharmaceutical field. Recently, there has been a noticeable rise of amino acids utilization throughout the world to include their use as raw materials in the production of various industrial chemicals: oil gelating agents (amino acid-based surfactants) to recover effluent oil in seas and rivers and poly(amino acids), which are attracting attention for biodegradable plastics manufacture. The amino acids can be obtained by biosynthesis or from protein hydrolysis, but their separation from the obtained mixtures can be challenging. In the last decades there has been a continuous interest in developing processes that will improve the selectivity and yield of downstream processing steps. The liquid-liquid extraction of amino acids (dissociated at any pH-value of the aqueous solutions) is possible only by using the reactive extraction technique, mainly with extractants of organophosphoric acid derivatives, high molecular weight amines and crown-ethers. The purpose of this study was to analyse the separation of nine amino acids of acidic character (l-aspartic acid, l-glutamic acid), basic character (l-histidine, l-lysine, l-arginine) and neutral character (l-glycine, l-tryptophan, l-cysteine, l-alanine) by reactive extraction with di-(2-ethylhexyl)phosphoric acid (D2EHPA) dissolved in butyl acetate. The results showed that the separation yield is controlled by the pH value of the aqueous phase: the reactive extraction of amino acids with D2EHPA is possible only if the amino acids exist in aqueous solution in their cationic forms (pH of aqueous phase below the isoeletric point). The studies for individual amino acids indicated the possibility of selectively separate different groups of amino acids with similar acidic properties as a function of aqueous solution pH-value: the maximum yields are reached for a pH domain of 2–3, then strongly decreasing with the pH increase. Thus, for acidic and neutral amino acids, the extraction becomes impossible at the isolelectric point (pHi) and for basic amino acids at a pH value lower than pHi, as a result of the carboxylic group dissociation. From the results obtained for the separation from the mixture of the nine amino acids, at different pH, it can be observed that all amino acids are extracted with different yields, for a pH domain of 1.5–3. Over this interval, the extract contains only the amino acids with neutral and basic character. For pH 5–6, only the neutral amino acids are extracted and for pH > 6 the extraction becomes impossible. Using this technique, the total separation of the following amino acids groups has been performed: neutral amino acids at pH 5–5.5, basic amino acids and l-cysteine at pH 4–4.5, l-histidine at pH 3–3.5 and acidic amino acids at pH 2–2.5.

Keywords: amino acids, di-(2-ethylhexyl) phosphoric acid, reactive extraction, selective extraction

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

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Model updating method has received increasing attention in damage detection structures based on measured modal parameters. Therefore, a probability-based damage detection (PBDD) procedure based on a model updating procedure is presented in this paper, in which a one-stage model-based damage identification technique based on the dynamic features of a structure is investigated. The presented framework uses a finite element updating method with a Monte Carlo simulation that considers the uncertainty caused by measurement noise. Enhanced ideal gas molecular movement (EIGMM) is used as the main algorithm for model updating. Ideal gas molecular movement (IGMM) is a multiagent algorithm based on the ideal gas molecular movement. Ideal gas molecules disperse rapidly in different directions and cover all the space inside. This is embedded in the high speed of molecules, collisions between them and with the surrounding barriers. In IGMM algorithm to accomplish the optimal solutions, the initial population of gas molecules is randomly generated and the governing equations related to the velocity of gas molecules and collisions between those are utilized. In this paper, an enhanced version of IGMM, which removes unchanged variables after specified iterations, is developed. The proposed method is implemented on two numerical examples in the field of structural damage detection. The results show that the proposed method can perform well and competitive in PBDD of structures.

Keywords: enhanced ideal gas molecular movement (EIGMM), ideal gas molecular movement (IGMM), model updating method, probability-based damage detection (PBDD), uncertainty quantification

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Authors: Bao Liu, Maarten Vanierschot, Frank Buysschaert

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The present work examines the wake dynamics of a rim-driven thruster (RDT) with Computational Fluid Dynamics (CFD). Unsteady Reynolds-averaged Navier-Stokes (URANS) equations were solved in the commercial solver ANSYS Fluent in combination with the SST k-ω turbulence model. The application of the moving reference frame (MRF) and sliding mesh (SM) approach to handling the rotational movement of the propeller were compared in the transient simulations. Validation and verification of the numerical model was performed to ensure numerical accuracy. Two representative scenarios were considered, i.e., the bollard condition (J=0) and a very light loading condition(J=0.7), respectively. From the results, it’s confirmed that compared to the SM method, the MRF method is not suitable for resolving the unsteady flow features as it only gives the general mean flow but smooths out lots of characteristic details in the flow field. By evaluating the simulation results with the SM technique, the instantaneous wake flow field under both conditions is presented and analyzed, most notably the helical vortex structure. It’s observed from the results that the tip vortices, blade shed vortices, and hub vortices are present in the wake flow field and convect downstream in a highly non-linear way. The shear layer vortices shedding from the duct displayed a strong interaction with the distorted tip vortices in an irregularmanner.

Keywords: computational fluid dynamics, rim-driven thruster, sliding mesh, wake dynamics

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Authors: Justine Kiiza, Xu Jiafang

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The world’s demand for energy is increasing rapidly due to population growth and a reduction in shallow conventional oil and gas reservoirs, resorting to deeper and mostly unconventional reserves like shale oil and gas. Most shale formations contain a large amount of expansive sodium montmorillonite (Na-Mnt), due to high water adsorption, hydration, and when the drilling fluid filtrate enters the formation with high Mnt content, the wellbore wall can be unstable due to hydration and swelling, resulting to shrinkage, sticking, balling, time wasting etc., and well collapse in extreme cases causing complex downhole accidents and high well costs. Recently, polyamines like 1, 6 – hexane diamine (HEDA) have been used as typical drilling fluid shale inhibitors to minimize and/or cab clay mineral swelling and maintain the wellbore stability. However, their application is limited to shallow drilling due to their sensitivity to elevated temperature and pressure. Inorganic potassium salts i.e., KCl, have long been applied for restriction of shale formation hydration expansion in deep wells, but their use is limited due to toxicity. Understanding the adsorption behaviour of HEDA on Na-Mnt surfaces in present of organo-salts, organic K-salts e.g., HCO₂K - main component of organo-salt drilling fluid, is of great significance in explaining the inhibitory performance of polyamine inhibitors. Molecular dynamic simulations (MD) were applied to investigate the influence of HCO₂K and KCl on the adsorption mechanism of HEDA on the Na-Mnt surface. Simulation results showed that adsorption configurations of HEDA are mainly by terminal amine groups with a flat-lying alkyl hydrophobic chain. Its interaction with the clay surface decreased the H-bond number between H₂O-clay and neutralized the negative charge of the Mnt surface, thus weakening the surface hydration ability of Na-Mnt. The introduction of HCO₂K greatly improved inhibition ability, coordination of interlayer ions with H₂O as they were replaced by K+, and H₂O-HCOO- coordination reduced H₂O-Mnt interactions, mobility and transport capability of H₂O molecules were more decreased. While KCl showed little ability and also caused more hydration with time, HCO₂K can be used as an alternative for offshore drilling instead of toxic KCl, with a maximum concentration noted in this study as 1.65 wt%. This study provides a theoretical elucidation for the inhibition mechanism and adsorption characteristics of HEDA inhibitor on Na-Mnt surfaces in the presence of K+-salts and may provide more insight into the evaluation, selection, and molecular design of new clay-swelling high-performance WBDF systems used in oil and gas complex offshore drilling well sections.

Keywords: shale, hydration, inhibition, polyamines, organo-salts, simulation

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Authors: Jorge Lopez

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In this work, we introduce fractional calculus in order to study the dynamics of a damped multistory building with some symmetry. Initially we make a review of the dynamics of a free and damped multistory building. Then we introduce those concepts of fractional calculus that will be involved in our study. It has been noticed that fractional calculus provides models with less parameters than those based on classical calculus. In particular, a damped classical oscilator is more naturally described by using fractional derivatives. Accordingly, we model our multistory building as a set of coupled fractional oscillators and compare its dynamics with the results coming from traditional methods.

Keywords: coupled oscillators, fractional calculus, fractional oscillator, structural dynamics

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Authors: Dino Carpentras, Alejandro Dinkelberg, Michael Quayle

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Within agent-based modeling, opinion dynamics is the field that focuses on modeling people's opinions. In this prolific field, most of the literature is dedicated to the exploration of the two 'degrees of freedom' and how they impact the model’s properties (e.g., the average final opinion, the number of final clusters, etc.). These degrees of freedom are (1) the interaction rule, which determines how agents update their own opinion, and (2) the network topology, which defines the possible interaction among agents. In this work, we show that the third degree of freedom exists. This can be used to change a model's output up to 100% of its initial value or to transform two models (both from the literature) into each other. Since opinion dynamics models are representations of the real world, it is fundamental to understand how people’s opinions can be measured. Even for abstract models (i.e., not intended for the fitting of real-world data), it is important to understand if the way of numerically representing opinions is unique; and, if this is not the case, how the model dynamics would change by using different representations. The process of measuring opinions is non-trivial as it requires transforming real-world opinion (e.g., supporting most of the liberal ideals) to a number. Such a process is usually not discussed in opinion dynamics literature, but it has been intensively studied in a subfield of psychology called psychometrics. In psychometrics, opinion scales can be converted into each other, similarly to how meters can be converted to feet. Indeed, psychometrics routinely uses both linear and non-linear transformations of opinion scales. Here, we analyze how this transformation affects opinion dynamics models. We analyze this effect by using mathematical modeling and then validating our analysis with agent-based simulations. Firstly, we study the case of perfect scales. In this way, we show that scale transformations affect the model’s dynamics up to a qualitative level. This means that if two researchers use the same opinion dynamics model and even the same dataset, they could make totally different predictions just because they followed different renormalization processes. A similar situation appears if two different scales are used to measure opinions even on the same population. This effect may be as strong as providing an uncertainty of 100% on the simulation’s output (i.e., all results are possible). Still, by using perfect scales, we show that scales transformations can be used to perfectly transform one model to another. We test this using two models from the standard literature. Finally, we test the effect of scale transformation in the case of finite precision using a 7-points Likert scale. In this way, we show how a relatively small-scale transformation introduces both changes at the qualitative level (i.e., the most shared opinion at the end of the simulation) and in the number of opinion clusters. Thus, scale transformation appears to be a third degree of freedom of opinion dynamics models. This result deeply impacts both theoretical research on models' properties and on the application of models on real-world data.

Keywords: degrees of freedom, empirical validation, opinion scale, opinion dynamics

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Authors: Santhosh Kumat T., Priya E.

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The control of a doubly fed induction generator by fuzzy is described. The active and reactive power can be controlled by rotor and grid side converters with fuzzy controller. The main objective is to maintain constant voltage and frequency at the output of the generator. However the Line Side Converter (LSC) can be controlled to supply up to 50% of the required reactive current. When the crowbar is not activated the DFIG can supply reactive power from the rotor side through the machine as well as through the LSC.

Keywords: Doubly Fed Induction Generator (DFIG), Rotor Side Converter (RSC), Grid Side Converter (GSC), Wind Energy Conversion Systems (WECS)

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Authors: Teewin Plangsrinont, Wasawat Nakkiew

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In this study, computational fluid dynamics (CFD) was utilized to simulate and predict the path of water from water soot blower through an ambient flow field in 300-megawatt tangentially burned pulverized coal boiler that utilizes a water soot blower as a cleaning device. To predict the position of the impact of water on the opposite side of the water soot blower under identical conditions, the nozzle size and water flow rate were fixed in this investigation. The simulation findings demonstrated a high degree of accuracy in predicting the direction of water flow to the boiler's water wall tube, which was validated by comparison to experimental data. Results show maximum deviation value of the water jet trajectory is 10.2 percent.

Keywords: computational fluid dynamics, tangentially fired boiler, thermal power plant, water soot blower

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Authors: Getachew Tilahun, Oluwole Makinde, David Malonza

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We propose and analyze a non-linear mathematical model for the transmission dynamics of pneumonia disease in a population of varying size. The deterministic compartmental model is studied using stability theory of differential equations. The effective reproduction number is obtained and also the local and global asymptotically stability conditions for the disease free and as well as for the endemic equilibria are established. The model exhibit a backward bifurcation and the sensitivity indices of the basic reproduction number to the key parameters are determined. Using Pontryagin’s maximum principle, the optimal control problem is formulated with three control strategies; namely disease prevention through education, treatment and screening. The cost effectiveness analysis of the adopted control strategies revealed that the combination of prevention and treatment is the most cost effective intervention strategies to combat the pneumonia pandemic. Numerical simulation is performed and pertinent results are displayed graphically.

Keywords: cost effectiveness analysis, optimal control, pneumonia dynamics, stability analysis, numerical simulation

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Authors: Isaac Quiros-Fernandez, Angel Cid-Arregui

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Tumor-reactive T cell receptors (TCRs) are being subject of intense investigation since they offer great potential in adoptive cell therapies against cancer. However, the identification of tumor-specific TCRs has proven challenging, for instance, due to the limited expansion capacity of tumor-infiltrating T cells (TILs) and the extremely low frequencies of tumor-reactive T cells in the repertoire of patients and healthy donors. We have developed an approach for rapid identification and characterization of neoepitope-reactive TCRs from the T cell repertoire of healthy donors. CD8 T cells isolated from multiple donors are subjected to a first sorting step after staining with HLA multimers carrying the peptide of interest. The isolated cells are expanded for two weeks, after which a second sorting is performed using the same peptide-HLA multimers. The cells isolated in this way are then processed for single-cell sequencing of their TCR alpha and beta chains. Newly identified TCRs are cloned in appropriate expression vectors for functional analysis on Jurkat, NK92, and primary CD8 T cells and tumor cells expressing the appropriate antigen. We have identified TCRs specifically binding HLA-A2 presenting epitopes of tumor antigens, which are capable of inducing TCR-mediated cell activation and cytotoxicity in target cancer cell lines. This method allows the identification of tumor-reactive TCRs in about two to three weeks, starting from peripheral blood samples of readily available healthy donors.

Keywords: cancer, TCR, tumor antigens, immunotherapy

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Authors: Anuradha Ranawakage, Chathurani Silva

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With the growing expansion of global businesses, supply chains are increasingly exposed to numerous disruptions. Organizations adopt various strategies to mitigate the impact of these disruptions. Depending on the variations in the conditions and characteristics of supply chains, the adoption of resilience strategies may vary across industries. However, these differences are largely unexplored in the existing literature. Hence, this study aims to evaluate the adoption of three proactive strategies: proactive collaboration, digital connectivity, integrated SC risk management, and three reactive strategies: reactive collaboration, inventory and reserve capacity, and lifeline maintenance in the apparel and construction industries in Sri Lanka. An online questionnaire was used to collect data on the implementation of resilience strategies from a sample of 162 apparel and 185 construction companies operating in Sri Lanka. This research makes a significant contribution to the field of supply chain management by assessing the extent to which different resilience strategies are functioned within the apparel and construction industries in Sri Lanka, particularly in an era after a global pandemic that significantly disrupted supply chains all around the world.

Keywords: apparel, construction, proactive strategies, reactive strategies, supply chain resilience

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Authors: Johns Paul, Santhosh J. Nalluveettil, P. Purushothaman, M. Premdas

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Lunar landing is one of the most critical phases of lunar mission. The lander is provided with a soft landing system to prevent structural damage of lunar module by absorbing the landing shock and also assure stability during landing. Presently available software are not capable to simulate the rigid body dynamics coupled with contact simulation and elastic/plastic deformation analysis. Hence a separate mathematical model has been generated for studying the dynamics of a typical lunar soft lander. Parameters used in the analysis includes lunar surface slope, coefficient of friction, initial touchdown velocity (vertical and horizontal), mass and moment of inertia of lander, crushing force due to energy absorbing material in the legs, number of legs and geometry of lander. The mathematical model is capable to simulate plastic and elastic deformation of honey comb, frictional force between landing leg and lunar soil, surface contact simulation, lunar gravitational force, rigid body dynamics and linkage dynamics of inverted tripod landing gear. The non linear differential equations generated for studying the dynamics of lunar lander is solved by numerical method. Matlab programme has been used as a computer tool for solving the numerical equations. The position of each kinematic joint is defined by mathematical equations for the generation of equation of motion. All hinged locations are defined by position vectors with respect to body fixed coordinate. The vehicle rigid body rotations and motions about body coordinate are only due to the external forces and moments arise from footpad reaction force due to impact, footpad frictional force and weight of vehicle. All these force are mathematically simulated for the generation of equation of motion. The validation of mathematical model is done by two different phases. First phase is the validation of plastic deformation of crushable elements by employing conservation of energy principle. The second phase is the validation of rigid body dynamics of model by simulating a lander model in ADAMS software after replacing the crushable elements to elastic spring element. Simulation of plastic deformation along with rigid body dynamics and contact force cannot be modeled in ADAMS. Hence plastic element of primary strut is replaced with a spring element and analysis is carried out in ADAMS software. The same analysis is also carried out using the mathematical model where the simulation of honeycomb crushing is replaced by elastic spring deformation and compared the results with ADAMS analysis. The rotational motion of linkages and 6 degree of freedom motion of lunar Lander about its CG can be validated by ADAMS software by replacing crushing element to spring element. The model is also validated by the drop test results of 4 leg lunar lander. This paper presents the details of mathematical model generated and its validation.

Keywords: honeycomb, landing leg tripod, lunar lander, primary link, secondary link

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Authors: Rajinder Pal Kaur, Amit Sharma, Anuj Kumar Sharma, Govind Prasad Sahu

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The existence of chaos in the marine ecosystems may cause planktonic blooms, disease outbreaks, extinction of some plankton species, or some complex dynamics in oceans, which can adversely affect the sustainable marine ecosystem. The control of the chaotic plankton-fish dynamics is one of the main motives of marine ecologists. In this paper, we have studied the impact of phytoplankton refuge, zooplankton refuge, and fear effect on the chaotic plankton-fish dynamics incorporating phytoplankton, zooplankton, and fish biomass. The fear of fish predation transfers the unpredictable(chaotic) behavior of the plankton system to a stable orbit. The defense mechanism developed by prey species due to fear of the predator population can also terminate chaos from the given dynamics. Moreover, the impact of external disturbances like seasonality, noise, periodic fluctuations, and time delay on the given chaotic plankton system has also been discussed. We have applied feedback mechanisms to control the complexity of the system through the parameter noise. The non-feedback schemes are implemented to observe the role of seasonal force, periodic fluctuations, and time delay in suppressing the given chaotic system. Analytical results are substantiated by numerical simulation.

Keywords: plankton, chaos, noise, seasonality, fluctuations, fear effect, prey refuge

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Authors: Vrushali Guhe, Shailza Singh

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Cutaneous leishmaniasis is neglected tropical disease present worldwide caused by the protozoan parasite Leishmania major, the therapeutic armamentarium for leishmaniasis are showing several limitations as drugs are showing toxic effects with increasing resistance by a parasite. Thus identification of novel therapeutic targets is of paramount importance. Previous studies have shown that autophagy, a cellular process, can either facilitate infection or aid in the elimination of the parasite, depending on the specific parasite species and host background in leishmaniasis. In the present study, our objective was to target the essential autophagy protein ATG8, which plays a crucial role in the survival, infection dynamics, and differentiation of the Leishmania parasite. ATG8 in Leishmania major and its homologue, LC3, in Homo sapiens, act as autophagic markers. Present study manifested the crucial role of ATG8 protein as a potential target for combating Leishmania major infection. Through bioinformatics analysis, we identified non-conserved motifs within the ATG8 protein of Leishmania major, which are not present in LC3 of Homo sapiens. Against these two non-conserved motifs, we generated a peptide library of 60 peptides on the basis of physicochemical properties. These peptides underwent a filtering process based on various parameters, including feasibility of synthesis and purification, compatibility with Selective Reaction Monitoring (SRM)/Multiple reaction monitoring (MRM), hydrophobicity, hydropathy index, average molecular weight (Mw average), monoisotopic molecular weight (Mw monoisotopic), theoretical isoelectric point (pI), and half-life. Further filtering criterion shortlisted three peptides by using molecular docking and molecular dynamics simulations. The direct interaction between ATG8 and the shortlisted peptides was confirmed through Surface Plasmon Resonance (SPR) experiments. Notably, these peptides exhibited the remarkable ability to penetrate the parasite membrane and exert profound effects on Leishmania major. The treatment with these peptides significantly impacted parasite survival, leading to alterations in the cell cycle and morphology. Furthermore, the peptides were found to modulate autophagosome formation, particularly under starved conditions, suggesting their involvement in disrupting the regulation of autophagy within Leishmania major. In vitro, studies demonstrated that the selected peptides effectively reduced the parasite load within infected host cells. Encouragingly, these findings were corroborated by in vivo experiments, which showed a reduction in parasite burden upon peptide administration. Additionally, the peptides were observed to affect the levels of LC3II within host cells. In conclusion, our findings highlight the efficacy of these novel peptides in targeting Leishmania major’s ATG8 and disrupting parasite survival. These results provide valuable insights into the development of innovative therapeutic strategies against leishmaniasis via targeting autophagy protein ATG8 of Leishmania major.

Keywords: ATG8, leishmaniasis, surface plasmon resonance, MD simulation, molecular docking, peptide designing, therapeutics

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Authors: Jonghyuk Yoon, Hyoungwoon Song

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Recently, there are lots of increasing interest in a smart farming that represents application of modern Information and Communication Technologies (ICT) into agriculture since it provides a methodology to optimize production efficiencies by managing growing conditions of crops automatically. In order to obtain high performance and stability for smart greenhouse, it is important to identify the effect of various working parameters such as capacity of ventilation fan, vent opening area and etc. In the present study, a 3-dimensional CFD (Computational Fluid Dynamics) simulation for single-span greenhouse was conducted using the commercial program, Ansys CFX 18.0. The numerical simulation for single-span greenhouse was implemented to figure out the internal thermal and flow characteristics. In order to numerically model solar radiation that spread over a wide range of wavelengths, the multiband model that discretizes the spectrum into finite bands of wavelength based on Wien’s law is applied to the simulation. In addition, absorption coefficient of vinyl varied with the wavelength bands is also applied based on Beer-Lambert Law. To validate the numerical method applied herein, the numerical results of the temperature at specific monitoring points were compared with the experimental data. The average error rates (12.2~14.2%) between them was shown and numerical results of temperature distribution are in good agreement with the experimental data. The results of the present study can be useful information for the design of various greenhouses. This work was supported by Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (IPET) through Advanced Production Technology Development Program, funded by Ministry of Agriculture, Food and Rural Affairs (MAFRA)(315093-03).

Keywords: single-span greenhouse, CFD (computational fluid dynamics), solar radiation, multiband model, absorption coefficient

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Authors: Maria Fontenele, Claude-Gilles Dussap, Vincent Dumouilla, Baptiste Boit

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Roquette Frères is a producer of plant-based ingredients that employs many processes to extract relevant molecules and often transforms them through chemical and physical processes to create desired ingredients with specific functionalities. In this context, Roquette encounters numerous multi-component complex systems in their processes, including fibers, proteins, and carbohydrates, in an aqueous environment. To develop, control, and optimize both new and old processes, Roquette aims to develop new in silico tools. Currently, Roquette uses process modelling tools which include specific thermodynamic models and is willing to develop computational methodologies such as molecular dynamics simulations to gain insights into the complex interactions in such complex media, and especially hydrogen bonding interactions. The issue at hand concerns aqueous mixtures of polyols with high dry matter content. The polyols mannitol and sorbitol molecules are diastereoisomers that have nearly identical chemical structures but very different physicochemical properties: for example, the solubility of sorbitol in water is 2.5 kg/kg of water, while mannitol has a solubility of 0.25 kg/kg of water at 25°C. Therefore, predicting liquid-solid equilibrium properties in this case requires sophisticated solution models that cannot be based solely on chemical group contributions, knowing that for mannitol and sorbitol, the chemical constitutive groups are the same. Recognizing the significance of solvation phenomena in polyols, the GePEB (Chemical Engineering, Applied Thermodynamics, and Biosystems) team at Institut Pascal has developed the COSMO-UCA model, which has the structural advantage of using quantum mechanics tools to predict formation and phase equilibrium properties. In this work, we use molecular dynamics simulations to elucidate the behavior of polyols in aqueous solution. Specifically, we employ simulations to compute essential metrics such as radial distribution functions and hydrogen bond autocorrelation functions. Our findings illuminate a fundamental contrast: sorbitol and mannitol exhibit disparate hydrogen bond lifetimes within aqueous environments. This observation serves as a cornerstone in elucidating the divergent physicochemical properties inherent to each compound, shedding light on the nuanced interplay between their molecular structures and water interactions. We also present a methodology to predict the physicochemical properties of complex solutions, taking as sole input the three-dimensional structure of the molecules in the medium. Finally, by developing knowledge models, we represent some physicochemical properties of aqueous solutions of sorbitol and mannitol.

Keywords: COSMO models, hydrogen bond, molecular dynamics, thermodynamics

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Authors: M. Cardenas-Garcia, P. P. Gonzalez-Perez

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Intercellular communication is a necessary condition for cellular functions and it allows a group of cells to survive as a population. Throughout this interaction, the cells work in a coordinated and collaborative way which facilitates their survival. In the case of cancerous cells, these take advantage of intercellular communication to preserve their malignancy, since through these physical unions they can send signs of malignancy. The Wnt/β-catenin signaling pathway plays an important role in the formation of intercellular communications, being also involved in a large number of cellular processes such as proliferation, differentiation, adhesion, cell survival, and cell death. The modeling and simulation of cellular signaling systems have found valuable support in a wide range of modeling approaches, which cover a wide spectrum ranging from mathematical models; e.g., ordinary differential equations, statistical methods, and numerical methods– to computational models; e.g., process algebra for modeling behavior and variation in molecular systems. Based on these models, different simulation tools have been developed from mathematical ones to computational ones. Regarding cellular and molecular processes in cancer, its study has also found a valuable support in different simulation tools that, covering a spectrum as mentioned above, have allowed the in silico experimentation of this phenomenon at the cellular and molecular level. In this work, we simulate and explore the complex interaction patterns of intercellular communication in cancer cells using the Cellulat bioinformatics tool, a computational simulation tool developed by us and motivated by two key elements: 1) a biochemically inspired model of self-organizing coordination in tuple spaces, and 2) the Gillespie’s algorithm, a stochastic simulation algorithm typically used to mimic systems of chemical/biochemical reactions in an efficient and accurate way. The main idea behind the Cellulat simulation tool is to provide an in silico experimentation environment that complements and guides in vitro experimentation in intra and intercellular signaling networks. Unlike most of the cell signaling simulation tools, such as E-Cell, BetaWB and Cell Illustrator which provides abstractions to model only intracellular behavior, Cellulat is appropriate for modeling both intracellular signaling and intercellular communication, providing the abstractions required to model –and as a result, simulate– the interaction mechanisms that involve two or more cells, that is essential in the scenario discussed in this work. During the development of this work we made evident the application of our computational simulation tool (Cellulat) for the modeling and simulation of intercellular communication between normal and cancerous cells, and in this way, propose key molecules that may prevent the arrival of malignant signals to the cells that surround the tumor cells. In this manner, we could identify the significant role that has the Wnt/β-catenin signaling pathway in cellular communication, and therefore, in the dissemination of cancer cells. We verified, using in silico experiments, how the inhibition of this signaling pathway prevents that the cells that surround a cancerous cell are transformed.

Keywords: cancer cells, in silico approach, intercellular communication, key molecules, modeling and simulation

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Authors: Oluwaseun Simon Adekanle, M'hammed Guisser, Elhassane Abdelmounim, Mohamed Aboulfatah

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In this paper, modeling and control of a grid connected 660KW Doubly-Fed Induction Generator wind turbine is presented. Stator flux orientation is used to realize active-reactive power decoupling to enable independent control of active and reactive power. The recursive Integral Backstepping technique is used to control generator speed to its optimum value and to obtain unity power factor. The controller is combined with High Gain Observer to estimate the mechanical torque of the machine. The most important advantage of this combination of High Gain Observer and the Integral Backstepping controller is the annulation of static error that may occur due to incertitude between the actual value of a parameter and its estimated value by the controller. Simulation results under Matlab/Simulink show the robustness of this control technique in presence of parameter variation.

Keywords: doubly-fed induction generator, field orientation control, high gain observer, integral backstepping control

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Authors: Sunita Gakkhar, Arti Mishra

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In this paper, a nonlinear host vector model has been proposed and analyzed for the two strain dengue dynamics incorporating ADE effect. The model considers that the asymptomatic infected people are more responsible for secondary infection than that of symptomatic ones and differentiates between them. The existence conditions are obtained for various equilibrium points. Basic reproduction number has been computed and analyzed to explore the effect of secondary infection enhancement parameter on dengue infection. Stability analyses of various equilibrium states have been performed. Numerical simulation has been done for the stability of endemic state.

Keywords: dengue, ade, stability, threshold, asymptomatic, infection

Procedia PDF Downloads 403

Authors: Yaseen Elhebshi, Abdulkareem Hamid, Nureddin Bin Issa, Xiaonong Chen

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A convenient method of preparing ultrafine polystyrene latex nano-particles with amino groups on the surface is developed. Polystyrene latexes in the size range 50–400 nm were prepared via emulsion polymerization, using sodium dodecyl sulfate (SDS) as surfactant. Polystyrene with amino groups on the surface will be fine to use as organic filler to modify rubber. Transmission electron microscopy (TEM) was used to observe the morphology of silicon dioxide and functionalized polystyrene nano-particles. The nature of bonding between the polymer and the reactive groups on the filler surfaces was analyzed using Fourier transform infrared spectroscopy (FTIR). Scanning electron microscopy (SEM) was employed to examine the filler surface.

Keywords: reactive filler, emulsion polymerization, particle size, polystyrene nanoparticles

Procedia PDF Downloads 332

Authors: Xie Kai, Laith K. Abbas, Chen Dongyang, Yang Fufeng, Rui Xiaoting

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Effect of plunging motion on the pitch oscillating NACA0012 airfoil is investigated using computational fluid dynamics (CFD). A simulation model based on overset grid technology and k - ω shear stress transport (SST) turbulence model is established, and the numerical simulation results are compared with available experimental data and other simulations. Two cases of phase angle φ = 0, μ which represents the phase difference between the pitching and plunging motions of an airfoil are performed. Airfoil vortex generation, moving, and shedding are discussed in detail. Good agreements have been achieved with the available literature. The upward plunging motion made the equivalent angle of attack less than the actual one during pitching analysis. It is observed that the formation of the stall vortex is suppressed, resulting in a decrease in the lift coefficient and a delay of the stall angle. However, the downward plunging motion made the equivalent angle of attack higher the actual one.

Keywords: dynamic stall, pitching-plunging, computational fluid dynamics, helicopter blade rotor, airfoil

Procedia PDF Downloads 203

Authors: Chuan-Wen Liu, Min-Hsien Liu, Chung-Chieh Tai, Bing-Cheng Kuo, Cheng-Lung Chen, Huazhen Shen

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A recent surge in research on magnetic radar absorbing materials (RAMs) has presented researchers with new opportunities and challenges. This study was performed to gain a better understanding of the wave-absorbing phenomenon of magnetic RAMs. First, we hypothesized that the absorbing phenomenon is dependent on the particle shape. Using the Material Studio program and the micro-dot magnetic dipoles (MDMD) method, we obtained results from magnetic RAMs to support this hypothesis. The total MDMD energy of disk-like iron particles was greater than that of spherical iron particles. In addition, the particulate aggregation phenomenon decreases the wave-absorbance, according to both experiments and computational data. To conclude, this study may be of importance in terms of explaining the wave- absorbing characteristic of magnetic RAMs. Combining molecular dynamics simulation results and the theory of magnetization of magnetic dots, we investigated the magnetic properties of iron materials with different particle shapes and degrees of aggregation under external magnetic fields. The MDMD of the materials under magnetic fields of various strengths were simulated. Our results suggested that disk-like iron particles had a better magnetization than spherical iron particles. This result could be correlated with the magnetic wave- absorbing property of iron material.

Keywords: wave-absorbing property, magnetic material, micro-dot magnetic dipole, particulate aggregation

Procedia PDF Downloads 465

Authors: Ali Oveysi Sarabi

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In this paper, controller design for the attitude and altitude dynamics of an outdoor quadrotor, which is constructed with low cost actuators and drivers, is aimed. Before designing the controller, the quadrotor is modeled mathematically in Matlab-Simulink environment. To control attitude dynamics, linear quadratic regulator (LQR) based controllers are designed, simulated and applied to the system. Two different proportional-integral-derivative action (PID) controllers are designed to control yaw and altitude dynamics. During the implementation of the designed controllers, different test setups are used. Designed controllers are implemented and tuned on the real system using xPC Target. Tests show that these basic control structures are successful to control the attitude and altitude dynamics.

Keywords: helicopter balance, flight dynamics, autonomous landing, control robotics

Procedia PDF Downloads 485

Authors: Cise Unluer

Abstract:

Reactive MgO hydrates to form brucite (Mg(OH)2, magnesium hydroxide), which can then react with CO2 and additional water to form a range of strength providing hydrated magnesium carbonates (HMCs) within cement-based formulations. The presented work focuses on the use of reactive MgO in a range of concrete mixes, where it carbonates by absorbing CO2 and gains strength accordingly. The main goal involves maximizing the amount of CO2 absorbed within construction products, thereby reducing the overall environmental impact of the designed formulations. Microstructural analyses including scanning electron microscopy (SEM), X-ray diffraction (XRD) and thermogravimetry/differential thermal analysis (TG/DTA) are used in addition to porosity, permeability and unconfined compressive strength (UCS) testing to understand the performance mechanisms. XRD Reference Intensity Ratio (RIR), acid digestion and TG/DTA are utilized to quantify the amount of CO2 sequestered, with the goal of achieving 100% carbonation through careful mix design, leading to a range of carbon neutral products with high strengths. As a result, samples stronger than those containing Portland cement (PC) were produced, revealing the link between the mechanical performance and microstructural development of the developed formulations with the amount of CO2 sequestered.

Keywords: carbonation, compressive strength, reactive MgO cement, sustainability

Procedia PDF Downloads 151

Authors: Sakshi Batra, Suresh Gupta, Pratik Pande, Navneet Kaur, Lovdeep Kaur

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The objective of this study is removal of Methylene blue dye or reactive orange-16 from industrial waste water or from soil using bioremediation technique. As huge amount of dyes are releasing from textile industry in water and soil environment during dyeing process. In this study, we focused on removal of Methylene blue dye and Reactive orange dye from industrial soil at different initial concentration of dye. An experiment study was carried out at methylene blue dye or Reactive orange-16 dye at varying concentration of both the dye as 50 ppm, 100ppm, 200 ppm, 300 ppm and 400 ppm. Maximum removal is obtained at 16-20 hours Experiments are carried out for pH, Temperature and MSM composition. The final concentration has been observed by UV-VIS. The two species has been isolated from the Industrial effluent. Finally the product analysis has been done by GC-MS.

Keywords: bioremediation, cultural growth, dyes, environment

Procedia PDF Downloads 287

Authors: J. Fernandez, N. Aguilar, R. Fernandez de Canete, J. C. Ramos-Diaz

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In this paper, a simulation model of the glucose-insulin system for a patient undergoing diabetes Type 1 is developed by using a causal modeling approach under system dynamics. The OpenModelica simulation environment has been employed to build the so called causal model, while the glucose-insulin model parameters were adjusted to fit recorded mean data of a diabetic patient database. Model results under different conditions of a three-meal glucose and exogenous insulin ingestion patterns have been obtained. This simulation model can be useful to evaluate glucose-insulin performance in several circumstances, including insulin infusion algorithms in open-loop and decision support systems in closed-loop.

Keywords: causal modeling, diabetes, glucose-insulin system, diabetes, causal modeling, OpenModelica software

Procedia PDF Downloads 307