Search results for: molecular simulation

Authors: Hyery Kang, Dong-Yeun Koh, Yun-Ho Ahn, Huen Lee

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Terahertz time-domain spectroscopy (THz-TDS) was used to observe the THF clathrate hydrate system with dosage of polyvinylpyrrolidone (PVP) with three different average molecular weights (10,000 g/mol, 40,000 g/mol, 360,000 g/mol). Distinct footprints of phase transition in the THz region (0.4 - 2.2 THz) were analyzed and absorption coefficients and complex refractive indices are obtained and compared in the temperature range of 253 K to 288 K. Along with the optical properties, ring breathing and stretching modes for different molecular weights of PVP in THF hydrate are analyzed by Raman spectroscopy.

Keywords: clathrate hydrate, terahertz, polyvinylpyrrolidone (PVP), THz-TDS, inhibitor

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Authors: Changshan Zhang, Zhijin Yu, Shixing Fan

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A comprehensive hazard evaluation for coal self-heating in composite long-wall gobs is heavily dependent on computational simulation. In this study, the spatial distributions of cracks which caused significant air leakage were simulated by universal distinct element code (UDEC) simulation. Based on the main routes of air leakage and characteristics of coal self-heating, a computational fluid dynamics (CFD) modeling was conducted to model the coal spontaneous combustion dangerous area in composite long-wall gobs. The results included the oxygen concentration distributions and temperature profiles showed that the numerical approach is validated by comparison with the test data. Furthermore, under the conditions of specific engineering, the major locations where some techniques for extinguishing and preventing long-wall gob fires need to be put into practice were also examined.

Keywords: computational simulation, UDEC simulation, coal self-heating, CFD modeling, long-wall gobs

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Authors: Asma Poursoroush

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Solid-supported lipid bilayers are often used as a simple model for studies of biological membranes. The presence of a solid substrate that interacts attractively with lipid head-groups is expected to affect the phase behavior of the supported bilayer. Molecular dynamics simulations of a coarse-grained model are thus performed to investigate the phase behavior of supported one-component lipid bilayer membranes. Our results show that the attraction of the lipid head groups to the substrate leads to a phase behavior that is different from that of a free standing lipid bilayer. In particular, we found that the phase behaviors of the two leaflets are decoupled in the presence of a substrate. The proximal leaflet undergoes a clear gel-to-fluid phase transition at a temperature lower than that of a free standing bilayer, and that decreases with increasing strength of the substrate-lipid attraction. The distal leaflet, however, undergoes a change from a homogeneous liquid phase at high temperatures to a heterogeneous state consisting of small liquid and gel domains, with the average size of the gel domains that increases with decreasing temperature. While the chain order parameter of the proximal leaflet clearly shows a gel-fluid phase transition, the chain order parameter of the distal leaflet does not exhibit a clear phase transition. The decoupling in the phase behavior of the two leaflets is due to a non-symmteric lipid distribution in the two leaflets resulting from the presence of the substrate.

Keywords: membrane, substrate, molecular dynamics, simulation

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Authors: Melvin Ballera, Aldrich Olivar, Mary Soriano

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Digital computers nowadays must be able to have a utility that is capable of generating random numbers. Usually, computer-generated random numbers are not random given predefined values such as starting point and end points, making the sequence almost predictable. There are many applications of random numbers such business simulation, manufacturing, services domain, entertainment sector and other equally areas making worthwhile to design a unique method and to allow unpredictable random numbers. Applying stochastic simulation using linear congruential algorithm, it shows that as it increases the numbers of the seed and range the number randomly produced or selected by the computer becomes unique. If this implemented in an environment where random numbers are very much needed, the reliability of the random number is guaranteed.

Keywords: stochastic simulation, random numbers, linear congruential algorithm, pseudorandomness

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Authors: Mahdi Golriz

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The aim of this work is to estimate the change in molecular structure of linear low-density polyethylene (LLDPE) during peroxide modification can be detected by a simple rheological method. For this purpose a commercial grade LLDPE (Exxon MobileTM LL4004EL) was reacted with different doses of dicumyl peroxide (DCP). The samples were analyzed by size-exclusion chromatography coupled with a light scattering detector. The dynamic shear oscillatory measurements showed a deviation of the δ-׀G ׀٭curve from that of the linear LLDPE, which can be attributed to the presence of long-chain branching (LCB). By the use of a simple rheological method that utilizes melt rheology, transformations in molecular architecture induced on an originally linear low density polyethylene during the early stages of reactive modification were indicated. Reasonable and consistent estimates are obtained, concerning the degree of LCB, the volume fraction of the various molecular species produced in peroxide modification of LLDPE.

Keywords: linear low-density polyethylene, peroxide modification, long-chain branching, rheological method

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Authors: Soraya Abtouche, Zeyneb Ghoualem, Syrine Daoudi, Lina Ouldmohamed, Xavier Assfeld

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This work reports density functional theory calculations of the optimized geometries, molecular reactivity, energy gap,and thermodynamic properties of the free base (H2P) and their Zn (II) metallated (ZnP), bearing one, two, or three carboxylic acid groups using the hybrid functional B3LYP, Cam-B3lYP, wb97xd with 6-31G(d,p) basis sets. When donating groups are attached to the molecular dye, the bond lengths are slightly decreased, which is important for the easy transfer of an electron from donating to the accepting group. For all dyes, the highest occupied molecular orbital/lowest occupied molecular orbital analysis results in positive outcomes upon electron injection to the semiconductor and subsequent dye regeneration by the electrolyte. The ionization potential increases with increasing conjugation; therefore, the compound dye attached to one carboxylic acid group has the highest ionization potential. The results show higher efficiencies of those sensitized with ZnP. These results have been explained, taking into account the electronic character of the metal ion, which acts as a mediator in the injection step, and, on the other hand, considering the number of anchoring groups to which it binds to the surface of TiO2.

Keywords: DSSC, porphyrin, TD-DFT, electronic properties, donor-acceptor groups

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Authors: Ali Mustafa Elshawesh, Mohamed Abdulali

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The paper presents an approach to dimension circuit switched networks and find the relationship between the parameters of the circuit switched networks on the condition of specific probability of call blocking. Our work is creating a Simulation code based on Erlang (B) formula to draw graphs which show two curves for each graph; one of simulation and the other of calculated. These curves represent the relationships between average number of calls and average call duration with the probability of call blocking. This simulation code facilitates to select the appropriate parameters for circuit switched networks.

Keywords: Erlang B formula, call blocking, telephone system dimension, Markov model, link capacity

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Authors: Kirti Gosavi, Anita Bhole

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The paper demonstrates simulation and steady-state performance of three phase squirrel cage induction motor and detection of rotor broken bar fault using MATLAB. This simulation model is successfully used in the fault detection of rotor broken bar for the induction machines. A dynamic model using PWM inverter and mathematical modelling of the motor is developed. The dynamic simulation of the small power induction motor is one of the key steps in the validation of the design process of the motor drive system and it is needed for eliminating advertent design errors and the resulting error in the prototype construction and testing. The simulation model will be helpful in detecting the faults in three phase induction motor using Motor current signature analysis.

Keywords: squirrel cage induction motor, pulse width modulation (PWM), fault diagnosis, induction motor

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Authors: Asghar Ebrahimi, Elyas Lakzian

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For the analysis of flow inside micro geometries, classical CFD methods can not accurately predict the behavior of flow. Alternatively, the gas flow through micro geometries can be investigated precisely using the direct simulation Monte Carlo (DSMC) method. In the present paper, a pressure boundary condition is utilized to simulate a gaseous flow inside a micro channel using the DSMC method. Accuracy of simulation is guaranteed by choosing proper cell dimension and number of particle per cell analysis. Also, results of simulation are compared with the results of reliable references. Good agreement with results certifies the correctness of new boundary condition implemented on the micro channel.

Keywords: pressure boundary condition, DSMC, micro channel, cell dimension, particle per cell

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Authors: Marianna Maiaru, Gregory M. Odegard, Josh Kemppainen, Ivan Gallegos, Michael Olaya

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Ceramic matrix composites (CMCs) are typically used in applications that require long-term mechanical integrity at elevated temperatures. CMCs are usually fabricated using a polymer precursor that is initially polymerized in situ with fiber reinforcement, followed by a series of cycles of pyrolysis to transform the polymer matrix into a rigid glass or ceramic. The pyrolysis step typically generates volatile gasses, which creates porosity within the polymer matrix phase of the composite. Subsequent cycles of monomer infusion, polymerization, and pyrolysis are often used to reduce the porosity and thus increase the durability of the composite. Because of the significant expense of such iterative processing cycles, new generations of CMCs with improved durability and manufacturability are difficult and expensive to develop using standard Edisonian approaches. The goal of this research is to develop a computational process-modeling-based approach that can be used to design the next generation of CMC materials with optimized material and processing parameters for maximum strength and efficient manufacturing. The process modeling incorporates computational modeling tools, including molecular dynamics (MD), to simulate the material at multiple length scales. Results from MD simulation are used to inform the continuum-level models to link molecular-level characteristics (material structure, temperature) to bulk-level performance (strength, residual stresses). Processing parameters are optimized such that process-induced residual stresses are minimized and laminate strength is maximized. The multiscale process modeling method developed with this research can play a key role in the development of future CMCs for high-temperature and high-strength applications. By combining multiscale computational tools and process modeling, new manufacturing parameters can be established for optimal fabrication and performance of CMCs for a wide range of applications.

Keywords: digital engineering, finite elements, manufacturing, molecular dynamics

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Authors: T. Kritsana, P. Sawitri, P. Teeratas

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This article aims to study the effect of pressure on rocket motor case by Finite Element Method simulation to select optimal material in rocket motor manufacturing process. In this study, cylindrical tubes with outside diameter of 122 mm and thickness of 3 mm are used for simulation. Defined rocket motor case materials are AISI4130, AISI1026, AISI1045, AL2024 and AL7075. Internal pressure used for the simulation is 22 MPa. The result from Finite Element Method shows that at a pressure of 22 MPa rocket motor case produced by AISI4130, AISI1045 and AL7075 can be used. A comparison of the result between AISI4130, AISI1045 and AL7075 shows that AISI4130 has minimum principal stress and confirm the results of Finite Element Method by the used of calculation method found that, the results from Finite Element Method has good reliability.

Keywords: rocket motor case, finite element method, principal stress, simulation

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Authors: Bina Kumari, Subir K. Sarkar, Pradipta Bandyopadhyay

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The autocorrelation function of the density fluctuation is studied in each of the two phases in a Gibbs Ensemble Monte Carlo (GEMC) simulation of the problem of phase separation for a square well potential with various values of its range. We find that the normalized autocorrelation function is described very well as a linear combination of an exponential function with a time scale τ₂ and a stretched exponential function with a time scale τ₁ and an exponent α. Dependence of (α, τ₁, τ₂) on the parameters of the GEMC algorithm and the range of the square well potential is investigated and interpreted. We also analyse the issue of how to choose the parameters of the GEMC simulation optimally.

Keywords: autocorrelation function, density fluctuation, GEMC, simulation

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Authors: Muthana Saleh Alalaki, Michael Opoku Agyeman

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The growth in the number of Intellectual Properties (IPs) or the number of cores on the same chip becomes a critical issue in System-on-Chip (SoC) due to the intra-communication problem between the chip elements. As a result, Network-on-Chip (NoC) has emerged as a system architecture to overcome intra-communication issues. This paper presents a study of recent contributions on simulation tools for NoC. Furthermore, an overview of NoC is covered as well as a comparison between some NoC simulators to help facilitate research in on-chip communication.

Keywords: WiNoC, simulation tool, network-on-chip, SoC

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Authors: Amir Doustgani

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Melt electrospinning is a safe and simple technique for the production of micro and nanofibers which can be an alternative to conventional solvent electrospinning. The effects of various melt-electrospinning parameters, including molecular weight, electric field strength, flow rate and temperature on the morphology and fiber diameter of polylactic acid were studied. It was shown that molecular weight was the predominant factor in determining the obtainable fiber diameter of the collected fibers. An orthogonal design was used to examine process parameters. Results showed that molecular weight is the most effective parameter on the average fiber diameter of melt electrospun PLA nanofibers and the flow rate has the less important impact. Mean fiber diameter increased by increasing MW and flow rate, but decreased by increasing electric field strength and temperature. MFD of optimized fibers was below 100 nm and the result of software was in good agreement with the experimental condition.

Keywords: fiber formation, processing, spinning, melt blowing

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Authors: Shuo Tian, Xuepiao Bai, Jianqin Shang, Pengtao Gai, Yuansong Zeng

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Shot peen forming is an essential forming process for aircraft metal wing panel. With the development of computer simulation technology, scholars have proposed a numerical simulation method of shot peen forming based on stress field. Three shot peen forming indexes of crater diameter, shot speed and surface coverage are required as simulation parameters in the stress field method. It is necessary to establish the relationship between simulation and experimental process parameters in order to simulate the deformation under different shot peen forming parameters. The shot peen forming tests of the 2024-T351 aluminum alloy workpieces were carried out using uniform test design method, and three factors of air pressure, feed rate and shot flow were selected. The second-order response surface model between simulation parameters and uniform test factors was established by stepwise regression method using MATLAB software according to the results. The response surface model was combined with the stress field method to simulate the shot peen forming deformation of the workpiece. Compared with the experimental results, the simulated values were smaller than the corresponding test values, the maximum and average errors were 14.8% and 9%, respectively.

Keywords: shot peen forming, process parameter, response surface model, numerical simulation

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Authors: E. Al Daoud

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In many cases, theoretical treatments are available for models for which there is no perfect physical realization. In this situation, the only possible test for an approximate theoretical solution is to compare with data generated from a computer simulation. In this paper, Monte Carlo tools are used to study and compare the elementary particles models. All the experiments are implemented using 10000 events, and the simulated energy is 13 TeV. The mean and the curves of several variables are calculated for each model using MadAnalysis 5. Anomalies in the results can be seen in the muons masses of the minimal supersymmetric standard model and the two Higgs doublet model.

Keywords: Feynman rules, hadrons, Lagrangian, Monte Carlo, simulation

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Authors: Ilya Kavalchuk, Hayrettin Arisoy, Alex Stojcevski, Aman Maun Than Oo

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Electric vehicles are one of the most complicated electric devices to simulate due to the significant number of different processes involved in electrical structure of it. There are concurrent processes of energy consumption and generation with different onboard systems, which make simulation tasks more complicated to perform. More accurate simulation on energy consumption can provide a better understanding of all energy management for electric transport. As a result of all those processes, electric transport can allow for a more sustainable future and become more convenient in relation to the distance range and recharging time. This paper discusses the problems of energy consumption simulations for electric vehicles using different software packages to provide ideas on how to make this process more precise, which can help engineers create better energy management strategies for electric vehicles.

Keywords: electric vehicles, EV, power consumption, power management, simulation

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Authors: S. Kohestani, R. Amrollahi, P. Daryabor

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Microwave diagnostics such as reflectometry are receiving growing attention in magnetic confinement fusionresearch. In order to obtain the better understanding of plasma confinement physics, more detailed measurements on density profile and its fluctuations might be required. A 2D full-wave simulation of ordinary mode propagation has been written in an effort to model effects seen in reflectometry experiment. The code uses the finite-difference-time-domain method with a perfectly-matched-layer absorption boundary to solve Maxwell’s equations.The code has been used to simulate the reflectometer measurement in Alborz Tokamak.

Keywords: reflectometry, simulation, ordinary mode, tokamak

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Authors: Mehvish Bilal, Navneet Singh, Jasir Mushtaq

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Water pollution puts people's health at risk, and it can also impact the ecology. For practitioners of integrated water resources management (IWRM), water quality modelling may be useful for informing decisions about pollution control (such as discharge permitting) or demand management (such as abstraction permitting). To comprehend the current pollutant load, movement of effective load movement of contaminants generates effective relation between pollutants, mathematical simulation, source, and water quality is regarded as one of the best estimating tools. The current study involves the Qual2k model, which includes manual simulation of the various physiochemical characteristics of water. To this end, various sensors could be installed for the automatic simulation of various physiochemical characteristics of water. An artificial intelligence model has been proposed for the automatic simulation of water quality parameters. Models of water quality have become an effective tool for identifying worldwide water contamination, as well as the ultimate fate and behavior of contaminants in the water environment. Water quality model research is primarily conducted in Europe and other industrialized countries in the first world, where theoretical underpinnings and practical research are prioritized.

Keywords: artificial intelligence, QUAL2K, simulation, physiochemical parameters

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Authors: Arunima Verma, Padmabati Mondal

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Serotonin-receptor binding plays a key role in several neurological and biological processes, including mood, sleep, hunger, cognition, learning, and memory. In this article, we performed molecular dynamics simulation to examine the key residues that play an essential role in the binding of serotonin to the G-protein-coupled 5-HT₁ᴮ receptor (5-HT₁ᴮ R) via electrostatic interactions. An end-point free energy calculation method (MM-PBSA) determines the stability of the 5-HT1B R due to serotonin binding. The single-point mutation of the polar or charged amino acid residues (Asp129, Thr134) on the binding sites and the calculation of binding free energy validate the importance of these residues in the stability of the serotonin-receptor complex. Principal component analysis indicates the serotonin-bound 5-HT1BR is more stabilized than the apo-receptor in terms of dynamical changes. The difference dynamic cross-correlations map shows the correlation between the transmembrane and mini-Go, which indicates signal transduction happening between mini-Go and the receptor. Allosteric communication reveals the key nodes for signal transduction in 5-HT1BR. These results provide useful insights into the signal transduction pathways and mutagenesis study to regulate the functionality of the complex. The developed protocols can be applied to study local non-covalent interactions and long-range allosteric communications in any protein-ligand system for computer-aided drug design.

Keywords: allostery, CADD, MD simulations, MM-PBSA

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Authors: Robert Ogbanje Okwori

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The research studied expository and simulation method of teaching woodwork at Federal University of Technology, Minna, Niger State, Nigeria. The purpose of the study was to compare expository and simulation method of teaching woodwork and determine the method that is more effective in improving performance of students in woodwork. Two research questions and two hypotheses were formulated to guide the study. Fifteen objective questions and two theory questions were used for data collection. The questions set were on structure of timber. The study used the quasi experimental design. The population of the study consisted of 25 woodwork students of Federal University of Technology, Minna, Niger State, Nigeria and three hundred (300) level students were used for the study. The lesson plans for expository method and questions were validated by three lecturers in the Department of Industrial and Technology Education, Federal University of Technology, Minna, Nigeria. The validators checked the appropriates of test items and all the corrections and inputs were effected before administration of the instrument. Data obtained were analyzed using mean, standard deviation and t-test statistical tool. The null hypotheses were formulated and tested using t-test statistics at 0.05 level of significance. The findings of the study showed that simulation method of teaching has improved students’ performance in woodwork and the performance of the students was not influenced by gender. Based on the findings of the study, it was concluded that there was a significant difference in the mean achievement scores of students taught woodwork using simulation method. This implies that simulation method is more effective than expository method of teaching woodwork. Therefore, woodwork teachers should adopt simulation method of teaching woodwork towards better performance. It was recommended that simulation method should be used by woodwork lecturers to teach woodwork since students perform better using the method and also the teachers needs to be trained and re-trained in using simulation method for teaching woodwork. Teachers should be encouraged to use simulation method for their instructional delivery because it will allow them to identify their areas of strength and weakness when imparting knowledge to woodwork students. Government and different agencies should assist in procuring materials and equipment for wood workshops to enable students effectively practice what they have been taught using simulation method.

Keywords: comparative, expository, simulation, woodwork

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

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

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

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Authors: Neha Kanodia, M. Kamil

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Properties of mono layers of Pluronic F127 at air/water interface have been investigated by using Langmuir trough method. Pluronic F127 is a triblock copolymer of poly (ethyleneoxide) (PEO groups)– poly (propylene oxide) (PO groups)–poly(ethylene oxide) (PEO groups). Surface pressure versus mean molecular area isotherms is studied. The isotherm of the mono layer showed the characteristics of a pancake-to-brush transition upon compression of the mono layer. The effect of adding surfactant (SDS) to polymer and the effect of increasing loading on polymer was also studied. The effect of repeated compression and expansion cycle (or hysteresis curve) is investigated to know about stability of the film formed. Static elasticity of mono layer gives information about molecular arrangement, phase structure and phase transition.

Keywords: surface-pressure, mean molecular area isotherms, hysteresis, static elasticity

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Authors: Jing Zhao, Yoshiharu Ishikawa, Chuan Xiao, Kento Sugiura

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In order to analyze large-scale scientific data, research on data exploration and visualization has gained popularity. In this paper, we focus on the exploration and visualization of scientific simulation data, and define a spatial V-Optimal histogram for data summarization. We propose histogram construction algorithms based on a general binary hierarchical partitioning as well as a more specific one, the l-grid partitioning. For effective data summarization and efficient data visualization in scientific data analysis, we propose an optimal algorithm as well as a heuristic algorithm for histogram construction. To verify the effectiveness and efficiency of the proposed methods, we conduct experiments on the massive evacuation simulation data.

Keywords: simulation data, data summarization, spatial histograms, exploration, visualization

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Authors: Hassan Nour, Nouh Mounadi, Oussama Abchir, Belaidi Salah, Samir Chtita

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Cholinesterase enzymes are biological catalysts essential for the transformation of acetylcholine, which is a neurotransmitter implicated in memory and learning, into acetic acid and choline, altering the neurotransmission process in Alzheimer’s disease patients. Therefore, inhibition of cholinesterase enzymes is a relevant strategy for the symptomatic treatment of Alzheimer’s disease. The current investigation aims to explore potential cholinesterase (ChE) inhibitors through a comprehensive computational approach. Forty-nine phytoconstituents extracted from Cannabis sativa L. were in-silico screened using molecular docking and pharmacokinetic and toxicological analysis to evaluate their possible inhibitory effect on the cholinesterase enzymes. Two phytoconstituents belonging to cannabinoid derivatives were revealed to be promising candidates for Alzheimer's therapy by acting as cholinesterase inhibitors. They have exhibited high binding affinities towards the cholinesterase enzymes and showed their ability to interact with key residues involved in cholinesterase enzymatic activity. In addition, they presented good ADMET profiles allowing them to be promising oral drug candidates. Furthermore, molecular dynamics (MD) simulations were executed to explore their interaction stability under mimetic biological conditions and thus support our findings. To corroborate the docking results, the binding free energy corresponding to the more stable ligand-ChE complexes was re-estimated by applying the MM-PBSA method. MD and MM-PBSA studies affirmed that the ligand-ChE recognition is a spontaneous reaction leading to stable complexes. The conducted investigations have led to great findings that would strongly guide the pharmaceutical industries toward the rational development of potent anti-Alzheimer agents.

Keywords: Alzheimer’s disease, molecular docking, Cannabis sativa L., cholinesterase inhibitors, molecular dynamics, ADMET, MM-PBSA

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Authors: A. Hossein Madadi-Najafabadi, Masoud Nasiri

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The discrete element method is a powerful technique for numerical modeling the flow of granular materials such as direct reduced iron. It would enable us to study processes and equipment related to the production and handling of the material. However, the characteristics and properties of the granules have to be adjusted precisely to achieve reliable results in a DEM simulation. The main properties for DEM simulation are size distribution, density, Young's modulus, Poisson's ratio and the contact coefficients of restitution, rolling friction and sliding friction. In the present paper, the mentioned properties are determined for DEM simulation of DRI pellets. A reliable DEM simulation would contribute to optimizing the handling system of DRIs in an iron-making plant. Among the mentioned properties, Young's modulus is the most important parameter, which is usually hard to get for particulate solids. Here, an especial method is utilized to precisely determine this parameter for DRI.

Keywords: discrete element method, direct reduced iron, simulation parameters, granular material

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Authors: N. V. Kuznetsov, O. A. Kuznetsova, G. A. Leonov, M. V. Yuldashev, R. V. Yuldashev

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Nonlinear analysis of the phase locked loop (PLL)-based circuits is a challenging task. Thus, the simulation is widely used for their study. In this work, we consider a mathematical model of the optical Costas loop and demonstrate the limitations of simulation approach related to the existence of so-called hidden oscillations in the phase space of the model.

Keywords: optical Costas loop, mathematical model, simulation, hidden oscillation

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Authors: Norbert Szulc, Jakub Wilk, Franciszek Górski

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This paper presents an approach for simulating and testing robotic systems based on PX4, using a local Kubernetes cluster. The approach leverages modern cloud-native tools and runs on single-board computers. Additionally, this solution enables the creation of datasets for computer vision and the evaluation of control system algorithms in an end-to-end manner. This paper compares this approach to method commonly used Docker based approach. This approach was used to develop simulation environment for an unmanned surface vehicle (USV) for RoboBoat 2023 by running a containerized configuration of the PX4 Open-source Autopilot connected to ROS and the Gazebo simulation environment.

Keywords: cloud computing, Kubernetes, single board computers, simulation, ROS

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Authors: Rozhgar A. Khailany, Mehri Igci, Emine Bayraktar, Sakip Erturhan, Metin Karakok, Ahmet Arslan

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Kidney cancer is the most lethal urological cancer accounting for 3% of adult malignancies. VHL, a tumor-suppressor gene, is best known to be associated with renal cell carcinoma (RCC). The VHL functions as negative regulator of hypoxia inducible factors. Recent sequencing efforts have identified several novel frequent mutations of histone modifying and chromatin remodeling genes in ccRCC (clear cell RCC) including PBRM1 and SETD2. The PBRM1 gene encodes the BAF180 protein, which involved in transcriptional activation and repression of selected genes. SETD2 encodes a histone methyltransferase, which may play a role in suppressing tumor development. In this study, RNAs of 30 paired tumor and normal samples that were grouped according to the types of kidney cancer and clinical characteristics of patients, including gender and average age were examined by RT-PCR, SSCP and sequencing techniques. VHL, PBRM1 and SETD2 expressions were relatively down-regulated. However, statistically no significance was found (Wilcoxon signed rank test, p > 0.05). Interestingly, no mutation was observed on the contrary of previous studies. Understanding the molecular mechanisms involved in the pathogenesis of RCC has aided the development of molecular-targeted drugs for kidney cancer. Further analysis is required to identify the responsible genes rather than VHL, PBRM1 and SETD2 in kidney cancer.

Keywords: kidney cancer, molecular biomarker, expression analysis, mutation screening

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Authors: M. Ali Mandegari, S. Farzad, J. F. Görgens

Abstract:

Sugar is one of the main agricultural industries in South Africa and approximately livelihoods of one million South Africans are indirectly dependent on sugar industry which is economically struggling with some problems and should re-invent in order to ensure a long-term sustainability. Second generation bio-refinery is defined as a process to use waste fibrous for the production of bio-fuel, chemicals animal food, and electricity. Bio-ethanol is by far the most widely used bio-fuel for transportation worldwide and many challenges in front of bio-ethanol production were solved. Bio-refinery annexed to the existing sugar mill for production of bio-ethanol and electricity is proposed to sugar industry and is addressed in this study. Since flow-sheet development is the key element of the bio-ethanol process, in this work, a bio-refinery (bio-ethanol and electricity production) annexed to a typical South African sugar mill considering 65ton/h dry sugarcane bagasse and tops/trash as feedstock was simulated. Aspen PlusTM V8.6 was applied as simulator and realistic simulation development approach was followed to reflect the practical behavior of the plant. Latest results of other researches considering pretreatment, hydrolysis, fermentation, enzyme production, bio-ethanol production and other supplementary units such as evaporation, water treatment, boiler, and steam/electricity generation units were adopted to establish a comprehensive bio-refinery simulation. Steam explosion with SO2 was selected for pretreatment due to minimum inhibitor production and simultaneous saccharification and fermentation (SSF) configuration was adopted for enzymatic hydrolysis and fermentation of cellulose and hydrolyze. Bio-ethanol purification was simulated by two distillation columns with side stream and fuel grade bio-ethanol (99.5%) was achieved using molecular sieve in order to minimize the capital and operating costs. Also boiler and steam/power generation were completed using industrial design data. Results indicates 256.6 kg bio ethanol per ton of feedstock and 31 MW surplus power were attained from bio-refinery while the process consumes 3.5, 3.38, and 0.164 (GJ/ton per ton of feedstock) hot utility, cold utility and electricity respectively. Developed simulation is a threshold of variety analyses and developments for further studies.

Keywords: bio-refinery, bagasse, tops, trash, bio-ethanol, electricity

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