Search results for: computational calculations

Authors: Kamal Haider

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Numerical simulations over landing gear of simplified and partially-dressed configurations with closed cavity have been performed to compute aerodynamically and aeroacoustics parameters using commercial engineering software. The objective of numerical computations is two folds. Firstly, to validate experimental data of newly built nose landing gear and secondly perform high-fidelity calculations using CFD/FW-H hybrid approach, as future engineering challenges need more advanced aircraft configurations such as performance noise and efficiency. Both geometries are used for multi-block structured, and unstructured/hybrid meshed to develop some understanding of physics in terms of aerodynamics and aeroacoustics. Detached Eddy Simulation (DES) approach is employed to compute surface pressure. Also far-field noise calculations have been generated by Ffowcs-William and Hawking solver. Both results of aerodynamics and aeroacoustics are compared with experimental data.

Keywords: landing gear, computational aeroacoustics, computational aerodynamics, detached eddy simulation

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Authors: Taher S. Ababneh, Taghreed M. A. Jazzazi, Tareq M. A. Alshboul

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The inhibiting action against aluminum corrosion by three derivatives of 1,8-bis (benzylideneamino) naphthalene (BN) Schiff base has been investigated by means of DFT quantum chemical calculations at the B3LYP/6-31G(d) level of theory. The derivatives (CBN, NBN and MBN) were prepared from the condensation reaction of 1,8-diaminonaphthalene with substituted benzaldehyde (4-CN, 3-NO₂ and 3,4-(OMe)₂, respectively). Calculations were conducted to study the adsorption of each Schiff base on aluminum surface to evaluate its potential as a corrosion inhibitor. The computational structural features and electronic properties of each derivative such as relative energies and energies of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) have been reported. Thermodynamic functions and quantum chemical parameters such as the hardness of the inhibitor, the softness and the electrophilicity index were calculated to determine the derivative of the highest inhibition efficiency.

Keywords: corrosion, aluminum, DFT calculation, 1, 8-diaminonaphthalene, benzaldehyde

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Authors: Dairo Jose Hernandez Paez

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The quantum theory of atoms in molecules (QTAIM) allows us to obtain topological information on electronic density in quantum mechanical systems. The QTAIM starts by considering the electron density as a continuous mathematical object. On the other hand, the discretization of electron density is also a mathematical object, which, from discrete mathematics, would allow a new approach to its topological study. From this point of view, it is necessary to develop a series of steps that provide the theoretical support that guarantees its application. Some of the steps that we consider most important are mentioned below: (1) obtain good representations of the electron density through computational calculations, (2) design a methodology for the discretization of electron density, and construct the simplicial complex. (3) Make an analysis of the discrete vector field associating the simplicial complex. (4) Finally, in this research, we propose to use the discrete Morse theory as a mathematical tool to carry out studies of electron density topology.

Keywords: discrete mathematics, Discrete Morse theory, electronic density, computational calculations

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Authors: Imad Eddine Charif, Sidi Mohamed Mekelleche, Didier Villemin

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The solvent effects on the keto-enol tautomeric equilibriums of acetylacetone and dimedone are theoretically investigated at the correlated Becke-3-parameter-Lee-Yang-Parr (B3LYP) and second-order Møller-Plesset (MP2) computational levels. The present study shows that the most stable keto tautomer of acetylacetone corresponds to the trans-diketo, E,Z form; while the most stable enol tautomer corresponds to the closed cis-enol,Z,Z form. The keto tautomer of dimedone prefers the trans diketo, E, E form; while the most stable enol tautomer corresponds to trans-enol form. The calculated free Gibbs enthalpies indicate that, in polar solvents, the keto-enol equilibrium of acetylacetone is shifted toward the keto tautomer; whereas the keto-enol equilibrium of dimedone is shifted towards the enol tautomer. The experimental trends of the change of equilibrium constants with respect to the change of solvent polarity are well reproduced by both B3LYP and MP2 calculations.

Keywords: acetylacetone, dimedone, solvent effects, keto-enol equilibrium, theoretical calculations

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Authors: Asmaa M. Fahim

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In this investigation, the (E)-2-cyano-3-(dimethylamino)-N-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)acrylam-ide (4) which used TAM as a template which interacts with Methacrylic Acid (MAA) monomer, in the presence of CH₃CN as progen. The TAM-MMA complex interactions are dependent on stable hydrogen bonding interaction between the carboxylic acid group of TAM(Template) and the hydroxyl group of MMA(methyl methacrylate) with minimal interference of porogen CH₃CN. The physical computational studies were used to optimize their structures and frequency calculations. The binding energies between TAM with different monomers showed the most stable molar ratio of 1:4, which was confirmed through experimental analysis. The optimized polymers were investigated in industrial applications.

Keywords: molecular imprinted polymer, computational studies, SEM, spectral analysis, industrial applications

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Authors: Pranav Gunhal., Krish Jhurani

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This study tackles the significant computational challenge of predicting excited state dynamics in organic photovoltaic (OPV) materials—a pivotal factor in the performance of solar energy solutions. Time-dependent density functional theory (TDDFT), though effective, is computationally prohibitive for larger and more complex molecules. As a solution, the research explores the application of transformer neural networks, a type of artificial intelligence (AI) model known for its superior performance in natural language processing, to predict excited state dynamics in OPV materials. The methodology involves a two-fold process. First, the transformer model is trained on an extensive dataset comprising over 10,000 TDDFT calculations of excited state dynamics from a diverse set of OPV materials. Each training example includes a molecular structure and the corresponding TDDFT-calculated excited state lifetimes and key electronic transitions. Second, the trained model is tested on a separate set of molecules, and its predictions are rigorously compared to independent TDDFT calculations. The results indicate a remarkable degree of predictive accuracy. Specifically, for a test set of 1,000 OPV materials, the transformer model predicted excited state lifetimes with a mean absolute error of 0.15 picoseconds, a negligible deviation from TDDFT-calculated values. The model also correctly identified key electronic transitions contributing to the excited state dynamics in 92% of the test cases, signifying a substantial concordance with the results obtained via conventional quantum chemistry calculations. The practical integration of the transformer model with existing quantum chemistry software was also realized, demonstrating its potential as a powerful tool in the arsenal of materials scientists and chemists. The implementation of this AI model is estimated to reduce the computational cost of predicting excited state dynamics by two orders of magnitude compared to conventional TDDFT calculations. The successful utilization of transformer neural networks to accurately predict excited state dynamics provides an efficient computational pathway for the accelerated discovery and design of new OPV materials, potentially catalyzing advancements in the realm of sustainable energy solutions.

Keywords: transformer neural networks, organic photovoltaic materials, excited state dynamics, time-dependent density functional theory, predictive modeling

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Authors: Paul Stonaha, Mariia Romashchenko, Xaio Xu

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Magnetic shape memory alloys (MSMAs) are promising technological materials for a range of fields, from biomaterials to energy harvesting. We have performed inelastic neutron scattering on two powder samples of cobalt-based high-entropy MSMAs across a range of temperatures in an effort to compare calculations of thermodynamic properties (entropy, specific heat, etc.) to the measured ones. The measurements were correct for multiphonon scattering and multiple scattering contributions. We present herein the neutron-weighted vibrational density of states. Future work will utilize DFT calculations of the disordered lattice to correct for the neutron weighting and retrieve the true thermodynamical properties.

Keywords: neutron scattering, vibrational dynamics, computational physics, material science

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Authors: Abdusalam Sharf

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In the oil and gas industries, one of the most important issues in drilling wells is understanding the behavior of a flow through an annulus gap in a vertical position, whose outer wall is stationary whilst the inner wall rotates. The main emphasis is placed on a comparison of experimental and computational investigations into the effects of the rotation speed of the inner pipe on the axial velocity profiles. The computational investigations were carried out by employing CFD software, and Gambit and Fluent. Three turbulence models were used: standard, RNG with enhanced wall treatment, and SST model. The profiles of the axial velocity had investigated at different rotation speeds of the inner pipe with three different volumetric flow rates. The comparison results showed that the calculations satisfactorily predict the qualitative features of the axial and swirl velocity profiles and the RNG model performs the best results.

Keywords: computational fluid dynamics (CFD), SST k−ω shear-stress transport (k−ω mode variant), RNG k–ε renormalisation group (k−ε mode variant), y+ dimensionless distance from wall

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Authors: Harsh Sadawarti, Kamal Malik

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Humans are the unique and the most powerful creature on this planet just because of the high level of intelligence gifted by nature. Computational Intelligence is highly influenced by the term natural intelligence, neurosciences and mathematics. To deal with the in-depth study of computational intelligence and to utilize it in real-life applications, it is quite important to understand its simulation with the human brain. In this paper, the three important parts, Frontal Lobe, Occipital Lobe and Parietal Lobe of the human brain, are compared with the ANN(Artificial Neural Network), CNN(Convolutional Neural network), and RNN(Recurrent Neural Network), respectively. Intelligent computational systems are created by combining deductive reasoning, logical concepts and high-level algorithms with the simulation and study of the human brain. Human brain is a combination of Physiology, Psychology, emotions, calculations and many other parameters which are of utmost importance that determines the overall intelligence. To create intelligent algorithms, smart machines and to simulate the human brain in an effective manner, it is quite important to have an insight into the human brain and the basic concepts of biological neurosciences.

Keywords: computational intelligence, neurosciences, convolutional neural network, recurrent neural network, artificial neural network, frontal lobe, occipital lobe, parietal lobe

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Authors: M. Ibrir, S. Berri, S. Lakel, D. Maouche And Y. Medkour

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We have performed first-principle calculations of the structural, electronic and magnetic properties of KFeF3, KCoF3, KMnF3, KVF3, using full-potential linearized augmented plane-wave (FP-LAPW) scheme within GGA. Features such as the lattice constant, bulk modulus and its pressure derivative are reported. Also, we have presented our results of the band structure and the density of states. The magnetic moments of KFeF3, KCoF3, KMnF3, KVF3 compounds are in most came from the exchange-splitting of X-3d orbital.

Keywords: Ab initio calculations, electronic structure, magnetic materials

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Authors: Roshanak Khodabakhsh Jolfaei, Javad Akbari Torkestani

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As a cooperative environment for problem-solving, it is necessary that grids develop efficient job scheduling patterns with regard to their goals, domains and structure. Since the Grid environments facilitate distributed calculations, job scheduling appears in the form of a critical problem for the management of Grid sources that influences severely on the efficiency for the whole Grid environment. Due to the existence of some specifications such as sources dynamicity and conditions of the network in Grid, some algorithm should be presented to be adjustable and scalable with increasing the network growth. For this purpose, in this paper a job scheduling algorithm has been presented on the basis of learning automata in computational Grid which the performance of its results were compared with FPSO algorithm (Fuzzy Particle Swarm Optimization algorithm) and GJS algorithm (Grid Job Scheduling algorithm). The obtained numerical results indicated the superiority of suggested algorithm in comparison with FPSO and GJS. In addition, the obtained results classified FPSO and GJS in the second and third position respectively after the mentioned algorithm.

Keywords: computational grid, job scheduling, learning automata, dynamic scheduling

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Authors: Brahim Bahloul, Khatir Babesse, Azzedine Dkhira, Yacine Bahloul, Dalila Hammoutene

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In this paper, we investigate with ab initio calculations some structural and optoelectronic properties of Li₂S compound. The structural and electronic properties of the Li₂S antifluorite structure have been studied by first-principles calculations within the density functional theory (DFT), whereas the optical properties have been obtained using empirical relationships such as the modified Moss relation. Our calculated lattice parameters are in good agreement with the experimental data and other theoretical calculations. The electronic band structures and density of states were obtained. The anti-fluorite Li₂S present an indirect band gap of 3.388 eV at equilibrium. The top of the valence bands reflects the p electronic character for both structures. The calculated energy gaps and optical constants are in good agreement with experimental measurements.

Keywords: Ab initio calculations, antifluorite, electronic properties, optical properties

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Authors: Rakesh Bhatia

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Students often face significant challenges in understanding and applying trigonometric identities, primarily due to the overwhelming need to memorize numerous formulas. This often leads to confusion, frustration, and difficulty in effectively using these formulas across diverse types of problems. Traditional methods of learning trigonometry demand considerable time and effort, which can further hinder comprehension and application. Vedic Mathematics offers an innovative and simplified approach to overcoming these challenges. This paper explores how Baudhayan Numbers, can be used to derive trigonometric identities and simplify calculations related to height and distance. Unlike conventional approaches, this method minimizes the need for extensive paper-based calculations, promoting a conceptual understanding. Using Vedic Mathematics Sutras such as Anurupyena and Vilokanam, this approach enables the derivation of over 100 trigonometric identities through a single, unified approach. The simplicity and efficiency of this technique not only make learning trigonometry more accessible but also foster computational thinking. Beyond academics, the practical applications of this method extend to engineering fields such as bridge design and construction, where precise trigonometric calculations are critical. This exploration underscores the potential of Vedic Mathematics to revolutionize the learning and application of trigonometry by offering a streamlined, intuitive, and versatile framework.

Keywords: baudhayan numbers, anurupyena, vilokanam, sutras

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Authors: Zair Mohammed El Amine, Chemouri Hafida, Derbal Habak Hassina

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Organic photovoltaic cells are electronic devices that convert sunlight into electricity. To this end, the number of studies on organic photovoltaic cells (OVCs) is growing, and this trend is expected to continue. Computational studies are still needed to verify and prove the capability of CVOs, specifically the nanometer molecule PCBM, based on successful experimental results. In this paper, we present a theoretical and computational investigation of PCBM and PC71BM derivatives using the DFT method. On this basis, we employ independent and time-dependent density theories. HOMO, LUMO and GAPH-L energies, ionization potentials and electronic affinity are determined and found to be in agreement with experiments. Using DFT theory based on B3LYP and M062X methods with bases 6-31G (d,p) and 6-311G (d), calculations show that the most efficient acceptors are presented in the group of PC71BM derivatives and are in substantial agreement with experiments. The geometries of the structures are optimized by Gaussian 09.

Keywords: PCBM, P3HT, organic cell solar, DFT, TD-DFT

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Authors: Ali Mohammadi

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One of the concerns that employers and contractors have in creating long tunnels is that when the excavation is completed, the tunnel will be exited in the correct position according to designed, the deviation of the tunnel from its path can have many costs for the employer and the contractor, lack of correct calculations by the surveying engineer or the employer and contractors lack of importance to the surveying team in guiding the tunnel can cause the tunnel to deviate from its path and this deviation becomes a disaster. But employers are able to make the right decisions so that the tunnel is guided with the highest precision if they consider some points. We are investigating two tunnels with lengths of 12 and 18 kilometers that were dug by Tunnel boring machine machines to transfer water, how the contractor’s decision to control the 12 kilometer tunnel caused the most accuracy of one centimeter to the next part of the tunnel will be connected. We will also investigate the reasons for the deviation of axis in the 18 km tunnel about 20 meters. Also we review the calculations of surveyor engineers in both tunnels and what challenges there will be in the calculations and teach how to solve these challenges. Surveying calculations are the most important part in controlling long tunnels.

Keywords: UTM, localization, scale factor, traverse

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Authors: Konrad Pietrykowski, Michał Gęca, Michał Bialy

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The paper presents the results of the crankshaft strength simulation. The crankshaft was taken from the opposed piston engine. Calculations were made using finite element method (FEM) in Abaqus software. This program allows to perform strength tests of individual machine parts as well as their assemblies. The crankshaft that was used in the calculations will be used in the two-stroke aviation research aircraft engine. The assumptions for the calculations were obtained from the AVL Boost software, from one-dimensional engine cycle model and from the multibody model using the method developed in the MSC Adams software. The research engine will be equipped with 3 combustion chambers and two crankshafts. In order to shorten the calculation time, only one crankcase analysis was performed. The cut of the shaft has been selected with the greatest forces resulting from the engine operation. Calculations were made for two cases. For maximum piston force when maximum bending load occurs and for the maximum torque. Cast iron material was adopted. For this material, Poisson's number, density, and Young's modulus were determined. The computational grid contained of 1,977,473 Tet elements. This type of elements was chosen because of the complex design of the crankshaft. Results are presented in the form of stress distributions maps and displacements on the surface and inside the geometry of the shaft. The results show the places of tension stresses, however, no stresses are exceeded at any place. The shaft can thus be applied to the engine in its present form. Acknowledgement: This work has been realized in the cooperation with The Construction Office of WSK 'PZL-KALISZ’ S.A. and is part of Grant Agreement No. POIR.01.02.00-00-0002/15 financed by the Polish National Centre for Research and Development.

Keywords: aircraft diesel engine, crankshaft, finite element method, two-stroke engine

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Authors: L. Yettou

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In this study, the calculations of proton emission spectra produced by ⁶³Cu(n,xp) and ⁶⁵Cu(n,xp) reactions are used in the framework of preequilibrium models using the EMPIRE code and TALYS code. Exciton Model predidtions combined with the Kalbach angular distribution systematics and the Hybrid Monte Carlo Simulation (HMS) were used. The effects of levels densities and those of a-parameter have been investigated for our calculations. The comparison with experimental data shows clear improvement over the Exciton Model and HMS calculations.

Keywords: Preequilibrium models , level density, level density a-parameter., Empire code, Talys code.

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Authors: Mohammad Sadeghian, Mohsen Sadeghian

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In this paper, planning catamaran and mono-hull vessels resistance and trim in calm waters were considered. Hydrodynamic analysis of fast mono-hull planning vessel was also investigated. For hull form geometry optimization, numerical methods of different parameters were used for this type of vessels. Hull material was selected as carbon fiber composite. Exact architectural aspects were specified and stability calculations were performed, as well. Hydrodynamic calculations to extract the resistance force using semi-analytical methods and numerical modeling were carried out. Free surface numerical analysis of vessel in designed draft using finite volume method and double phase were evaluated and verified by experimental tests.

Keywords: fast vessel, hydrostatic and hydrodynamic optimization, free surface flow, computational fluid dynamics

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Authors: Mohammad Ali Badri, Pouya Molana, Amin Rezvanpour

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In this paper, planning catamaran and mono-hull vessels resistance and trim in calm waters were considered. Hydrodynamic analysis of fast mono-hull planning vessel was also investigated. In order to hull form geometry optimization, numerical methods of different parameters were used for this type of vessels. Hull material was selected in carbon fiber composite. Exact architectural aspects were specified and stability calculations were performed as well. Hydrodynamic calculations to extract the resistance force using semi-analytical methods and numerical modeling were carried out. Free surface numerical analysis of vessel in designed draft using finite volume method and double phase were evaluated and verified by experimental tests.

Keywords: fast vessel, hydrostatic and hydrodynamic optimization, free surface flow, computational fluid dynamics

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Authors: Olaide O. Wahab, Lukman O. Olasunkanmi, Krishna K. Govender, Penny P. Govender

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The economic and environmental challenges associated with azo disperse dyes applications are due to poor aqueous solubility and low degradation tendency which stems from low chemical reactivity. Poor aqueous solubility property of this group of dyes necessitates the use of dispersing agents which increase operational costs and also release toxic chemical components into the environment, while their low degradation tendency is due to the high stability of the azo functional group (-N=N-) in their chemical structures. To address these problems, this study investigated theoretically the effects of some polar substituents on the aqueous solubility and reactivity properties of disperse yellow (DY) 119 dye with a view to theoretically develop new azo disperse dyes with improved solubility in water and higher degradation tendency in the environment using DMol³ computational code. All calculations were carried out using the Becke and Perdew version of Volsko-Wilk-Nusair (VWN-BP) level of density functional theory in conjunction with double numerical basis set containing polarization function (DNP). The aqueous solubility determination was achieved with conductor-like screening model for realistic solvation (COSMO-RS) in conjunction with known empirical solubility model, while the reactivity was predicted using frontier molecular orbital calculations. Most of the new derivatives studied showed evidence of higher aqueous solubility and degradation tendency compared to the parent dye. We conclude that these derivatives are promising alternative dyes for more economic and environmental benign dyeing practice and therefore recommend them for synthesis.

Keywords: aqueous solubility, azo disperse dye, degradation, disperse yellow 119, DMol³, reactivity

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Authors: Arzu K. Kamberli

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This article examines the relationship between economics and physics, starting with Adam Smith, with a new econophysics approach in Economics-Physics with the Gauss Law model proposal using for the Electric Field calculation, which will allow us to anticipate the Global Financial Crisis. For this purpose, the similarities between the Gauss Law using the electric field calculations and the global financial crisis have been explained on the formula, and a model has been suggested to predict the risks of the financial systems from the electricity field calculations. Thus, this study is expected to help for preventing the Global Financial Crisis with the contribution of the science of economics and physics from the aspect of econophysics.

Keywords: econophysics, electric field, financial system, Gauss law, global financial crisis

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Authors: Piotr Ciuman, Barbara Lipska

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The aim of presented research was to improve numerical predictions of air parameters distribution in the actual natatorium by the selection of calculation formula of mass flux of moisture emitted from the pool. Selected correlation should ensure the best compliance of numerical results with the measurements' results of these parameters in the facility. The numerical model of the natatorium was developed, for which boundary conditions were prepared on the basis of measurements' results carried out in the actual facility. Numerical calculations were carried out with the use of ANSYS CFX software, with six formulas being implemented, which in various ways made the moisture emission dependent on water surface temperature and air parameters in the natatorium. The results of calculations with the use of these formulas were compared for air parameters' distributions: Specific humidity, velocity and temperature in the facility. For the selection of the best formula, numerical results of these parameters in occupied zone were validated by comparison with the measurements' results carried out at selected points of this zone.

Keywords: experimental validation, indoor swimming pool, moisture emission, natatorium, numerical calculations CFD, thermal and humidity conditions, ventilation

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Authors: G. Levacic, A. Zupan

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Application of new technological solutions and installation of new elements into the network requires special attention when investigating its interaction with the existing power system. Special attention needs to be devoted to the occurrence of harmonic resonance. Sources of increasing harmonic penetration could be wind power plants, Flexible Alternating Current Transmission System (FACTS) devices, underground and submarine cable installations etc. Calculation in frequency domain with various software, for example, the software for power systems transients EMTP-RV presents one of the most common ways to obtain the harmonic impedance of the system. Along calculations in frequency domain, such software allows performing of different type of calculations as well as steady-state domain. This paper describes a power system modeling with software EMTP-RV based on data from SCADA/EMS system. The power flow results on 220 kV and 400 kV voltage levels retrieved from EMTP-RV are verified by comparing with power flow results from power transmissions system planning software PSS/E. The determination of the harmonic impedance for the case of remote power plant connection with cable up to 2500 Hz is presented as an example of calculations in frequency domain.

Keywords: power system modeling, frequency domain, steady state, EMTP-RV, PSS/E

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Authors: Ahmed El-Banbi

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Several PVT models exist to represent how PVT properties are handled in sub-surface and surface engineering calculations for oil and gas production. The most commonly used models include black oil, modified black oil (MBO), and compositional models. These models are used in calculations that allow engineers to optimize and forecast well and reservoir performance (e.g., reservoir simulation calculations, material balance, nodal analysis, surface facilities, etc.). The choice of which model is dependent on fluid type and the production process (e.g., depletion, water injection, gas injection, etc.). Based on close to 2,000 reservoir fluid samples collected from different basins and locations, this paper presents some conclusions on the occurrence of reservoir fluids. It also reviews the common methods used to classify reservoir fluid types. Based on new criteria related to the production behavior of different fluids and economic considerations, an updated classification of reservoir fluid types is presented in the paper. Recommendations on the use of different PVT models to simulate the behavior of different reservoir fluid types are discussed. Each PVT model requirement is highlighted. Available methods for the calculation of PVT properties from each model are also discussed. Practical recommendations and tips on how to control the calculations to achieve the most accurate results are given.

Keywords: PVT models, fluid types, PVT properties, fluids classification

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Authors: Abdelouaheb Rouabhi

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In order to study the plastic resource of structures, the elastic-plastic single degree of freedom model described by Prandtl diagram is widely used. The generalization of this model to tow degree of freedom beyond the scope of a simple rigid-plastic system allows investigating the plastic resource of structures under complex disproportionate by individual components of deformation (earthquake). This macro-model greatly increases the accuracy of the calculations carried out. At the same time, the implementation of the proposed macro-model calculations easier than the detailed dynamic elastic-plastic calculations existing software systems such as ANSYS.

Keywords: elastic-plastic, single degree of freedom model, rigid-plastic system, plastic resource, complex plastic deformation, macro-model

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Authors: Zaaraoui Abdelkader, Kerfah Rabeh, Noura Belkheir, Matene Elhacene

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The trapezoidal bluff body is a typical configuration of vortex shedding bodies. The aim of this work is to study flow behaviour over a trapezoidal cylinder at low Reynolds number. The geometry was constructed from a prototype device for measuring the volumetric flow-rate by counting vortices. Simulations were run for this geometry under steady and unsteady flow conditions using finite volume discretization. Laminar flow was investigated in this model with rigid walls and homogeneous incompressible Newtonian fluid. Calculations were performed for Reynolds number range 5 ≤ Re ≤ 180 and several flow parameters were documented. The present computations are in good agreement with the experimental observations and the numerical calculations by several investigators.

Keywords: bluff body, confined flow, numerical calculations, steady and unsteady flow, vortex shedding flow meter

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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: Shahriar Ghammamy, Masomeh Shahsavary

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In this paper, the optimized geometries and frequencies of the stationary point and the minimum energy paths of C13H12F7ClN2O are calculated by using the DFT (B3LYP) methods with LANL2DZ basis sets. B3LYP/ LANL2DZ calculation results indicated that some selected bond length and bond angles values for the C13H12F7ClN2O.

Keywords: C13H12F7ClN2O, vatural bond orbital, fluorous compounds, functional calculations

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Authors: Titus A. Beu

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Many modern gene-delivery protocols rely on condensed complexes of DNA with polycations to introduce the genetic payload into cells by endocytosis. In particular, polyethyleneimine (PEI) stands out by a high buffering capacity (enabling the efficient condensation of DNA) and relatively simple fabrication. Realistic computational studies can offer essential insights into the formation process of DNA-PEI polyplexes, providing hints on efficient designs and engineering routes. We present comprehensive computational investigations of solvated PEI and DNA-PEI polyplexes involving calculations at three levels: ab initio, all-atom (AA), and coarse-grained (CG) molecular mechanics. In the first stage, we developed a rigorous AA CHARMM (Chemistry at Harvard Macromolecular Mechanics) force field (FF) for PEI on the basis of accurate ab initio calculations on protonated model pentamers. We validated this atomistic FF by matching the results of extensive molecular dynamics (MD) simulations of structural and dynamical properties of PEI with experimental data. In a second stage, we developed a CG MARTINI FF for PEI by Boltzmann inversion techniques from bead-based probability distributions obtained from AA simulations and ensuring an optimal match between the AA and CG structural and dynamical properties. In a third stage, we combined the developed CG FF for PEI with the standard MARTINI FF for DNA and performed comprehensive CG simulations of DNA-PEI complex formation and condensation. Various technical aspects which are crucial for the realistic modeling of DNA-PEI polyplexes, such as options of treating electrostatics and the relevance of polarizable water models, are discussed in detail. Massive CG simulations (with up to 500 000 beads) shed light on the mechanism and provide time scales for DNA polyplex formation independence of PEI chain size and protonation pattern. The DNA-PEI condensation mechanism is shown to primarily rely on the formation of DNA bundles, rather than by changes of the DNA-strand curvature. The gained insights are expected to be of significant help for designing effective gene-delivery applications.

Keywords: DNA condensation, gene-delivery, polyethylene-imine, molecular dynamics.

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Authors: Ali S. Gargoum

Abstract:

Graphical modeling plays an important role in providing efficient probability calculations in high dimensional problems (computational efficiency). In this paper, we address one of such problems where we discuss fragmenting puff models and some distributional assumptions concerning models for the instantaneous, emission readings and for the fragmenting process. A graphical representation in terms of a junction tree of the conditional probability breakdown of puffs and puff fragments is proposed.

Keywords: graphical models, influence diagrams, junction trees, Bayesian nets

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