Search results for: computational calculations

Authors: Tivani Phosa Mashamba-Thompson, Mahmoud E. S. Soliman

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To date, the cause of neurodegeneration is not well understood and diseases that stem from neurodegeneration currently have no known cures. Cathepsin B (CB) enzyme is known to be involved in the production of peptide neurotransmitters and toxic peptides in neurodegenerative diseases (NDs). CA-074Me is a membrane-permeable irreversible selective cathepsin B (CB) inhibitor as confirmed by in vivo studies. Due to the lack of the crystal structure, the binding mode of CA-074Me with the human CB at molecular level has not been previously reported. The main aim of this study is to gain an insight into the binding mode of CB CA-074Me to human CB using various computational tools. Herein, molecular dynamics simulations, binding free energy calculations and per-residue energy decomposition analysis were employed to accomplish the aim of the study. Another objective was to identify novel CB inhibitors based on the structure of CA-074Me using fragment based drug design using scaffold hoping drug design approach. Results showed that two of the designed ligands (hit 1 and hit 2) were found to have better binding affinities than the prototype inhibitor, CA-074Me, by ~2-3 kcal/mol. Per-residue energy decomposition showed that amino acid residues Cys29, Gly196, His197 and Val174 contributed the most towards the binding. The Van der Waals binding forces were found to be the major component of the binding interactions. The findings of this study should assist medicinal chemist towards the design of potential irreversible CB inhibitors.

Keywords: cathepsin B, scaffold hopping, docking, molecular dynamics, binding-free energy, neurodegerative diseases

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Authors: R. Khenata, T. Djied, R. Ahmed, H. Baltache, S. Bin-Omran, A. Bouhemadou

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We predict structural, phase transition as well as opto-electronic properties of the filled-tetrahedral (Nowotny-Juza) NaZnAs compound in this study. Calculations are carried out by employing the full potential (FP) linearized augmented plane wave (LAPW) plus local orbitals (lo) scheme developed within the structure of density functional theory (DFT). Exchange-correlation energy/potential (EXC/VXC) functional is treated using Perdew-Burke and Ernzerhof (PBE) parameterization for generalized gradient approximation (GGA). In addition to Trans-Blaha (TB) modified Becke-Johnson (mBJ) potential is incorporated to get better precision for optoelectronic properties. Geometry optimization is carried out to obtain the reliable results of the total energy as well as other structural parameters for each phase of NaZnAs compound. Order of the structural transitions as a function of pressure is found as: Cu2Sb type → β → α phase in our study. Our calculated electronic energy band structures for all structural phases at the level of PBE-GGA as well as mBJ potential point out; NaZnAs compound is a direct (Γ–Γ) band gap semiconductor material. However, as compared to PBE-GGA, mBJ potential approximation reproduces higher values of fundamental band gap. Regarding the optical properties, calculations of real and imaginary parts of the dielectric function, refractive index, reflectivity coefficient, absorption coefficient and energy loss-function spectra are performed over a photon energy ranging from 0.0 to 30.0 eV by polarizing incident radiation in parallel to both [100] and [001] crystalline directions.

Keywords: NaZnAs, FP-LAPW+lo, structural properties, phase transition, electronic band-structure, optical properties

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Authors: Mouhamadou Diop, Mohamed I. Hassan

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Molten metallic flow in metallurgical plant is highly turbulent and presents a complex coupling with heat transfer, phase transfer, chemical reaction, momentum transport, etc. Molten silicon flow has significant effect in directional solidification of multicrystalline silicon by affecting the temperature field and the emerging crystallization interface as well as the transport of species and impurities during casting process. Owing to the complexity and limits of reliable measuring techniques, computational models of fluid flow are useful tools to study and quantify these problems. The overall objective of this study is to investigate the potential of a traveling magnetic field for an efficient operating control of the molten metal flow. A multidimensional numerical model will be developed for the calculations of Lorentz force, molten metal flow, and the related phenomenon. The numerical model is implemented in a laboratory-scale silicon crystallization furnace. This study presents the potential of traveling magnetic field approach for an efficient operating control of the molten flow. A numerical model will be used to study the effects of magnetic force applied on the molten flow, and their interdependencies. In this paper, coupled and decoupled, steady and unsteady models of molten flow and crystallization interface will be compared. This study will allow us to retrieve the optimal traveling magnetic field parameter range for crystallization furnaces and the optimal numerical simulations strategy for industrial application.

Keywords: multidimensional, numerical simulation, solidification, multicrystalline, traveling magnetic field

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Authors: Keaghan Brown

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The prioritization of drug resistance mutations impacting protein folding or protein-drug and protein-DNA interactions within macromolecular systems is critical to the success of treatment regimens. With a continual increase in computational tools to assess these impacts, the need for scalability and reproducibility became an essential component of computational analysis and experimental research. Here it introduce a bioinformatics pipeline that combines several structural analysis tools in a simplified workflow, by optimizing the present computational hardware and software to automatically ease the flow of data transformations. Utilizing preestablished software tools, it was possible to develop a pipeline with a set of pre-defined functions that will automate mutation introduction into the HIV-1 Integrase protein structure, calculate the gain and loss of polar interactions and calculate the change in energy of protein fold. Additionally, an automated molecular dynamics analysis was implemented which reduces the constant need for user input and output management. The resulting pipeline, Automated Mutation Introduction and Analysis (AMIA) is an open source set of scripts designed to introduce and analyse the effects of mutations on the static protein structure as well as the results of the multi-conformational states from molecular dynamic simulations. The workflow allows the user to visualize all outputs in a user friendly manner thereby successfully enabling the prioritization of variant systems for experimental validation.

Keywords: automated workflow, variant prioritization, drug resistance, HIV Integrase

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Authors: Giorgio Visentin, Alexei A. Buchachenko

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Recent proposals to use Yb dimer as an optical clock and as a sensor for non-Newtonian gravity imply the knowledge of its interaction potential. Here, the ground-state Born-Oppenheimer Yb₂ potential energy curve is represented by a semi-analytical function, consisting of short- and long-range contributions. For the former, the systematic ab initio all-electron exact 2-component scalar-relativistic CCSD(T) calculations are carried out. Special care is taken to saturate diffuse basis set component with the atom- and bond-centered primitives and reach the complete basis set limit through n = D, T, Q sequence of the correlation-consistent polarized n-zeta basis sets. Similar approaches are used to the long-range dipole and quadrupole dispersion terms by implementing the CCSD(3) polarization propagator method for dynamic polarizabilities. Dispersion coefficients are then computed through Casimir-Polder integration. The semiclassical constraint on the number of the bound vibrational levels known for the ¹⁷⁴Yb isotope is used to scale the potential function. The scaling, based on the most accurate ab initio results, bounds the interaction energy of two Yb atoms within the narrow 734 ± 4 cm⁻¹ range, in reasonable agreement with the previous ab initio-based estimations. The resulting potentials can be used as the reference for more sophisticated models that go beyond the Born-Oppenheimer approximation and provide the means of their uncertainty estimations. The work is supported by Russian Science Foundation grant # 17-13-01466.

Keywords: ab initio coupled cluster methods, interaction potential, semi-analytical function, ytterbium dimer

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Authors: Diane Vassallo., Leonard Busuttil

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Recent educational developments have seen increasing attention attributed to Computational Thinking (CT) and its integration into primary and secondary school curricula. CT is more than simply being able to use technology but encompasses fundamental Computer Science concepts which are deemed to be very important in developing the correct mindset for our future digital citizens. The case study presented in this article explores the journey of a Maltese secondary school teacher in his efforts to plan, develop and integrate CT within the context of a local classroom. The teacher participant was recruited from the Malta EU Code week summer school, a pilot initiative that stemmed from the EU Code week Team’s Train the Trainer program. The qualitative methodology involved interviews with the participant teacher as well as an analysis of the artefacts created by the students during the lessons. The results shed light on the numerous challenges and obstacles that the teacher encountered in his integration of CT, as well as portray some brilliant examples of good practices which can substantially inform further research and practice around the integration of CT in classroom practice.

Keywords: computational thinking, digital citizens, digital literacy, technology integration

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Authors: Sedat Yayla, Mehmet Oruc, Shakhwan Yaseen

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Cavitation phenomena might rigorously impair machine parts such as pumps, propellers and impellers or devices as the pressure in the fluid declines under the liquid's saturation pressure. To evaluate the influence of cavitation, in this research two-dimensional computational fluid dynamics (CFD) venturi models with variety of inlet pressure values, throat lengths and vapor fluid contents were applied. In this research three different vapor contents (0%, 5% 10%), four inlet pressures (2, 4, 6, 8 and 10 atm) and two venturi models were employed at different throat lengths ( 5, 10, 15 and 20 mm) for discovering the impact of each parameter on the cavitation number. It is uncovered that there is a positive correlation between pressure inlet and vapor fluid content and cavitation number. Furthermore, it is unveiled that velocity remains almost constant at the inlet pressures of 6, 8,10atm, nevertheless increasing the length of throat results in the substantial escalation in the velocity of the throat at inlet pressures of 2 and 4 atm. Furthermore, velocity and cavitation number were negatively correlated. The results of the cavitation number varied between 0.092 and 0.495 depending upon the velocity values of the throat.

Keywords: cavitation number, computational fluid dynamics, mixture of fluid, two-phase flow, velocity of throat

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Authors: Muzna Tariq, Ihtzaz Qamar

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In most engineering cases, the working temperatures inside a combustion chamber are high enough that they lie beyond the operational range of thermocouples. Furthermore, design and manufacturing limitations restrict the use of internal thermocouples in many applications. Heat transfer inside a combustion chamber is caused due to interaction of the post-combustion hot fluid with the chamber wall. Heat transfer that involves an interaction between the fluid and solid is categorized as Conjugate Heat Transfer (CHT). Therefore, to satisfy the needs of CHT, CHT Analysis is performed by using ANSYS CFD tool to estimate theoretically precise thermocouple positions at the combustion chamber wall where excessive temperatures (beyond thermocouple range) can be avoided. In accordance with these Computational Fluid Dynamics (CFD) results, a combustion chamber is designed, and a prototype is manufactured with multiple thermocouple ports positioned at the specified distances so that the temperature of hot gases can be measured on the chamber wall where the temperatures do not exceed the thermocouple working range.

Keywords: computational fluid dynamics, conduction, conjugate heat transfer, convection, fluid flow, thermocouples

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Authors: Francesco Pandolfi, Georgios Baltzopoulos, Iunio Iervolino

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The impact of extreme winds on industrial assets and the built environment is gaining increasing attention from stakeholders, including the corporate insurance industry. This has led to a progressively more in-depth study of building vulnerability and fragility to wind. Wind vulnerability models are used in probabilistic risk assessment to relate a loss metric to an intensity measure of the natural event, usually a gust or a mean wind speed. In fact, vulnerability models can be integrated with the wind hazard, which consists of associating a probability to each intensity level in a time interval (e.g., by means of return periods) to provide an assessment of future losses due to extreme wind. This has also given impulse to the world- and regional-scale wind hazard studies.Another approach often adopted for the probabilistic description of building vulnerability to the wind is the use of fragility functions, which provide the conditional probability that selected building components will exceed certain damage states, given wind intensity. In fact, in wind engineering literature, it is more common to find structural system- or component-level fragility functions rather than wind vulnerability models for an entire building. Loss assessment based on component fragilities requires some logical combination rules that define the building’s damage state given the damage state of each component and the availability of a consequence model that provides the losses associated with each damage state. When risk calculations are based on numerical simulation of a structure’s behavior during extreme wind scenarios, the interaction of component fragilities is intertwined with the computational procedure. However, simulation-based approaches are usually computationally demanding and case-specific. In this context, the present work introduces the ExtReMe wind risk assESsment prototype Software, ERMESS, which is being developed at the University of Naples Federico II. ERMESS is a wind risk assessment tool for insurance applications to industrial facilities, collecting a wide assortment of available wind vulnerability models and fragility functions to facilitate their incorporation into risk calculations based on in-built or user-defined wind hazard data. This software implements an alternative method for building-specific risk assessment based on existing component-level fragility functions and on a number of simplifying assumptions for their interactions. The applicability of this alternative procedure is explored by means of an illustrative proof-of-concept example, which considers four main building components, namely: the roof covering, roof structure, envelope wall and envelope openings. The application shows that, despite the simplifying assumptions, the procedure can yield risk evaluations that are comparable to those obtained via more rigorous building-level simulation-based methods, at least in the considered example. The advantage of this approach is shown to lie in the fact that a database of building component fragility curves can be put to use for the development of new wind vulnerability models to cover building typologies not yet adequately covered by existing works and whose rigorous development is usually beyond the budget of portfolio-related industrial applications.

Keywords: component wind fragility, probabilistic risk assessment, vulnerability model, wind-induced losses

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Authors: Goran Baloevic, Jure Radnic, Nikola Grgic

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The application of frames with masonry or panel infill is common in the engineering practice. In these cases, a frame is often considered to be a primary structure, while an infill is considered to be a secondary structure. In past calculations, the infill was rarely included in the design of frame structures in terms of their bearing capacity and safety. Recent calculations of such structures necessarily include the effect of infill since it contributes to stiffness and bearing capacity of overall system, especially under horizontal loads. In certain cases, if the infill is not included in the seismic design of frame structures, the result can be lower design safety. However, since the different configuration of the infill through the building’s height can be made, it is possible that contribution of such infill to the overall bearing capacity can be lower and seismic forces on the building can be increased due to greater stiffness of the structure. So far, many experimental and numerical researches on the behavior of infilled frames under horizontal static forces and earthquake have been performed. In this paper, several masonry-infilled concrete and steel frames under horizontal static forces and earthquake are analysed. The experimental results by shake-table and numerical results are compared in terms of the bearing capacity of bare and infilled frames. Herein, the stiffness of frames and infill were varied, with different position of the infill and different types of openings. Cases with positive and negative effects of the infill to the bearing capacity of the frames were considered. Finally, main conclusions and recommendations for practical application and design of masonry-infilled concrete and steel frames are given.

Keywords: bearing capacity, infilled frame, numerical model, shake table

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Authors: Adil Loya, Kamran Maqsood, Muhammad Duraid

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Aerodynamic stability coefficients are necessary to be known before any unmanned aircraft flight is performed. This requires expertise on aerodynamics and stability control of the aircraft. To enable efficacious performance of aircraft requires that a well-defined flight path and aerodynamics should be defined beforehand. This paper presents a study on the aerodynamics of an unmanned aero vehicle (UAV) during flight conditions. Current research holds comparative studies of different parameters for flight aerodynamic, measured using two different open source analytical software programs. These software packages are DATCOM and XLRF5, which help in depicting the flight aerodynamic variables. Computational fluid dynamics (CFD) was also used to perform aerodynamic analysis for which Star CCM+ was used. Output trends of the study demonstrate high accuracies between the two software programs with that of CFD. It can be seen that the Coefficient of Lift (CL) obtained from DATCOM and XFLR is similar to CL of CFD simulation. In the similar manner, other potential aerodynamic stability parameters obtained from analytical software are in good agreement with CFD.

Keywords: XFLR5, DATCOM, computational fluid dynamic, unmanned aero vehicle

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Authors: Thiago M. R Dias, Gray F. Moita

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The analysis of scientific collaboration networks has contributed significantly to improving the understanding of how does the process of collaboration between researchers and also to understand how the evolution of scientific production of researchers or research groups occurs. However, the identification of collaborations in large scientific databases is not a trivial task given the high computational cost of the methods commonly used. This paper proposes a method for identifying collaboration in large data base of curriculum researchers. The proposed method has low computational cost with satisfactory results, proving to be an interesting alternative for the modeling and characterization of large scientific collaboration networks.

Keywords: extraction, data integration, information retrieval, scientific collaboration

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Authors: Zdzislaw Kaminski, Zbigniew Czyz, Krzysztof Skiba

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This paper discusses the CFD simulation of a flow around a rotor of a Vertical Axis Wind Turbine. Numerical simulation, unlike experiments, enables us to validate project assumptions when it is designed and avoid a costly preparation of a model or a prototype for a bench test. CFD simulation enables us to compare characteristics of aerodynamic forces acting on rotor working surfaces and define operational parameters like torque or power generated by a turbine assembly. This research focused on the rotor with the blades capable of modifying their working surfaces, i.e. absorbing wind kinetic energy. The operation of this rotor is based on adjusting angular aperture α of the top and bottom parts of the blades mounted on an axis. If this angular aperture α increases, the working surface which absorbs wind kinetic energy also increases. The operation of turbines is characterized by parameters like the angular aperture of blades, power, torque, speed for a given wind speed. These parameters have an impact on the efficiency of assemblies. The distribution of forces acting on the working surfaces in our turbine changes according to the angular velocity of the rotor. Moreover, the resultant force from the force acting on an advancing blade and retreating blade should be as high as possible. This paper is part of the research to improve an efficiency of a rotor assembly. Therefore, using simulation, the courses of the above parameters were studied in three full rotations individually for each of the blades for three angular apertures of blade working surfaces, i.e. 30 °, 60 °, 90 °, at three wind speeds, i.e. 4 m / s, 6 m / s, 8 m / s and rotor speeds ranging from 100 to 500 rpm. Finally, there were created the characteristics of torque coefficients and power as a function of time for each blade separately and for the entire rotor. Accordingly, the correlation between the turbine rotor power as a function of wind speed for varied values of rotor rotational speed. By processing this data, the correlation between the power of the turbine rotor and its rotational speed for each of the angular aperture of the working surfaces was specified. Finally, the optimal values, i.e. of the highest output power for given wind speeds were read. The research results in receiving the basic characteristics of turbine rotor power as a function of wind speed for the three angular apertures of the blades. Given the nature of rotor operation, the growth in the output turbine can be estimated if angular aperture of the blades increases. The controlled adjustment of angle α enables a smooth adjustment of power generated by a turbine rotor. If wind speed is significant, this type of adjustment enables this output power to remain at the same level (by reducing angle α) with no risk of damaging a construction. This work has been financed by the Polish Ministry of Science and Higher Education.

Keywords: computational fluid dynamics, numerical analysis, renewable energy, wind turbine

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Authors: Dominic Wentworth-Linton, Shian Gao

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This project was aimed at investigating the effect of velocity stacks on the intakes of internal combustion engines for motorsport applications. The intake systems in motorsport are predominantly fuel injection with a plate mounted for the stacks. Using Computational Fluid Dynamics software, the relationship between the stack length and power and torque delivery across the engine’s rev range was investigated and the results were used to choose the best option for its intended motorsport discipline. The test results are expected to vary with engine geometry and its natural manufacturer characteristics. The test was also relevant in bridging between computational data and real simulation as the results show flow, pressure and velocity readings but the behaviour of the engine is inferred from the nature of each test. The results of the data analysis were tested in a real-life simulation on a dynamometer to prove the theory of stack length on power and torque delivery, which helps determine the most suitable stack for the Vauxhall engine for rallying in the Caribbean.

Keywords: CFD simulation, Internal combustion engine, Intake system, Dynamometer test

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Authors: David Ryan, Martin Breugst, Turlough Downes, Peter A. Byrne, Gerard P. McGlacken

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An ambident nucleophile is a nucleophile that possesses two or more distinct nucleophilic sites that are linked through resonance and are effectively “in competition” for reaction with an electrophile. Examples include enolates, pyridone anions, and nitrite anions, among many others. Reactions of ambident nucleophiles and electrophiles are extremely prevalent at all levels of organic synthesis. The principle of hard and soft acids and bases (the “HSAB principle”) is most commonly cited in the explanation of selectivities in such reactions. Although this rationale is pervasive in any discussion on ambident reactivity, the HSAB principle has received considerable criticism. As a result, the principle’s supplantation has become an area of active interest in recent years. This project focuses on developing a model for rationalizing ambident reactivity. Presented here is an approach that incorporates computational calculations and experimental kinetic data to construct Gibbs energy profile diagrams. The preferred site of alkylation of nitrite anion with a range of ‘hard’ and ‘soft’ alkylating agents was established by ¹H NMR spectroscopy. Pseudo-first-order rate constants were measured directly by ¹H NMR reaction monitoring, and the corresponding second-order constants and Gibbs energies of activation were derived. These, in combination with computationally derived standard Gibbs energies of reaction, were sufficient to construct Gibbs energy wells. By representing the ambident system as a series of overlapping Gibbs energy wells, a more intuitive picture of ambident reactivity emerges. Here, previously unexplained switches in reactivity in reactions involving closely related electrophiles are elucidated.

Keywords: ambident, Gibbs, nucleophile, rates

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Authors: Yuxi Liu, Boris Belousov, Mehrzad Esmaeili Charkhab, Oliver Tessmann

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This paper presents a computational solution for designing reconfigurable interlocking structures that are fully assembled with SL Blocks. Formed by S-shaped and L-shaped tetracubes, SL Block is a specific type of interlocking puzzle. Analogous to molecular self-assembly, the aggregation of SL blocks will build a reversible hierarchical and discrete system where a single module can be numerously replicated to compose semi-interlocking components that further align, wrap, and braid around each other to form complex high-order aggregations. These aggregations can be disassembled and reassembled, responding dynamically to design inputs and changes with a unique capacity for reconfiguration. To use these aggregations as architectural structures, we developed computational tools that automate the configuration of SL blocks based on architectural design objectives. There are three critical phases in our work. First, we revisit the hierarchy of the SL block system and devise a top-down-type design strategy. From this, we propose two key questions: 1) How to translate 3D polyominoes into SL block assembly? 2) How to decompose the desired voxelized shapes into a set of 3D polyominoes with interlocking joints? These two questions can be considered the Hamiltonian path problem and the 3D polyomino tiling problem. Then, we derive our solution to each of them based on two methods. The first method is to construct the optimal closed path from an undirected graph built from the voxelized shape and translate the node sequence of the resulting path into the assembly sequence of SL blocks. The second approach describes interlocking relationships of 3D polyominoes as a joint connection graph. Lastly, we formulate the desired shapes and leverage our methods to achieve their reconfiguration within different levels. We show that our computational strategy will facilitate the efficient design of hierarchical interlocking structures with a self-replicating geometric module.

Keywords: computational design, SL-blocks, 3D polyomino puzzle, combinatorial problem

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Authors: Ming-Hwi Yao, Su-Szu Yang

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Typhoons are one of the major types of disasters that affect Taiwan each year and that cause severe damage to agriculture. Indeed, the damage exacted during a typical typhoon season can be up to $1 billion, and is responsible for nearly 75% of yearly agricultural losses. However, there is no consensus on how to reduce the damage caused by the strong winds and heavy precipitation engendered by typhoons. One suggestion is the use of windbreak nets, which are a low-cost and easy-to-use disaster mitigation strategy for crop production. In the present study, we conducted an evaluation to determine the optimal conditions of a windbreak net by using a computational fluid dynamics (CFD) model. This model may be used as a reference for crop protection. The results showed that CFD simulation validated windbreak nets of different mesh sizes and heights in the experimental area; thus, CFD is an efficient tool for evaluating the effectiveness of windbreak nets. Specifically, the effective wind protection length and height were found to be 6 and 1.3 times the length and height of the windbreak net, respectively. During a real typhoon, maximum wind gusts of 18 m s-1 can be reduced to 4 m s-1 by using a windbreak net that has a 70% blocking rate. In short, windbreak nets are significantly effective in protecting typhoon-affected areas.

Keywords: computational fluid dynamics, disaster, typhoon, windbreak net

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Authors: S. V. Boroznin, I. V. Zaporotskova, N. P. Polikarpova

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Studing of nanotubes sorption properties is very important for researching. These processes for carbon and boron nanotubes described in the high number of papers. But the sorption properties of boron containing nanotubes, susch as BC3-nanotubes haven’t been studied sufficiently yet. In this paper we present the results of theoretical research into the mechanism of atomic surface adsorption on the two types of boron-carbon nanotubes (BCNTs) within the framework of an ionic-built covalent-cyclic cluster model and an appropriately modified MNDO quantum chemical scheme and DFT method using B3LYP functional with 6-31G basis. These methods are well-known and the results, obtained using them, were in good agreement with the experiment. Also we studied three position of atom location above the nanotube surface. These facts suggest us to use them for our research and quantum-chemical calculations. We studied the mechanism of sorption of Cl, O and F atoms on the external surface of single-walled BC3 arm-chair nanotubes. We defined the optimal geometry of the sorption complexes and obtained the values of the sorption energies. Analysis of the band structure suggests that the band gap is insensitive to adsorption process. The electron density is located near atoms of the surface of the tube. Also we compared our results with others, which have been obtained earlier for pure carbon and boron nanotubes. The most stable adsorption complex has been between boron-carbon nanotube and oxygen atom. So, it suggests us to make a research of oxygen molecule adsorption on the BC3 nanotube surface. We modeled five variants of molecule orientation above the nanotube surface. The most stable sorption complex has been defined between the oxygen molecule and nanotube when the oxygen molecule is located above the nanotube surface perpendicular to the axis of the tube.

Keywords: Boron-carbon nanotubes, nanostructures, nanolayers, quantum-chemical calculations, nanoengineering

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Authors: Xavier Bertrand, Alexandre Cayrel

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The early phase of an aircraft development is instrumental as it really drives the potential of a new concept. Any weakness in the high-level design (wing planform, moveable surfaces layout etc.) will be extremely difficult and expensive to recover later in the aircraft development process. Aerodynamic evaluation in this very early development phase is driven by two main criteria: a short lead-time to allow quick iterations of the geometrical design, and a high quality of the calculations to get an accurate & reliable assessment of the current status. These two criteria are usually quite contradictory. Actually, short lead time of a couple of hours from end-to-end can be obtained with very simple tools (semi-empirical methods for instance) although their accuracy is limited, whereas higher quality calculations require heavier/more complex tools, which obviously need more complex inputs as well, and a significantly longer lead time. At this point, the choice has to be done between accuracy and lead-time. A brand new approach has been developed within Airbus, aiming at obtaining quickly high quality evaluations of the aerodynamic of an aircraft. This methodology is based on a joint use of Surrogate Modelling and a lifting line code. The Surrogate Modelling is used to get the wing sections characteristics (e.g. lift coefficient vs. angle of attack), whatever the airfoil geometry, the status of the moveable surfaces (aileron/spoilers) or the high-lift devices deployment. From these characteristics, the lifting line code is used to get the 3D effects on the wing whatever the flow conditions (low/high Mach numbers etc.). This methodology has been applied successfully to a concept of medium range aircraft.

Keywords: aerodynamics, lifting line, surrogate model, CFD

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Authors: Halim Djerroud, Arab Ali Cherif

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We assume that conscious functions are implemented automatically. In other words that consciousness as well as the non-consciousness aspect of human thought, planning, and perception, are produced by biologically adaptive algorithms. We propose that the mechanisms of consciousness can be produced using similar adaptive algorithms to those executed by the mechanism. In this paper, we propose a computational model of consciousness, the ”Global Abstraction Workspace” which is an internal environmental modelling perceived as a multi-agent system. This system is able to evolve and generate new data and processes as well as actions in the environment.

Keywords: artificial consciousness, cognitive architecture, global abstraction workspace, multi-agent system

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Authors: Oleg Ye Sysoyev, Artem Yu Dobryshkin, Nyein Sitt Naing

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Cylindrical shells are widely used in the construction of buildings and structures, as well as in the air structure. Thin-walled casings made of aluminum alloys are an effective substitute for reinforced concrete and steel structures in construction. The correspondence of theoretical calculations and the actual behavior of aluminum alloy structures is to ensure their trouble-free operation. In the laboratory of our university, "Building Constructions" conducted an experimental study to determine the effect of the system of attached masses on the natural oscillations of shallow cylindrical shells of aluminum alloys, the results of which were compared with theoretical calculations. The purpose of the experiment is to measure the free oscillations of an open, sloping cylindrical shell for various variations of the attached masses. Oscillations of an open, slender, thin-walled cylindrical shell, rectangular in plan, were measured using induction accelerometers. The theoretical calculation of the shell was carried out on the basis of the equations of motion of the theory of shallow shells, using the Bubnov-Galerkin method. A significant splitting of the flexural frequency spectrum is found, influenced not only by the systems of attached маsses but also by the values of the wave formation parameters, which depend on the relative geometric dimensions of the shell. The correspondence of analytical and experimental data is found, using the example of an open shell of alloy D19, which allows us to speak about the high quality of the study. A qualitative new analytical solution of the problem of determining the value of the oscillation frequency of the shell, carrying a system of attached masses is shown.

Keywords: open hollow shell, nonlinear oscillations, associated mass, frequency

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Authors: Kumar Sambhav Pandey, Anamika Singh

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The continuous researches in the field of computer architecture basically aims at accelerating the computational speed and to gain enhanced performance. In this era, the superscalar, sub-scalar concept has not gained enough attention for improving the computation performance. In this paper, we have presented a sub-scalar approach to utilize the parallelism present with in the data while processing. The main idea is to split the data into individual smaller entities and these entities are processed with a defined known set of instructions. This sub-scalar approach to the MIPS architecture can bring out significant improvement in the computational speedup. MIPS-I is the basic design taken in consideration for the development of sub-scalar MIPS64 for increasing the instruction level parallelism (ILP) and resource utilization.

Keywords: dataword, MIPS, processor, sub-scalar

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Authors: R. Chanajaree, D. Luanwiset, K. Pongpratea

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Dye removal is an environmental concern because the textile industries have been increasing by world population and industrialization. Adsorption is the technique to find adsorbents to remove dyes from wastewater. This method is low-cost and effective for dye removal. This work tries to develop effective adsorbents using the computational approach because it will be able to predict the possibility of the adsorbents for specific dyes in terms of binding free energies. The computational approach is faster and cheaper than the experimental approach in case of finding the best adsorbents. All starting structures of dyes and adsorbents are optimized by quantum calculation. The complexes between dyes and adsorbents are generated by the docking method. The obtained binding free energies from docking are compared to binding free energies from the experimental data. The calculated energies can be ranked as same as the experimental results. In addition, this work also shows the possible orientation of the complexes. This work used two experimental groups of the complexes of the dyes and adsorbents. In the first group, there are chitosan (adsorbent) and two dyes (reactive red (RR) and direct sun yellow (DY)). In the second group, there are poly(1,2-epoxy-3-phenoxy) propane (PEPP), which is the adsorbent, and 2 dyes of bromocresol green (BCG) and alizarin yellow (AY).

Keywords: dyes removal, binding free energies, quantum calculation, docking

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Authors: Fatemeh Faramarzi, Hosein Mahjoob

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Building dams on rivers for utilization of water resources causes problems in hydrodynamic equilibrium and results in leaving all or part of the sediments carried by water in dam reservoir. This phenomenon has also significant impacts on water and sediment flow regime and in the long term can cause morphological changes in the environment surrounding the river, reducing the useful life of the reservoir which threatens sustainable development through inefficient management of water resources. In the past, empirical methods were used to predict the sedimentation amount in dam reservoirs and to estimate its efficient lifetime. But recently the mathematical and computational models are widely used in sedimentation studies in dam reservoirs as a suitable tool. These models usually solve the equations using finite element method. This study compares the results from tow software packages, GSTARS4 & HEC-6, in the prediction of the sedimentation amount in Dez dam, southern Iran. The model provides a one-dimensional, steady-state simulation of sediment deposition and erosion by solving the equations of momentum, flow and sediment continuity and sediment transport. GSTARS4 (Generalized Sediment Transport Model for Alluvial River Simulation) which is based on a one-dimensional mathematical model that simulates bed changes in both longitudinal and transverse directions by using flow tubes in a quasi-two-dimensional scheme to calibrate a period of 47 years and forecast the next 47 years of sedimentation in Dez Dam, Southern Iran. This dam is among the highest dams all over the world (with its 203 m height), and irrigates more than 125000 square hectares of downstream lands and plays a major role in flood control in the region. The input data including geometry, hydraulic and sedimentary data, starts from 1955 to 2003 on a daily basis. To predict future river discharge, in this research, the time series data were assumed to be repeated after 47 years. Finally, the obtained result was very satisfactory in the delta region so that the output from GSTARS4 was almost identical to the hydrographic profile in 2003. In the Dez dam due to the long (65 km) and a large tank, the vertical currents are dominant causing the calculations by the above-mentioned method to be inaccurate. To solve this problem, we used the empirical reduction method to calculate the sedimentation in the downstream area which led to very good answers. Thus, we demonstrated that by combining these two methods a very suitable model for sedimentation in Dez dam for the study period can be obtained. The present study demonstrated successfully that the outputs of both methods are the same.

Keywords: Dez Dam, prediction, sedimentation, water resources, computational models, finite element method, GSTARS4, HEC-6

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Authors: A. Bahmanpour, I. Eames, C. Klettner, A. Dimakopoulos

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We develop a new set of diagnostic tools to analyze inundation into a model district using three-dimensional CFD simulations, with a view to generating a database against which to test simpler models. A three-dimensional model of Oregon city with different-sized groups of building next to the coastline is used to run calculations of the movement of a long period wave on the shore. The initial and boundary conditions of the off-shore water are set using a nonlinear inverse method based on Eulerian spatial information matching experimental Eulerian time series measurements of water height. The water movement is followed in time, and this enables the pressure distribution on every surface of each building to be followed in a temporal manner. The three-dimensional numerical data set is validated against published experimental work. In the first instance, we use the dataset as a basis to understand the success of reduced models - including 2D shallow water model and reduced 1D models - to predict water heights, flow velocity and forces. This is because models based on the shallow water equations are known to underestimate drag forces after the initial surge of water. The second component is to identify critical flow features, such as hydraulic jumps and choked states, which are flow regions where dissipation occurs and drag forces are large. Finally, we describe how future tsunami inundation models should be modified to account for the complex effects of buildings through drag and blocking.Financial support from UCL and HR Wallingford is greatly appreciated. The authors would like to thank Professor Daniel Cox and Dr. Hyoungsu Park for providing the data on the Seaside Oregon experiment.

Keywords: computational fluid dynamics, extreme events, loading, tsunami

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Authors: Junting Xiang, Jörg Uwe Schlüter, Fei Duan

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The miniaturization of gas turbines promises many advantages. Miniature gas turbines can be used for local power generation or the propulsion of small aircraft, such as UAV and MAV. However, experience shows that the miniaturization of conventional gas turbines, which are optimized at their current large size, leads to a substantial loss of efficiency and performance at smaller scales. This may be due to a number of factors, such as the Reynolds-number effect, the increased heat transfer, and manufacturing tolerances. In the present work, we focus on computational investigations of the Reynolds number effect and the wall heat transfer on the performance of axial compressor during its size change. The NASA stage 35 compressors are selected as the configuration in this study and Computational Fluid Dynamics (CFD) is used to carry out the miniaturization process and simulations. We perform parameter studies on the effect of Reynolds number and wall thermal conditions. Our results indicate a decrease of efficiency, if the compressor is miniaturized based on its original geometry due to the increase of viscous effects. The increased heat transfer through wall has only a small effect and will actually benefit compressor performance based on our study.

Keywords: axial compressor, CFD, heat transfer, miniature gas turbines, Reynolds number

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Authors: Deepshikha Shukla, C. H. Solanki, Mayank K. Desai

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Amongst all the natural hazards, earthquakes have the potential for causing the greatest damages. Since the earthquake forces are random in nature and unpredictable, the quantification of the hazards becomes important in order to assess the hazards. The time and place of a future earthquake are both uncertain. Since earthquakes can neither be prevented nor be predicted, engineers have to design and construct in such a way, that the damage to life and property are minimized. Seismic hazard analysis plays an important role in earthquake design structures by providing a rational value of input parameter. In this paper, both mathematical, as well as computational methods adopted by researchers globally in the past five years, will be discussed. Some mathematical approaches involving the concepts of Poisson’s ratio, Convex Set Theory, Empirical Green’s Function, Bayesian probability estimation applied for seismic hazard and FOSM (first-order second-moment) algorithm methods will be discussed. Computational approaches and numerical model SSIFiBo developed in MATLAB to study dynamic soil-structure interaction problem is discussed in this paper. The GIS-based tool will also be discussed which is predominantly used in the assessment of seismic hazards.

Keywords: computational methods, MATLAB, seismic hazard, seismic measurements

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Authors: Ram Mohan, Richard Haney, Ajit Kelkar

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Current developments in computing have shown the advantage of using one or more Graphic Processing Units (GPU) to boost the performance of many computationally intensive applications but there are still limits to these GPU-enhanced systems. The major factors that contribute to the limitations of GPU(s) for High Performance Computing (HPC) can be categorized as hardware and software oriented in nature. Understanding how these factors affect performance is essential to develop efficient and robust applications codes that employ one or more GPU devices as powerful co-processors for HPC computational modeling. This research and technical presentation will focus on the analysis and understanding of the intrinsic interrelationship of both hardware and software categories on computational performance for single and multiple GPU-enhanced systems using a computationally intensive application that is representative of a large portion of challenges confronting modern HPC. The representative application uses unstructured finite element computations for transient composite resin infusion process flow modeling as the computational core, characteristics and results of which reflect many other HPC applications via the sparse matrix system used for the solution of linear system of equations. This work describes these various software and hardware factors and how they interact to affect performance of computationally intensive applications enabling more efficient development and porting of High Performance Computing applications that includes current, legacy, and future large scale computational modeling applications in various engineering and scientific disciplines.

Keywords: graphical processing unit, software development and engineering, performance analysis, system architecture and software performance

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Authors: Reena Murali, David Peter S.

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The small interfering RNA (siRNA) alters the regulatory role of mRNA during gene expression by translational inhibition. Recent studies shows that up regulation of mRNA cause serious diseases like Cancer. So designing effective siRNA with good knockdown effects play an important role in gene silencing. Various siRNA design tools had been developed earlier. In this work, we are trying to analyze the existing good scoring second generation siRNA predicting tools and to optimize the efficiency of siRNA prediction by designing a computational model using Artificial Neural Network and whole stacking energy (ΔG), which may help in gene silencing and drug design in cancer therapy. Our model is trained and tested against a large data set of siRNA sequences. Validation of our results is done by finding correlation coefficient of experimental versus observed inhibition efficacy of siRNA. We achieved a correlation coefficient of 0.727 in our previous computational model and we could improve the correlation coefficient up to 0.753 when the threshold of whole tacking energy is greater than or equal to -32.5 kcal/mol.

Keywords: artificial neural network, double stranded RNA, RNA interference, short interfering RNA

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Authors: H. Shamoradifar, B. Teimuri, P. Parvaresh, S. Mohammadi

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One of the main characteristics of Heavy Water Moderated Reactors is their high production of plutonium. This article demonstrates the possibility of reduction of plutonium and other actinides in Heavy Water Research Reactor. Among the many ways for reducing plutonium production in a heavy water reactor, in this research, changing the fuel from natural Uranium fuel to Thorium-Uranium mixed fuel was focused. The main fissile nucleus in Thorium-Uranium fuels is U-233 which would be produced after neutron absorption by Th-232, so the Thorium-Uranium fuels have some known advantages compared to the Uranium fuels. Due to this fact, four Thorium-Uranium fuels with different compositions ratios were chosen in our simulations; a) 10% UO₂-90% THO₂ (enriched= 20%); b) 15% UO₂-85% THO₂ (enriched= 10%); c) 30% UO₂-70% THO₂ (enriched= 5%); d) 35% UO₂-65% THO₂ (enriched= 3.7%). The natural Uranium Oxide (UO₂) is considered as the reference fuel, in other words all of the calculated data are compared with the related data from Uranium fuel. Neutronic parameters were calculated and used as the comparison parameters. All calculations were performed by Monte Carol (MCNPX2.6) steady state reaction rate calculation linked to a deterministic depletion calculation (CINDER90). The obtained computational data showed that Thorium-Uranium fuels with four different fissile compositions ratios can satisfy the safety and operating requirements for Heavy Water Research Reactor. Furthermore, Thorium-Uranium fuels have a very good proliferation resistance and consume less fissile material than uranium fuels at the same reactor operation time. Using mixed Thorium-Uranium fuels reduced the long-lived α emitter, high radiotoxic wastes and the radio toxicity level of spent fuel.

Keywords: Heavy Water Reactor, Burn up, Minor Actinides, Neutronic Calculation

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