Search results for: molecular dynamics simulations

Authors: Firman Riyudha, Endrik Mifta Shaiful

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The spread of drug users is one kind of behavioral epidemiology that becomes a threat to every country in the world. This problem caused various crisis simultaneously, including financial or economic crisis, social, health, until human crisis. Most drug users are teenagers at school age. A new deterministic model would be constructed to determine the dynamics of the spread of drug users by considering level of education in a susceptible population. Based on the analytical model, two equilibria points were obtained; there were E₀ (zero user) and E₁ (endemic equilibrium). Existence of equilibrium and local stability of equilibria depended on the Basic Reproduction Ratio (R₀). This parameter was defined as the expected rate of secondary prevalence and primary prevalence in virgin population along spreading primary prevalence. The zero-victim equilibrium would be locally asymptotically stable if R₀ < 1 while if R₀ > 1 the endemic equilibrium would be locally asymptotically stable. The result showed that R₀ was proportional to the rate of interaction of each susceptible population based on educational level with the users' population. It is concluded that there was a need to be given a control in interaction, so that drug users population could be minimized. Numerical simulations were also provided to support analytical results.

Keywords: drugs users, level education, mathematical model, stability

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Authors: M. W. Sun, Y. Zhang, L. M. Zhang, Z. H. Wang, Z. Q. Chen

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In the realm of flight control, the Proportional- Derivative (PD) control is still widely used for the attitude control in practice, particularly for the pitch control, and the attitude dynamics using PD controller should be investigated deeply. According to the empirical knowledge about the unstable flight dynamics, the control parameter combination conditions to generate sole or finite number of closed-loop oscillations, which is a quite smooth response and is more preferred by practitioners, are presented in analytical or numerical manners. To analyze the effects of the combination conditions of the control parameters, the roots of several polynomials are sought to obtain feasible solutions. These conditions can also be plotted in a 2-D plane which makes the conditions be more explicit by using multiple interval operations. Finally, numerical examples are used to validate the proposed methods and some comparisons are also performed.

Keywords: attitude control, dynamic performance, numerical solving method, interval, unstable flight dynamics

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Authors: Hamza Javar Magnier, Leslie V. Woodcock

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We report extensive molecular dynamics (MD) computational investigations into the thermodynamic description of supercritical properties for a model fluid that is the simplest realistic representation of atoms or molecules. The pair potential is a hard-sphere repulsion of diameter σ with a very short attraction of length λσ. When λ = 1.005 the range is so short that the model atoms are referred to as “adhesive spheres”. Molecular dimers, trimers …etc. up to large clusters, or droplets, of many adhesive-sphere atoms are unambiguously defined. This then defines percolation transitions at the molecular level that bound the existence of gas and liquid phases at supercritical temperatures, and which define the existence of a supercritical mesophase. Both liquid and gas phases are seen to terminate at the loci of percolation transitions, and below a second characteristic temperature (Tc2) are separated by the supercritical mesophase. An analysis of the distribution of clusters in gas, meso- and liquid phases confirms the colloidal nature of this mesophase. The general phase behaviour is compared with both experimental properties of the water-steam supercritical region and also with formally exact cluster theory of Mayer and Mayer. Both are found to be consistent with the present findings that in this system the supercritical mesophase narrows in density with increasing T > Tc and terminates at a higher Tc2 at a confluence of the primary percolation loci. The expended plot of the MD data points in the mesophase of 7 critical and supercritical isotherms in highlight this narrowing in density of the linear-slope region of the mesophase as temperature is increased above the critical. This linearity in the mesophase implies the existence of a linear combination rule between gas and liquid which is an extension of the Lever rule in the subcritical region, and can be used to obtain critical parameters without resorting to experimental data in the two-phase region. Using this combination rule, the calculated critical parameters Tc = 0.2007 and Pc = 0.0278 are found be agree with the values found by of Largo and coworkers. The properties of this supercritical mesophase are shown to be consistent with an alternative description of the phenomenon of critical opalescence seen in the supercritical region of both molecular and colloidal-protein supercritical fluids.

Keywords: critical opalescence, supercritical, square-well, percolation transition, critical parameters.

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Authors: Abishek Rajkumar

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Antibiotic resistance can occur naturally given the selective pressure placed on antibiotics. Within a large population of bacteria, there is a significant chance that some of those bacteria can develop resistance via mutations or genetic recombination. However, a growing public health concern has arisen over the fact that antibiotic resistance has increased significantly over the past few decades. This is because humans have been over-consuming and producing antibiotics, which has ultimately accelerated the antibiotic resistance seen in these bacteria. The product of all of this is an ongoing race between scientists and the bacteria as bacteria continue to develop resistance, which creates even more demand for an antibiotic that can still terminate the newly resistant strain of bacteria. This paper will focus on a myriad of aspects of antibiotic resistance in bacteria starting with how it occurs on a molecular level and then focusing on the antibiotic concentrations and how they affect the resistance and fitness seen in bacteria.

Keywords: antibiotic, molecular, mutation, resistance

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Authors: Mahdi Hamzehei, Seyyed Amin Hakim, Nahid Taherian

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Fins play an important role in increasing the efficiency of compact shell and tube heat exchangers by increasing heat transfer. The objective of this paper is to determine the optimum fin wave angle, as one of the geometric parameters affecting the efficiency of the heat exchangers. To this end, finite volume method is used to model and simulate the flow in heat exchanger. In this study, computational fluid dynamics simulations of wave channel are done. The results show that the wave angle affects the temperature output of the heat exchanger.

Keywords: fin wave angle, tube, intercooler, optimum, performance

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Authors: Avichal Malhotra, Jerome Frisch, Christoph van Treeck

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The utilization of semantic, cadastral and topological data from geographic information systems (GIS) has exponentially increased for building and urban-scale energy performance simulations. Urban planners, simulation scientists, and researchers use virtual 3D city models for energy analysis, algorithms and simulation tools. For dynamic energy simulations at city and district level, this paper provides an overview of the available GIS data models and their levels of detail. Adhering to different norms and standards, these models also intend to describe building and construction industry data. For further investigations, CityGML data models are considered for simulations. Though geographical information modelling has considerably many different implementations, extensions of virtual city data can also be made for domain specific applications. Highlighting the use of the extended CityGML models for energy researches, a brief introduction to the Energy Application Domain Extension (ADE) along with its significance is made. Consequently, addressing specific input simulation data, a workflow using Modelica underlining the usage of GIS information and the quantification of its significance over annual heating energy demand is presented in this paper.

Keywords: CityGML, EnergyADE, energy performance simulation, GIS

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Authors: Boukli Hacene Faiza, Soufi Wassila, Ghalem Said

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The oral antidiabetics drugs such as alpha glucosidase inhibitors present undesirable effects like acarbose. Flavonoids are class of molecules widely distributed in plants, for this reason we are interested in our work to study the inhibition in silico of alpha glucosidase by natural ligands ( flavonoids analogues) using molecular modeling methods using MOE (Molecular Operating Environment) software to predict their interaction with this enzyme with score energy, ADME /T tests and druglikeness properties experiments. Two flavonoids Beicalein and Apigenin have high binding affinity with alpha glucosidase with lower IC50 supposed potent inhibitors.

Keywords: alpha glucosidase, flavonoides analogues, drug research, molecular modeling

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Authors: Xiuxia Sun, Yan Jin, Zilong Liu, Shiming Wei

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As a critical mineral component of shale, illite is essential in oil exploration and development due to its surface hydration characteristics and action mechanism. This paper, starting from the perspective of the molecular structure of organic matter, uses molecular dynamics simulation technology to deeply explore the interaction mechanism between organic molecules and the illite surface. In the study, we thoroughly considered the forces such as van der Waals force, electrostatic force, and steric hindrance and constructed an illite crystal model covering C8-C18 modifiers. Subsequently, we systematically analyzed surfactants' adsorption behavior and hydration characteristics with different alkyl chain numbers, lengths, and concentrations on the illite surface. The simulation results show that surfactant molecules with shorter alkyl chains present a lateral monolayer or inclined double-layer arrangement on the illite surface, and these two arrangements may coexist under different concentration conditions. In addition, with the increase in the number of alkyl chains, the interlayer spacing of illite increases significantly. In contrast, the change in alkyl chain length has a limited effect on surface properties. It is worth noting that the change in functional group structure has a particularly significant effect on the wettability of the illite surface, and its influence even exceeds the change in the alkyl chain structure. This discovery gives us a new perspective on understanding and regulating the wetting properties. The results obtained are consistent with the XRD analysis and wettability experimental data in this paper, further confirming the reliability of the research conclusions. This study deepened our understanding of illite's hydration characteristics and mechanism. We provided new ideas and directions for the molecular design and application development of oilfield chemicals.

Keywords: illite, surfactant, hydration, wettability, adsorption

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Authors: H. M. D. Prabhashana Herath, M. D. Anuradha Wickramasinghe, A. M. C. Kalpani Polgolla, R. A. C. Prasad Ranasinghe, M. Anusha Wijewardane

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The demand for thermal comfort in buildings in hot and humid climates increases progressively. In general, buildings in hot and humid climates spend more than 60% of the total energy cost for the functionality of the air conditioning (AC) system. Hence, it is required to install energy efficient AC systems or integrate energy recovery systems for both new and/or existing AC systems whenever possible, to reduce the energy consumption by the AC system. Integrate a Rotary Thermal Wheel as the energy recovery device of an existing AC system has shown very promising with attractive payback periods of less than 5 years. A rotary thermal wheel can be located in the Air Handling Unit (AHU) of a central AC system to recover the energy available in the return air stream. During this study, a sensitivity analysis was performed using a CFD (Computational Fluid Dynamics) software to determine the optimum design parameters (i.e., rotary speed and parameters of the matrix profile) of a rotary thermal wheel for hot and humid climates. The simulations were performed for a sinusoidal matrix geometry. Variation of sinusoidal matrix parameters, i.e., span length and height, were also analyzed to understand the heat exchanging performance and the induced pressure drop due to the air flow. The results show that the heat exchanging performance increases when increasing the wheel rpm. However, the performance increment rate decreases when increasing the rpm. As a result, it is more advisable to operate the wheel at 10-20 rpm. For the geometry, it was found that the sinusoidal geometries with lesser spans and higher heights have higher heat exchanging capabilities. Considering the sinusoidal profiles analyzed during the study, the geometry with 4mm height and 3mm width shows better performance than the other combinations.

Keywords: air conditioning, computational fluid dynamics, CFD, energy recovery, heat exchangers

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Authors: Rui Mao, Heming Ji, Xiaoyu Wang

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Keystroke dynamics are widely used in identity recognition. It has the advantage that the individual typing rhythm is difficult to imitate. It also supports continuous authentication through the keyboard without extra devices. The existing keystroke dynamics authentication methods based on machine learning have a drawback in supporting relatively complex scenarios with massive data. There are drawbacks to both feature extraction and model optimization in these methods. To overcome the above weakness, an authentication model of keystroke dynamics based on deep learning is proposed. The model uses feature vectors formed by keystroke content and keystroke time. It ensures efficient continuous authentication by cooperating attention mechanisms with the combination of CNN and Bi-LSTM. The model has been tested with Open Data Buffalo dataset, and the result shows that the FRR is 3.09%, FAR is 3.03%, and EER is 4.23%. This proves that the model is efficient and accurate on continuous authentication.

Keywords: keystroke dynamics, identity authentication, deep learning, CNN, LSTM

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Authors: Sanja O. Podunavac-Kuzmanović, Strahinja Z. Kovačević, Lidija R. Jevrić

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Prion is a protein substance whose certain form is considered as infectious agent. It is presumed to be the cause of the transmissible spongiform encephalopathies (TSEs). The protein it is composed of, called PrP, can fold in structurally distinct ways. At least one of those 3D structures is transmissible to other prion proteins. Prions can be found in brain tissue of healthy people and have certain biological role. The structure of prions naturally occurring in healthy organisms is marked as PrPc, and the structure of infectious prion is labeled as PrPSc. PrPc may play a role in synaptic plasticity and neuronal development. Also, it may be required for neuronal myelin sheath maintenance, including a role in iron uptake and iron homeostasis. PrPSc can be considered as an environmental pollutant. The main aim of this study was to carry out the molecular modeling and calculation of molecular descriptors (lipophilicity, physico-chemical and topological descriptors) of structurally diverse compounds which can be considered as anti-prion agents. Molecular modeling was conducted applying ChemBio3D Ultra version 12.0 software. The obtained 3D models were subjected to energy minimization using molecular mechanics force field method (MM2). The cutoff for structure optimization was set at a gradient of 0.1 kcal/Åmol. The Austin Model 1 (AM-1) was used for full geometry optimization of all structures. The obtained set of molecular descriptors is applied in analysis of similarities and dissimilarities among the tested compounds. This study is an important step in further development of quantitative structure-activity relationship (QSAR) models, which can be used for prediction of anti-prion activity of newly synthesized compounds.

Keywords: chemometrics, molecular modeling, molecular descriptors, prions, QSAR

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Authors: Sara Soltanpour, Adolfo Foriero

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Frost heave is arguably the most problematic adverse phenomenon in cold region areas. Frost heave is a complex process that depends on heat and water transfer. These coupled physical fields generate considerable heave stresses as well as deformations. In the present study, a coupled thermal-hydraulic-mechanical (THM) model using COMSOL Multiphysics in frozen unsaturated soils, such as fine sand, is investigated. Particular attention to the frost heave and temperature distribution, as well as the water migrating during soil freezing, is assessed. The results obtained from the numerical simulations are consistent with the results measured in the full-scale tests conducted by Cold Regions Research and Engineering Laboratory (CRREL).

Keywords: frost heave, numerical simulations, COMSOL software, unsaturated freezing soil

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Authors: Sabyasachi Mukhopadhyay, Joseph Ogutu, Hans-Peter Piepho

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We aim to model dynamics of wildlife or pastoral livestock population for understanding of their population change and hence for wildlife conservation and promoting human welfare. The study is motivated by an age-sex structured population counts in different regions of Serengeti-Mara during the period 1989-2003. Developing reliable and realistic models for population dynamics of large herbivore population can be a very complex and challenging exercise. However, the Bayesian statistical domain offers some flexible computational methods that enable the development and efficient implementation of complex population dynamics models. In this work, we have used a novel Bayesian state-space model to analyse the dynamics of topi and hartebeest populations in the Serengeti-Mara Ecosystem of East Africa. The state-space model involves survival probabilities of the animals which further depend on various factors like monthly rainfall, size of habitat, etc. that cause recent declines in numbers of the herbivore populations and potentially threaten their future population viability in the ecosystem. Our study shows that seasonal rainfall is the most important factors shaping the population size of animals and indicates the age-class which most severely affected by any change in weather conditions.

Keywords: bayesian state-space model, Markov Chain Monte Carlo, population dynamics, conservation

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Authors: S. Altmeyer, B. Hof, F. Marques, J. M. Lopez

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We present numerical simulations concerning the reversal of spiraling vortices in short highly counter-rotating cylinders. Increasing the differential cylinder rotation results in global flow-inversion is which develops various different and complex flow dynamics of several quasi-periodic solutions that differ in their number of vortex cells in the bulk. The dynamics change from being dominated of the inner cylinder boundary layer with ’passive’ only responding outer one to be dominated by the outer cylinder boundary layer with only responding inner one. Solutions exist on either two or three tori invariant manifolds whereby they appear as symmetric or asymmetric states. We find for either moderate and high inner cylinder rotation speed the quasiperiodic flow to consist of only two vortex cells but differ as the vortices has opposite spiraling direction. These both flows live on 2-tori but differ in number of symmetries. While for the quasi-periodic flow (q^a_2) at lower rotation speed a pair of symmetrically related 2-tori T2 exists the quasi-periodic flow (q^s_2) at higher rotation speeds is symmetric living on a single 2-torus T2. In addition these both flows differ due to their dominant azimuthal m modes. The first is dominated by m=1 whereas for the latter m=3 contribution is largest. The 2-tori states are separated by a further quasi-periodic flow (q^a_3) living on pair of symmetrically related 3-tori T3. This flow offers a ’periodical’ competition between a two and three vortex cell states in the bulk. This flow is also an m=1 solution as for the quasiperiodic flows living on the pair of symmetrically-related 2-tori states. Moreover we find hysteresis resulting in coexisting regions of different quasiperiodic flows q^s_2 and q^a_3 with increasing and decreasing the differential rotation.

Keywords: transition, bifurcation, torus, symmetries

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Authors: Yuri V. Kim

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This article presents a new approach to the Functional Testing of Space Systems (SS). It can be considered as a generic test and used for a wide class of SS that from the point of view of System Dynamics and Control may be described by the ordinary differential equations. Suggested methodology is based on using semi-natural experiment- laboratory stand that doesn’t require complicated, precise and expensive technological control-verification equipment. However, it allows for testing system as a whole totally assembled unit during Assembling, Integration and Testing (AIT) activities, involving system hardware (HW) and software (SW). The test physically activates system input (sensors) and output (actuators) and requires recording their outputs in real time. The data is then inserted in laboratory PC where it is post-experiment processed by Matlab/Simulink Identification Toolbox. It allows for estimating system dynamics in form of estimation of system differential equations by the experimental way and comparing them with expected mathematical model prematurely verified by mathematical simulation during the design process.

Keywords: system dynamics, space system ground tests and space qualification, system dynamics identification, satellite attitude control, assembling, integration and testing

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Authors: Haowen Xi

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We propose and solve exactly a class of non-linear generalization of the Black-Scholes process of stochastic differential equations describing price bubble and crashes dynamics. As a result of nonlinear positive feedback, the faster-than-exponential price positive growth (bubble forming) and negative price growth (crash forming) are found to be the power-law finite-time singularity in which bubbles and crashes price formation ending at finite critical time tc. While most literature on the market bubble and crash process focuses on the nonlinear positive feedback mechanism aspect, very few studies concern the noise level on the same process. The present work adds to the market bubble and crashes literature by studying the external sources noise influence on the critical time tc of the bubble forming and crashes forming. Two main results will be discussed: (1) the analytical expression of expected value of the critical time is found and unexpected critical slowing down due to the coupling external noise is predicted; (2) numerical simulations of the nonlinear stochastic equation is presented, and the probability distribution of Prob(tc) is found to be the inverse gamma function.

Keywords: bubble, crash, finite-time-singular, numerical simulation, price dynamics, stochastic differential equations

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Authors: Abdulmannan Fadel

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Arabinoxylan is a non-starch polysaccharide (NSP), which is one of the most important polysaccharides contained within cereal grains. Wheat endosperm pentosan and rice bran contain a significant amount of arabinoxylan (7% in rice bran and 10-12% in wheat endosperm pentosan). Several methods have been used for arabinoxylan extraction with varying degrees of success e.g. enzymatic and alkaline treatment. Yet, the use of extrusion alone as a pre-treatment to increase the yield and reduce the molecular weight in wheat endosperm pentosan and rice bran has not been investigated. The samples (wheat pentosan and rice bran) were extruded using a Twin-screw extruder at a range of screw speeds (80 and 160 rpm) and barrel temperatures range (80 to 140°C) with a throughput of 30 Kg hr-1 and moisture content of 25%. Arabinoxylans were extracted with water and the extraction yield and molecular weight was determined using size exclusion high-pressure liquid chromatography system. It was found that increasing screw speed from 80 rpm to 160 rpm, did not effect the extraction yield (p < 0.05) of arabinoxylan from either the wheat endosperm pentosan or the rice bran. However, the molecular weight of the extracted arabinoxylans from pentosan was found to decrease with increasing screw speed in wheat endosperm pentosan. These low molecular weight arabinoxylans have been suggested as immunomodulators.

Keywords: arabinoxylans, extrusion, wheat endosperm pentosan, rice bran

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Authors: Ehsan Gholamalizadeh, Jae Dong Chung

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Solar chimney power plant is a feasible solar thermal system which produces electricity from the Sun. The objective of this study is to investigate buoyancy-driven flow and heat transfer through a built pilot solar chimney system called 'Kerman Project'. The system has a chimney with the height and diameter of 60 m and 3 m, respectively, and the average radius of its solar collector is about 20 m, and also its average collector height is about 2 m. A three-dimensional simulation was conducted to analyze the system, using computational fluid dynamics (CFD). In this model, radiative transfer equation was solved using the discrete ordinates (DO) radiation model taking into account a non-gray radiation behavior. In order to modelling solar irradiation from the sun’s rays, the solar ray tracing algorithm was coupled to the computation via a source term in the energy equation. The model was validated with comparing to the experimental data of the Manzanares prototype and also the performance of the built pilot system. Then, based on the numerical simulations, velocity and temperature distributions through the system, the temperature profile of the ground surface and the system performance were presented. The analysis accurately shows the flow and heat transfer characteristics through the pilot system and predicts its performance.

Keywords: buoyancy-driven flow, computational fluid dynamics, heat transfer, renewable energy, solar chimney power plant

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Authors: P. Deepak Kumar, P. R. Maiti

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In recent years, sediment scour near bridge piers and abutment is a serious problem which causes nationwide concern because it has resulted in more bridge failures than other causes. Scour is the formation of scour hole around the structure mounted on and embedded in erodible channel bed due to the erosion of soil by flowing water. The formation of scour hole around the structures depends upon shape and size of the pier, depth of flow as well as angle of attack of flow and sediment characteristics. The flow characteristics around these structures change due to man-made obstruction in the natural flow path which changes the kinetic energy of the flow around these structures. Excessive scour affects the stability of the foundation of the structure by the removal of the bed material. The accurate estimation of scour depth around bridge pier is very difficult. The foundation of bridge piers have to be taken deeper and to provide sufficient anchorage length required for stability of the foundation. In this study, computational model simulations using a 3D Computational Fluid Dynamics (CFD) model were conducted to examine the mechanism of scour around a cylindrical pier. Subsequently, the flow characteristics around these structures are presented for different flow conditions. Mechanism of scouring phenomenon, the formation of vortex and its consequent effect is discussed for a straight channel. Effort was made towards estimation of scour depth around bridge piers under different flow conditions.

Keywords: bridge pier, computational fluid dynamics, multigrid, pier shape, scour

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Authors: Tomoaki Hashimoto

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Model predictive control is a kind of optimal feedback control in which control performance over a finite future is optimized with a performance index that has a moving initial time and a moving terminal time. This paper examines the stability of model predictive control for linear discrete-time systems with additive stochastic disturbances. A sufficient condition for the stability of the closed-loop system with model predictive control is derived by means of a linear matrix inequality. The objective of this paper is to show the results of computational simulations in order to verify the validity of the obtained stability condition.

Keywords: computational simulations, optimal control, predictive control, stochastic systems, discrete-time systems

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Authors: Shachi Pathak

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We are living in knowledge based economy where firms can gain competitive advantage with the help of managing knowledge within the organization. The purpose the study is to develop a conceptual model to explain the relationship between factors affecting knowledge sharing, called as knowledge enablers, in an organization, knowledge sharing activities and organizational performance, using system dynamics approach. This research is important since it will provide better understandings on what are the key knowledge enablers to support knowledge sharing activities, and how knowledge sharing activities will affect the capability of an organization to enhance the performance of the organization.

Keywords: knowledge management, knowledge sharing, organizational performance, system dynamics

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Authors: R. F. B. Gonçalves, E. N. Iwama, J. A. F. F. Rocco, K. Iha

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Propellants based on Hydroxyl Terminated Polybutadiene/Ammonium Perchlorate (HTPB/AP) are the most commonly used in most of the rocket engines used by the Brazilian Armed Forces. This work aimed at the possibility of extending its useful life (currently in 10 years) by performing kinetic-chemical analyzes of its energetic material via Differential Scanning Calorimetry (DSC) and also performing computer simulation of aging process using the software Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). Thermal analysis via DSC was performed in triplicates and in three heating ratios (5 ºC, 10 ºC, and 15 ºC) of rocket motor with 11 years shelf-life, using the Arrhenius equation to obtain its activation energy, using Ozawa and Kissinger kinetic methods, allowing comparison with manufacturing period data (standard motor). In addition, the kinetic parameters of internal pressure of the combustion chamber in 08 rocket engines with 11 years of shelf-life were also acquired, for comparison purposes with the engine start-up data.

Keywords: shelf-life, thermal analysis, Ozawa method, Kissinger method, LAMMPS software, thrust

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Authors: Hafiz Md. HasanBabu, Khandaker Mohammad Mohi Uddin, Md. IstiakJaman Ami, Rahat Hossain Faisal

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Computing in biomolecular programming performs through the different types of reactions. Proteins and nucleic acids are used to store the information generated by biomolecular programming. DNA (Deoxyribose Nucleic Acid) can be used to build a molecular computing system and operating system for its predictable molecular behavior property. The DNA device has clear advantages over conventional devices when applied to problems that can be divided into separate, non-sequential tasks. The reason is that DNA strands can hold so much data in memory and conduct multiple operations at once, thus solving decomposable problems much faster. Programmable Logic Array, abbreviated as PLA is a programmable device having programmable AND operations and OR operations. In this paper, a DNA PLA is designed by different molecular operations using DNA molecules with the proposed algorithms. The molecular PLA could take advantage of DNA's physical properties to store information and perform calculations. These include extremely dense information storage, enormous parallelism, and extraordinary energy efficiency.

Keywords: biological systems, DNA computing, parallel computing, programmable logic array, PLA, DNA

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Authors: Martins Onyekwelu Onuorah, Jnr Dahiru Usman

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Introduction: In the realm of public health, the threat posed by Monkeypox continues to elicit concern, prompting rigorous studies to understand its dynamics and devise effective containment strategies. Particularly significant is its recurrence in variable populations, such as the observed outbreak in Nigeria in 2022. In light of this, our study undertakes a meticulous analysis, employing a data-driven approach to explore, validate, and propose optimized intervention strategies tailored to the distinct dynamics of Monkeypox within varying demographic structures. Utilizing a deterministic mathematical model, we delved into the intricate dynamics of Monkeypox, with a particular focus on a variable population context. Our qualitative analysis provided insights into the disease-free equilibrium, revealing its stability when R0 is less than one and discounting the possibility of backward bifurcation, as substantiated by the presence of a single stable endemic equilibrium. The model was rigorously validated using real-time data from the Nigerian 2022 recorded cases for Epi weeks 1 – 52. Transitioning from qualitative to quantitative, we augmented our deterministic model with optimal control, introducing three time-dependent interventions to scrutinize their efficacy and influence on the epidemic's trajectory. Numerical simulations unveiled a pronounced impact of the interventions, offering a data-supported blueprint for informed decision-making in containing the disease. A comprehensive cost-effectiveness analysis employing the Infection Averted Ratio (IAR), Average Cost-Effectiveness Ratio (ACER), and Incremental Cost-Effectiveness Ratio (ICER) facilitated a balanced evaluation of the interventions’ economic and health impacts. In essence, our study epitomizes a holistic approach to understanding and mitigating Monkeypox, intertwining rigorous mathematical modeling, empirical validation, and economic evaluation. The insights derived not only bolster our comprehension of Monkeypox's intricate dynamics but also unveil optimized, cost-effective interventions. This integration of methodologies and findings underscores a pivotal stride towards aligning public health imperatives with economic sustainability, marking a significant contribution to global efforts in combating infectious diseases.

Keywords: monkeypox, equilibrium states, stability, bifurcation, optimal control, cost-effectiveness

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Authors: Vigen Barkhudaryan

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The influence of external effects (γ-, UV–radiations, high temperature) in presence of air oxygen on structural transformations of low-density polyethylene (LDPE) have been investigated dependent on the polymers’ thickness, the intensity and the dose of external actions. The methods of viscosimetry, light scattering, turbidimetry and gelation measuring were used for this purpose. The comparison of influence of external effects on LDPE shows, that the destruction and cross-linking processes of macromolecules proceed simultaneously with all kinds of external effects. A remarkable growth of average molecular mass of LDPE along with the irradiation doses and heat treatment exposure growth was established. It was linear for the mass average molecular mass and at the initial doses is mainly the result of the increase of the macromolecular branching. As a result, the macromolecular hydrodynamic volumes have been changed, and therefore the dependence of viscosity average molecular mass on the doses was going through the minimum at initial doses. A significant change of molecular mass, sizes and shape of macromolecules of LDPE occurs under the influence of external effects. The influence is limited only by diffusion of oxygen during -irradiation and heat treatment. At UV–irradiation the influence is limited both by diffusion of oxygen and penetration of radiation. Consequently, the molecular transformations are deeper and evident in case of -irradiation, as soon as the polymer is transformed in a whole volume. It was also established, that the mechanism of molecular transformations in polymers from the surface layer distinctly differs from those of the sample deeper layer. A comparison of the results of these investigations allows us to conclude, that the mechanisms of influence of investigated external effects on polyethylene are similar.

Keywords: cross-linking, destruction, high temperature, LDPE, γ-radiations, UV-radiations

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Authors: Shashi Kant Verma, S. L. Sinha, D. K. Chandraker

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Numerical simulations of selected subchannel tracer (Potassium Nitrate) based experiments have been performed to study the capabilities of state-of-the-art of Computational Fluid Dynamics (CFD) codes. The Computational Fluid Dynamics (CFD) methodology can be useful for investigating the spacer effect on turbulent mixing to predict turbulent flow behavior such as Dimensionless mixing scalar distributions, radial velocity and vortices in the nuclear fuel assembly. A Gibson and Launder (GL) Reynolds stress model (RSM) has been selected as the primary turbulence model to be applied for the simulation case as it has been previously found reasonably accurate to predict flows inside rod bundles. As a comparison, the case is also simulated using a standard k-ε turbulence model that is widely used in industry. Despite being an isotropic turbulence model, it has also been used in the modeling of flow in rod bundles and to produce lateral velocities after thorough mixing of coolant fairly. Both these models have been solved numerically to find out fully developed isothermal turbulent flow in a 30º segment of a 54-rod bundle. Numerical simulation has been carried out for the study of natural mixing of a Tracer (Passive scalar) to characterize the growth of turbulent diffusion in an injected sub-channel and, afterwards on, cross-mixing between adjacent sub-channels. The mixing with water has been numerically studied by means of steady state CFD simulations with the commercial code STAR-CCM+. Flow enters into the computational domain through the mass inflow at the three subchannel faces. Turbulence intensity and hydraulic diameter of 1% and 5.9 mm respectively were used for the inlet. A passive scalar (Potassium nitrate) is injected through the mass fraction of 5.536 PPM at subchannel 2 (Upstream of the mixing section). Flow exited the domain through the pressure outlet boundary (0 Pa), and the reference pressure was 1 atm. Simulation results have been extracted at different locations of the mixing zone and downstream zone. The local mass fraction shows uniform mixing. The effect of the applied turbulence model is nearly negligible just before the outlet plane because the distributions look like almost identical and the flow is fully developed. On the other hand, quantitatively the dimensionless mixing scalar distributions change noticeably, which is visible in the different scale of the colour bars.

Keywords: single-phase flow, turbulent mixing, tracer, sub channel analysis

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Authors: Etsuo Morishita

Abstract:

This paper presents the project and experiment-based fluid dynamics education in Meisei University, a private institution in Tokyo, Japan. We pay attention not only to the basic engineering courses but also to the practical aspect of engineering experience. So, we prepare courses called the Projects from I to VI. The Projects I and II are designed for the first year, III and IV are designated for the second year, V and VI are prepared for the third year, respectively. Each supervisor is responsible for two of these projects every year. When students take the Project V and VI at the third year, we automatically assume that these students will join the lab of the project for the graduation thesis. We would like to show our experience in the Project I in the summer term, 2016. In this project, we introduce a traction flight vehicle called Cat Flyer. This is a kind of a kite towed by a car for example. This is very similar to parasailing, but flight is possible even on the roads. Experiments in mechanical engineering education are also very important, and we would like to explain our course on centrifugal pump, venture, and orifice. Although these are described in detail in the text books of fluid dynamics, it is still crucial to have practical experiments as a student.

Keywords: aerodynamics, experiment, fluid dynamics, project

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Authors: T. G. Kassem, A. K. Adunchezor, J. P. Chollom

Abstract:

This paper describes a mathematical model developed to predict the dynamics of Hepatitis B virus (HBV) infection and to evaluate the potential impact of vaccination and treatment on its dynamics. We used a compartmental model expressed by a set of differential equations based on the characteristic of HBV transmission. With these, we find the threshold quantity R0, then find the local asymptotic stability of disease free equilibrium and endemic equilibrium. Furthermore, we find the global stability of the disease free and endemic equilibrium.

Keywords: hepatitis B virus, epidemiology, vaccination, mathematical model

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Authors: Salem El-Tohami Ashoor

Abstract:

A novel new vanadium (IV) complexes incorporating the chelating diamido cyclopentadienyl {ArN(CH2)3NAr)}2-((ηn-Cp)Cp)} (Ar = 2,6-Pri2C6H3)(Cp = C5H5 and n = 1,2,3,4 and 5) have been studied with calculation of the properties of species involved in various of cyclopentadienyl reaction. These were carried out under investigation of density functional theory (DFT) calculation, and comparing together. Other methods, explicitly including electron correlation, are necessary for more accurate calculations; MB3LYP (Becke) (Lee–Yang–Parr) level of theory often being used to obtain more exact results. These complexes were estimated of electronic energy for molecular system, because it accounts for all electron correlation interactions. The optimised of [V(ArN(CH2)3NAr)2Cl(η5-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) was found to be thermally more stable than others of vanadium cyclopentadienyl. In the meantime the complex [V(ArN(CH2)3NAr)2Cl(η1-Cp)] (Ar = 2,6-Pri2C6H3 and Cp= C5H5) which is showed a low thermal stability in case of the just one carbon of cyclopentadienyl can be insertion with vanadium metal centre. By using Dewar-Chatt-Duncanson model, as a basis of the molecular orbital (MO) analysis and showed the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital LUMO.

Keywords: vanadium (IV) cyclopentadienyl complexes, DFT, MO, HOMO, LUMO

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Authors: Khaled Suleiman Mohammed Al-Mashrafi

Abstract:

A compositional plume is a fluid flow in a directional channel of finite width in another fluid of different material composition. The study of the dynamics of compositional plumes plays an essential role in many real-life applications like industrial applications (e.g., iron casting), environmental applications (e.g., salt fingers and sea ice), and geophysical applications (e.g., solidification at the inner core boundary (ICB) of the Earth, and mantle plumes). The dynamics of compositional plumes have been investigated experimentally and theoretically. The experimental works observed that the plume flow seems to be stable, although some experiments showed that it can be unstable. At the same time, the theoretical investigations showed that the plume flow is unstable. This is found to be true even if the plume is subject to rotation or/and in the presence of a magnetic field and even if another plume of different composition is also present. It is noticeable that all the theoretical studies on the dynamics of compositional plumes are conducted in unbounded domains. The present work is to investigate theoretically the influence of vertical walls (boundaries) on the dynamics of compositional plumes in the absence/presence of a rotation field. The mathematical model of the dynamics of compositional plumes used the equations of continuity, motion, heat, concentration of light material, and state. It is found that the presence of boundaries has a strong influence on the basic state solution as well as the stability of the plume, particularly when the plume is close to the boundary, but the compositional plume remains unstable.

Keywords: compositional plumes, stability, bounded domain, vertical boundaries

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