Search results for: computational fluid dynamics "CFD"

Authors: Snigdha Sahai, Devaki Chikkavenkatappa Yellappa

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This study outlines approaches for testing and validating stochastic models used in epidemiology, focusing on the integration and functional testing of simulation code. It details methods for combining simple functions into comprehensive simulations, distinguishing between deterministic and stochastic components, and applying tests to ensure robustness. Techniques include isolating stochastic elements, utilizing large sample sizes for validation, and handling special cases. Practical examples are provided using R code to demonstrate integration testing, handling of incorrect inputs, and special cases. The study emphasizes the importance of both functional and defensive programming to enhance code reliability and user-friendliness.

Keywords: computational epidemiology, epidemiology, public health, infectious disease modeling, statistical analysis, health data analysis, disease transmission dynamics, predictive modeling in health, population health modeling, quantitative public health, random sampling simulations, randomized numerical analysis, simulation-based analysis, variance-based simulations, algorithmic disease simulation, computational public health strategies, epidemiological surveillance, disease pattern analysis, epidemic risk assessment, population-based health strategies, preventive healthcare models, infection dynamics in populations, contagion spread prediction models, survival analysis techniques, epidemiological data mining, host-pathogen interaction models, risk assessment algorithms for disease spread, decision-support systems in epidemiology, macro-level health impact simulations, socioeconomic determinants in disease spread, data-driven decision making in public health, quantitative impact assessment of health policies, biostatistical methods in population health, probability-driven health outcome predictions

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Authors: Mina Rabipour, Elena Pallaske, Floyd Hassenrück, Rocio Rebollido-Rios

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Protein tyrosine kinases, including Lyn kinase of the Src family kinases (SFK), regulate cell proliferation, survival, and differentiation. Lyn kinase has been implicated in various cancers, positioning it as a promising therapeutic target. However, the conserved ATP-binding pocket across SFKs makes developing selective inhibitors challenging. This study aims to address this limitation by exploring the potential for allosteric modulation of Lyn kinase, focusing on how its structural dynamics and specific oncogenic mutations impact its conformation and function. To achieve this, we combined homology modeling, molecular dynamics simulations, and data science techniques to conduct microsecond-length simulations. Our approach allowed a detailed investigation into the interplay between Lyn’s catalytic and regulatory domains, identifying key conformational states involved in allosteric regulation. Additionally, we evaluated the structural effects of Dasatinib, a competitive inhibitor, and ATP binding on Lyn active conformation. Notably, our simulations show that cancer-related mutations, specifically I364L/N and E290D/K, shift Lyn toward an inactive conformation, contrasting with the active state of the wild-type protein. This may suggest how these mutations contribute to aberrant signaling in cancer cells. We conducted a dynamical network analysis to assess residue-residue interactions and the impact of mutations on the Lyn intramolecular network. This revealed significant disruptions due to mutations, especially in regions distant from the ATP-binding site. These disruptions suggest potential allosteric sites as therapeutic targets, offering an alternative strategy for Lyn inhibition with higher specificity and fewer off-target effects compared to ATP-competitive inhibitors. Our findings provide insights into Lyn kinase regulation and highlight allosteric sites as avenues for selective drug development. Targeting these sites may modulate Lyn activity in cancer cells, reducing toxicity and improving outcomes. Furthermore, our computational strategy offers a scalable approach for analyzing other SFK members or kinases with similar properties, facilitating the discovery of selective allosteric modulators and contributing to precise cancer therapies.

Keywords: lyn tyrosine kinase, mutation analysis, conformational changes, dynamic network analysis, allosteric modulation, targeted inhibition

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Authors: Bang-Fuh Chen, Chih-Chun Chu

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The flow induced cylinder vibration or earthquake-induced cylinder motion are moving in an arbitrary direction with time. The phenomenon of flow across cylinder is highly nonlinear and a linear-superposition of flow pattern across separated oscillating direction of cylinder motion is not valid to obtain the flow pattern across a cylinder oscillating in multiple directions. A novel finite difference scheme is developed to simulate the viscous flow across an arbitrary moving circular cylinder and we call this a complete 2D (two-dimensional) flow-cylinder interaction. That is, the cylinder is simultaneously oscillating in x- and y- directions. The time-dependent domain and meshes associated with the moving cylinder are mapped to a fixed computational domain and meshes, which are time independent. The numerical results are validated by several bench mark studies. Several examples are introduced including flow across steam-wise, transverse oscillating cylinder and flow across rotating cylinder and flow across arbitrary moving cylinder. The Morison’s formula can not describe the complex interaction phenomenon between cross flow and oscillating circular cylinder. And the completed 2D computational fluid dynamic analysis should be made to obtain the correct hydrodynamic force acting on the cylinder.

Keywords: 2D cylinder, finite-difference method, flow-cylinder interaction, flow induced vibration

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Authors: Nazeef, Suleiman, Umar, Danladi Muhammad, Ja'afar Ali, Zaliha Adamu Umar

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The population dynamics of Auchenoglanis occidentalis from the Dadin-Kowa reservoir were studied. Population dynamic parameters such as growth, mortality and recruitment patterns were analyzed using length frequency data over a 12-month period employing FiSAT II software. Findings revealed that LWR (b - constant) = 2.88, K = 0.72 -yr., L∞ = 40.91 cm and Tmax = 3.57 years and Ɵ’ = 3.14. Mortality indices revealed that natural mortality (M = 1.39), fishing mortality (F = 0.22) and exploitation ratio (E = 0.14), Lc/L∞ = 0.48, Emax = 0.64, while Lopt = 26.4 cm. Uni-modal recruitment peak observed with Lm = 27.3 cm. A restocking program is suitable to ensure its continuous existence as it seems to have a low population.

Keywords: fish population dynamics, auchenoglanis occidentalis, FISAT II, natural mortality

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Authors: M. Salmanpour, O. Nourani Zonouz

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In this research, a numerical simulation of an Electrohydrodynamic (EHD) actuator’s effects on the flow around a square cylinder by using a finite volume method has been investigated. This is one of the newest ways for controlling the fluid flows. Two plate electrodes are flush-mounted on the surface of the cylinder and one wire electrode is placed on the line with zero angle of attack relative to the stagnation point and excited with DC power supply. The discharge produces an electric force and changes the local momentum behaviors in the fluid layers. For this purpose, after selecting proper domain and boundary conditions, the electric field relating to the problem has been analyzed and then the results in the form of electrical body force have been entered in the governing equations of fluid field (Navier-Stokes equations). The effect of ionic wind resulted from the Electrohydrodynamic actuator, on the velocity, pressure and the wake behind cylinder has been considered. According to the results, it is observed that the fluid flow accelerates in the nearest wall of the frontal half of the cylinder and the pressure difference between frontal and hinder cylinder is increased.

Keywords: CFD, corona discharge, electro hydrodynamics, flow around square cylinders, simulation

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Authors: Gamaliel Salazar, Adriana Chazaro, Oscar Madrigal

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The evolution of Unmanned Aerial Systems (UAS) has made it possible to develop new vehicles capable to perform microgravity experiments which due its cost and complexity were beyond the reach for many institutions. In this study, the aerodynamic behavior of an UAS is studied through its deceleration stage after an initial free fall phase (where the microgravity effect is generated) using Computational Fluid Dynamics (CFD). Due to the fact that the payload would be analyzed under a microgravity environment and the nature of the payload itself, the speed of the UAS must be reduced in a smoothly way. Moreover, the terminal speed of the vehicle should be low enough to preserve the integrity of the payload and vehicle during the landing stage. The UAS model is made by a study pod, control surfaces with fixed and mobile sections, landing gear and two semicircular wing sections. The speed of the vehicle is decreased by increasing the angle of attack (AoA) of each wing section from 2° (where the airfoil S1091 has its greatest aerodynamic efficiency) to 80°, creating a circular wing geometry. Drag coefficients (Cd) and forces (Fd) are obtained employing CFD analysis. A simplified 3D model of the vehicle is analyzed using Ansys Workbench 16. The distance between the object of study and the walls of the control volume is eight times the length of the vehicle. The domain is discretized using an unstructured mesh based on tetrahedral elements. The refinement of the mesh is made by defining an element size of 0.004 m in the wing and control surfaces in order to figure out the fluid behavior in the most important zones, as well as accurate approximations of the Cd. The turbulent model k-epsilon is selected to solve the governing equations of the fluids while a couple of monitors are placed in both wing and all-body vehicle to visualize the variation of the coefficients along the simulation process. Employing a statistical approximation response surface methodology the case of study is parametrized considering the AoA of the wing as the input parameter and Cd and Fd as output parameters. Based on a Central Composite Design (CCD), the Design Points (DP) are generated so the Cd and Fd for each DP could be estimated. Applying a 2nd degree polynomial approximation the drag coefficients for every AoA were determined. Using this values, the terminal speed at each position is calculated considering a specific Cd. Additionally, the distance required to reach the terminal velocity at each AoA is calculated, so the minimum distance for the entire deceleration stage without comprising the payload could be determine. The Cd max of the vehicle is 1.18, so its maximum drag will be almost like the drag generated by a parachute. This guarantees that aerodynamically the vehicle can be braked, so it could be utilized for several missions allowing repeatability of microgravity experiments.

Keywords: microgravity effect, response surface, terminal speed, unmanned system

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Authors: Ya Lv

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This article presents the application of the semi-analytic method (SAM) in the thermal management solution (TMS) of the energy storage system (ESS). The TMS studied in this work is fluid cooling. In fluid cooling, both effective heat conduction and heat convection are indispensable due to the heat transfer from solid to fluid. Correspondingly, an efficient TMS requires a design investigation of the following parameters: fluid inlet temperature, ESS initial temperature, fluid flow rate, working c rate, continuous working time, and materials properties. Their variation induces a change of thermal performance in the battery module, which is usually evaluated by numerical simulation. Compared to complicated computation resources and long computation time in simulation, the SAM is developed in this article to predict the thermal influence within a few seconds. In SAM, a fast prediction model is reckoned by combining numerical simulation with theoretical/empirical equations. The SAM can explore the thermal effect of boundary parameters in both steady-state and transient heat transfer scenarios within a short time. Therefore, the SAM developed in this work can simplify the design cycle of TMS and inspire more possibilities in TMS design.

Keywords: semi-analytic method, fast prediction model, thermal influence of boundary parameters, energy storage system

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Authors: Islam Tarek, Moataz Soliman

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With the amazing development of nanoscience’s and the discovery of the unique properties of nanometric materials, the ideas of scientists and researchers headed to take advantage of this progress in various fields, and one of the most important of these areas is the field of heat transfer and benefit from it in saving energy used for heat transfer, so nanometric materials were used to improve the properties of heat transfer fluids and increase the efficiency of the liquid. In this paper, we will compare two types of heat transfer fluid, one industrial type (the base fluid is a mix of ethylene glycol and deionized water ) and another natural oils(the base fluid is a mix of jatropha oil and expired olive oil), explaining the method of preparing each of them, starting from the method of preparing CNT, collecting and sorting jatropha seeds, and the most appropriate method for extracting oil from them, and characterization the both of two fluids and when to use both.

Keywords: nanoscience, heat transfer, thermal conductivity, jatropha oil

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Authors: G. V. Novikov, V. S. Sivozhelezov, S. S. Kolesnikov, K. V. Shaitan

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The study reports about the influence of binding of orthosteric ligands as well as point mutations on the conformational dynamics of β-2-adrenoreceptor. Using molecular dynamics simulation we found that there was a little fraction of active states of the receptor in its apo (ligand free) ensemble corresponded to its constitutive activity. Analysis of MD trajectories indicated that such spontaneous activation of the receptor is accompanied by the motion in intracellular part of its alpha-helices. Thus receptor’s constitutive activity directly results from its conformational dynamics. On the other hand the binding of a full agonist resulted in a significant shift of the initial equilibrium towards its active state. Finally, the binding of the inverse agonist stabilized the receptor in its inactive state. It is likely that the binding of inverse agonists might be a universal way of constitutive activity inhibition in vivo. Our results indicate that ligand binding redistribute pre-existing conformational degrees of freedom (in accordance to the Monod-Wyman-Changeux-Model) of the receptor rather than cause induced fit in it. Therefore, the ensemble of biologically relevant receptor conformations is encoded in its spatial structure, and individual conformations from that ensemble might be used by the cell in conformity with the physiological behaviour.

Keywords: seven-transmembrane receptors, constitutive activity, activation, x-ray crystallography, principal component analysis, molecular dynamics simulation

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Authors: Benkherbache Souad

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This work presents the numerical results of the mixed convective heat transfer of a three-dimensional flow around a radial heat sink composed of horizontal circular base fitted with rectangular fins. The governing equations of mass, momentum, and energy equation are solved by the finite volume method using the commercially available CFD software Fluent 6.3.26. The circular base of the heat sink is subjected to uniform heat generation; the flow enters through the sides of the heat sink around the fins then the heat is transmitted from the base to the fins afterwards the fluid. In this study two fluids are utilized, in the first case, the air for the following Reynolds numbers Re=600,900,1200 and a Grashof number Gr=3.7x10⁶, in the second case a water based nano fluid for which two types of nano particles (Cu and Al₂O₃) are carried out for Re=25 and a Richardson number Ri=2.7(Ri=Gr/Re²). The effect of the number of the fins of the heat sink as well as the type and the volume fraction of nano particles of the nano fluid were investigated. Results have been presented for N=15 and N=20 fins. The effect of the nano particles concentrations and the number of fins on the temperature in the heat sink and the Nusselt number has been studied.

Keywords: heat sink, mixed convection, nano fluid, volumetric heat generation

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Authors: Sang Ho Lee, Tae Heon Moon, Youn Taik Leem, Kwang Woo Nam

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Knowledge and IT inputs to other industrial production have become more important as a key factor for the competitiveness of national and regional economies, such as knowledge economies in smart cities. Knowledge and IT industries lead the industrial innovation and technical (r)evolution through low cost, high efficiency in production, and by creating a new value chain and new production path chains, which is referred as knowledge and IT dynamics. This study aims to investigate the knowledge and IT dynamics in Korea, which are analyzed through the input-output model and structural path analysis. Twenty-eight industries were reclassified into seven categories; Agriculture and Mining, IT manufacture, Non-IT manufacture, Construction, IT-service, Knowledge service, Non-knowledge service to take close look at the knowledge and IT dynamics. Knowledge and IT dynamics were analyzed through the change of input output coefficient and multiplier indices in terms of technical innovation, as well as the changes of the structural paths of the knowledge and IT to other industries in terms of new production value creation from 1985 and 2010. The structural paths of knowledge and IT explain not only that IT foster the generation, circulation and use of knowledge through IT industries and IT-based service, but also that knowledge encourages IT use through creating, sharing and managing knowledge. As a result, this paper found the empirical investigation on the knowledge and IT dynamics of the Korean economy. Knowledge and IT has played an important role regarding the inter-industrial transactional input for production, as well as new industrial creation. The birth of the input-output production path has mostly originated from the knowledge and IT industries, while the death of the input-output production path took place in the traditional industries from 1985 and 2010. The Korean economy has been in transition to a knowledge economy in the Smart City.

Keywords: knowledge and IT industries, input-output model, structural path analysis, dynamics of knowledge and it, knowledge economy, knowledge city and smart city

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Authors: Karim Kheloufi, El Hachemi Amara

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In the present study, a three-dimensional transient numerical model was developed to study the temperature field and cutting kerf shape during laser fusion cutting. The finite volume model has been constructed, based on the Navier–Stokes equations and energy conservation equation for the description of momentum and heat transport phenomena, and the Volume of Fluid (VOF) method for free surface tracking. The Fresnel absorption model is used to handle the absorption of the incident wave by the surface of the liquid metal and the enthalpy-porosity technique is employed to account for the latent heat during melting and solidification of the material. To model the physical phenomena occurring at the liquid film/gas interface, including momentum/heat transfer, a new approach is proposed which consists of treating friction force, pressure force applied by the gas jet and the heat absorbed by the cutting front surface as source terms incorporated into the governing equations. All these physics are coupled and solved simultaneously in Fluent CFD®. The main objective of using a transient phase change model in the current case is to simulate the dynamics and geometry of a growing laser-cutting generated kerf until it becomes fully developed. The model is used to investigate the effect of some process parameters on temperature fields and the formed kerf geometry.

Keywords: laser cutting, numerical simulation, heat transfer, fluid flow

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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: Taher M. Abou-deif, Esmail M. El-Bialy, Essam E. Khalil

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The paper is devoted to numerically investigating the influence of the air supply outlets geometry on human comfort inside living looms. A computational fluid dynamics model is developed to examine the air flow characteristics of a room with different supply air diffusers. The work focuses on air flow patterns, thermal behavior in the room with few number of occupants. As an input to the full-scale 3-D room model, a 2-D air supply diffuser model that supplies direction and magnitude of air flow into the room is developed. Air distribution effect on thermal comfort parameters was investigated depending on changing the air supply diffusers type, angles and velocity. Air supply diffusers locations and numbers were also investigated. The pre-processor Gambit is used to create the geometric model with parametric features. Commercially available simulation software “Fluent 6.3” is incorporated to solve the differential equations governing the conservation of mass, three momentum and energy in the processing of air flow distribution. Turbulence effects of the flow are represented by the well-developed two equation turbulence model. In this work, the so-called standard k-ε turbulence model, one of the most widespread turbulence models for industrial applications, was utilized. Basic parameters included in this work are air dry bulb temperature, air velocity, relative humidity and turbulence parameters are used for numerical predictions of indoor air distribution and thermal comfort. The thermal comfort predictions through this work were based on ADPI (Air Diffusion Performance Index),the PMV (Predicted Mean Vote) model and the PPD (Percentage People Dissatisfied) model, the PMV and PPD were estimated using Fanger’s model.

Keywords: thermal comfort, Fanger's model, ADPI, energy effeciency

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Authors: H. Abchiche, M. Mellal

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The aim of this work is to study the parameters that influence the rheological behavior of a complex fluid (sodium Carboxyméthylcellulose solution), on a capillary rheometer. An installation has been made to be able to vary the diameter of trial conducts. The obtained results allowed us to deduce that: the diameter of trial conducts have a remarkable effect on the rheological responds.

Keywords: bingham’s fluid, CMC, cylindrical conduit, rheological behavior

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Authors: K. P. Mredula, D. C. Vakaskar

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The article traces developments and evolution of various algorithms developed for solving partial differential equations using the significant combination of wavelet with few already explored solution procedures. The approach depicts a study over a decade of traces and remarks on the modifications in implementing multi-resolution of wavelet, finite difference approach, finite element method and finite volume in dealing with a variety of partial differential equations in the areas like plasma physics, astrophysics, shallow water models, modified Burger equations used in optical fibers, biology, fluid dynamics, chemical kinetics etc.

Keywords: multi-resolution, Haar Wavelet, partial differential equation, numerical methods

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Authors: W. Hamaidia, T. Zebbiche

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This paper presents the design of axisymmetric supersonic nozzles, in order to accelerate a supersonic flow to the desired Mach number and that having a small weight, in the same time gives a high thrust. The concerned nozzle gives a parallel and uniform flow at the exit section. The nozzle is divided into subsonic and supersonic regions. The supersonic portion is independent to the upstream conditions of the sonic line. The subsonic portion is used to give a sonic flow at the throat. In this case, nozzle gives a uniform and parallel flow at the exit section. It’s named by minimum length Nozzle. The study is done at high temperature, lower than the dissociation threshold of the molecules, in order to improve the aerodynamic performances. Our aim consists of improving the performances both by the increase of exit Mach number and the thrust coefficient and by reduction of the nozzle's mass. The variation of the specific heats with the temperature is considered. The design is made by the Method of Characteristics. The finite differences method with predictor-corrector algorithm is used to make the numerical resolution of the obtained nonlinear algebraic equations. The application is for air. All the obtained results depend on three parameters which are exit Mach number, the stagnation temperature, the chosen mesh in characteristics. A numerical simulation of nozzle through Computational Fluid Dynamics-FASTRAN was done to determine and to confirm the necessary design parameters.

Keywords: flux supersonic flow, axisymmetric minimum length nozzle, high temperature, method of characteristics, calorically imperfect gas, finite difference method, trust coefficient, mass of the nozzle, specific heat at constant pressure, air, error

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Authors: Akram Rasheed

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Background: Simulation in the health care field has been increasingly used over the last years in the training of resuscitation and life support practices. It has shown the advantage of improving the decision-making and technical skills through deliberate practice and return demonstration. Local Problem: This article reports on the integration of simulation-based training (SBT) in the training program about proper team dynamics and leadership skills during cardiopulmonary resuscitation (CPR) in the intensive care unit (ICU). Method and Intervention: Training of 180 critical care nurses was conducted using SBT between 1st January and 30th 2020. We had conducted 15 workshops, with the integration of SBT using high fidelity manikins and using demonstration and return-demonstration approach to train the nursing staff about proper team dynamics and leadership skills during CPR. Results: After completing the SBT session, all 180 nurses completed the evaluation form. The majority of evaluation items were rated over 95% for the effectiveness of the education; four items were less than 95% (88–94%). Lower rated items considered training and practice time, improved competency, and commitment to apply to learn. The team dynamics SBT was evaluated as an effective means to improve team dynamics and leadership skills during CPR in the intensive care unit (ICU). Conclusion: The use of simulation-based training to improve team dynamics and leadership skills is an effective method for better patient management during CPR. Besides skills competency, closed-loop communication, clear messages, clear roles, and assignments, knowing one’s limitations, knowledge sharing, constructive interventions, re-evaluating and summarizing, and mutual respect are all important concepts that should be considered during team dynamics training. However, participants reported the need for a repeated practice opportunity to build competency.

Keywords: cardiopulmonary resuscitation, high fidelity manikins, simulation-based training, team dynamics

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Authors: Kiran Kumar K., Ramesh Babu Bejjam, Atul Najan

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A thermosyphon system is a heat transfer loop which operates on the basis of gravity and buoyancy forces. It guarantees a good reliability and low maintenance cost as it does not involve any mechanical pump. Therefore it can be used in many industrial applications such as refrigeration and air conditioning, electronic cooling, nuclear reactors, geothermal heat extraction, etc. But flow instabilities and loop configuration are the major problems in this system. Several previous researchers studied that stabilities can be suppressed by using nanofluids as loop fluid. In the present study a rectangular thermosyphon loop with end heat exchangers are considered for the study. This configuration is more appropriate for many practical applications such as solar water heater, geothermal heat extraction, etc. In the present work, steady-state analysis is carried out on thermosyphon loop with parallel flow coaxial heat exchangers at heat source and heat sink. In this loop nano fluid is considered as the loop fluid and water is considered as the external fluid in both hot and cold heat exchangers. For this analysis one-dimensional homogeneous model is developed. In this model, conservation equations like conservation of mass, momentum, energy are discretized using finite difference method. A computer code is written in MATLAB to simulate the flow in thermosyphon loop. A comparison in terms of heat transfer is made between water and nano fluid as working fluids in the loop.

Keywords: heat exchanger, heat transfer, nanofluid, thermosyphon loop

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Authors: Adam Abate, Elham Rasti, Philip Romero

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Beta-glucosidase is the key enzyme component present in cellulase and completes the final step during cellulose hydrolysis by converting the cellobiose to glucose. The regulatory properties of beta-glucosidases are most commonly found for the retaining and inverting enzymes. Hydrolysis of a glycoside typically occurs with general acid and general base assistance from two amino acid side chains, normally glutamic or aspartic acids. In order to obtain more detailed information on the dynamic events origination from the interaction with enzyme active site, we carried out molecular dynamics simulations of beta-glycosidase in protonated state (Glu-H178) and deprotonated state (Glu178). The theoretical models generated from our molecular dynamics simulations complement and advance the structural information currently available, leading to a more detailed understanding of Beta-glycosidase structure and function. This article presents the important role of Asn307 in enzyme activity of beta-glucosidase

Keywords: Beta-glucosidase, GROMACS, molecular dynamics simulation, structural parameters

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Authors: Eunae Lee, Oh-Kuen Kwon, Ki-Sub Kim, Jeong Won Kang

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We investigated the dynamic properties of graphene-nanoribbon (GNR) memory encapsulating graphene-nanoflake (GNF) shuttle in the potential to be applicable as a non-volatile random access memory via molecular dynamics simulations. This work explicitly demonstrates that the GNR encapsulating the GNF shuttle can be applied to nonvolatile memory. The potential well was originated by the increase of the attractive vdW energy between the GNRs when the GNF approached the edges of the GNRs. So the bistable positions were located near the edges of the GNRs. Such a nanoelectromechanical non-volatile memory based on graphene is also applicable to the development of switches, sensors, and quantum computing.

Keywords: graphene nanoribbon, graphene nanoflake, shuttle memory, molecular dynamics

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Authors: Exa Heydemans, Jessica Sjah, Dwinanti Rika Marthanty

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This paper presents numerical simulations using an open boundary algorithm with modified dynamic boundary condition (mDBC) for weakly compressible smoothed particle hydrodynamics models from particle-based code Dualsphysics. The problems of piping erosion in dams and dikes are aimed for studying the algorithm. The case 2D model of unsteady fluid flow past around a fixed cylinder is simulated, where various values of Reynold’s numbers (Re40, Re60, Re80, and Re100) and different model’s resolution are considered. A constant velocity with different values of viscosity for generating various Reynold’s numbers and different numbers of particles over a cylinder for the resolution are modeled. The interaction between solid particles of the cylinder and fluid particles is concerned. The cylinder is affected by the hydrodynamics force caused by the flow of fluid particles. The solid particles of the cylinder are the observation points to obtain force and pressure due to the hydrodynamics forces. As results of the simulation, which is to show the capability to model 2D unsteady with various Reynold’s numbers, the pressure coefficient, drag coefficient, lift coefficient, and Strouhal number are compared to the previous work from literature.

Keywords: hydrodynamics, internal erosion, dualsphysics, viscous fluid flow

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Authors: Yu Zhang, Kohei Inoue, Kiichi Urahama

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We propose a simplified bilateral filter with binarized coefficients for accelerating it. Its computational cost is further decreased by sampling pixels. This computationally low cost filter is useful for smoothing or denoising images by using mobile devices with limited computational power.

Keywords: bilateral filter, binarized-weight bilateral filter, image smoothing, image denoising, pixel sampling

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Authors: Abdelkader Harrouz, Omar Harrouz, Ali Benatiallah

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This paper is to present the essential definitions, roles and characteristics of automation of metering system. We discuss measurement, data acquisition and metrological control of a signal sensor from dynamic metering system. After that, we present control of instruments of metering system of fluid with more detailed discussions to the reference standards.

Keywords: communication, metering, computer, sensor

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Authors: Roghayyeh Motallebzadeh, Shahin Hajizadeh, Mohammad Reza Ghasemi

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Laminar mixed convection heat transfer of a nanofluid with prescribed constant heat flux on the inner wall of horizontal annular tube has been studied numerically based on two-phase mixture model in different Rayleigh numbers and Azimuth angles. Effects of applying of different volume fractions of Al2O3 nanoparticles in water as a base fluid on hydrodynamic and thermal behaviours of the fluid flow such as axial velocity, secondary flow, temperature, heat transfer coefficient and friction coefficient at the inner and outer wall region, has been investigated. Conservation equations in elliptical form has been utilized and solved in three dimensions for a steady flow. It is observed that, there is a good agreement between results in this work and previously published experimental and numerical works on mixed convection in horizontal annulus. These particles cause to increase convection heat transfer coefficient of the fluid, meanwhile there is no considerable effect on friction coefficient.

Keywords: buoyancy force, laminar mixed convection, mixture model, nano-fluid, two-phase

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Authors: Khachatur V. Nerkararyan, Sergey I. Bozhevolnyi

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We investigate relaxation dynamics of a quantum dipole emitter (QDE), e.g., a molecule or quantum dot, located near a metal nanoparticle (MNP) exhibiting a dipolar localized surface plasmon (LSP) resonance at the frequency of the QDE radiative transition. It is shown that under the condition of the QDE-MNP characteristic relaxation time being much shorter than that of the QDE in free-space but much longer than the LSP lifetime. It is also shown that energy dissipation in the QDE-MNP system is relatively weak with the probability of the photon emission being about 0.75, a number which, rather surprisingly, does not explicitly depend on the metal absorption characteristics. The degree of entanglement measured by the concurrency takes the maximum value, while the distances between the QDEs and metal ball approximately are equal.

Keywords: metal nanoparticle, localized surface plasmon, quantum dipole emitter, relaxation dynamics

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Authors: Masato Saeki

Abstract:

Presented herein is a novel algorithms for calculating the damping performance of particle dampers. The particle damper is a passive vibration control technique and has many practical applications due to simple design. It consists of granular materials constrained to move between two ends in the cavity of a primary vibrating system. The damping effect results from the exchange of momentum during the impact of granular materials against the wall of the cavity. This damping has the advantage of being independent of the environment. Therefore, particle damping can be applied in extreme temperature environments, where most conventional dampers would fail. It was shown experimentally in many papers that the efficiency of the particle dampers is high in the case of resonant vibration. In order to use the particle dampers effectively, it is necessary to solve the equations of motion for each particle, considering the granularity. The discrete element method (DEM) has been found to be effective for revealing the dynamics of particle damping. In this method, individual particles are assumed as rigid body and interparticle collisions are modeled by mechanical elements as springs and dashpots. However, the computational cost is significant since the equation of motion for each particle must be solved at each time step. In order to improve the computational efficiency of the DEM, the new algorithms are needed. In this study, new algorithms are proposed for implementing the high performance DEM. On the assumption that behaviors of the granular particles in the each divided area of the damper container are the same, the contact force of the primary system with all particles can be considered to be equal to the product of the divided number of the damper area and the contact force of the primary system with granular materials per divided area. This convenience makes it possible to considerably reduce the calculation time. The validity of this calculation method was investigated and the calculated results were compared with the experimental ones. This paper also presents the results of experimental studies of the performance of particle dampers. It is shown that the particle radius affect the noise level. It is also shown that the particle size and the particle material influence the damper performance.

Keywords: particle damping, discrete element method (DEM), granular materials, numerical analysis, equivalent noise level

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Authors: S. Jurado, E. Pazmino

Abstract:

Determination of the medial axis of a porous media sample is a non-trivial problem of interest for several disciplines, e.g., hydrology, fluid dynamics, contaminant transport, filtration, oil extraction, etc. However, the computational tools available for researchers are limited and restricted. The primary aim of this work was to develop a series of algorithms to extract porosity, medial axis structure, and pore-throat size distributions from porous media domains. A complementary objective was to provide the algorithms as free computational software available to the academic community comprising researchers and students interested in 3D data processing. The burn algorithm was tested on porous media data obtained from High-Resolution X-Ray Microtomography (HRXMT) and idealized computer-generated domains. The real data and idealized domains were discretized in voxels domains of 550³ elements and binarized to denote solid and void regions to determine porosity. Subsequently, the algorithm identifies the layer of void voxels next to the solid boundaries. An iterative process removes or 'burns' void voxels in sequence of layer by layer until all the void space is characterized. Multiples strategies were tested to optimize the execution time and use of computer memory, i.e., segmentation of the overall domain in subdomains, vectorization of operations, and extraction of single burn layer data during the iterative process. The medial axis determination was conducted identifying regions where burnt layers collide. The final medial axis structure was refined to avoid concave-grain effects and utilized to determine the pore throat size distribution. A graphic user interface software was developed to encompass all these algorithms, including the generation of idealized porous media domains. The software allows input of HRXMT data to calculate porosity, medial axis, and pore-throat size distribution and provide output in tabular and graphical formats. Preliminary tests of the software developed during this study achieved medial axis, pore-throat size distribution and porosity determination of 100³, 320³ and 550³ voxel porous media domains in 2, 22, and 45 minutes, respectively in a personal computer (Intel i7 processor, 16Gb RAM). These results indicate that the software is a practical and accessible tool in postprocessing HRXMT data for the academic community.

Keywords: medial axis, pore-throat distribution, porosity, porous media

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Authors: Juan Antonio Mondragon Sanchez, Ruben Santamaria

Abstract:

The DNA G-quadruplex is a four-stranded DNA structure formed by stacked planes of four base paired guanines (G-quartet). Guanine rich DNA sequences appear in many sites of genomic DNA and can potential form G-quadruplexes, such as those occurring at 3'-terminus of the human telomeric DNA. The formation and stabilization of a G-quadruplex by small ligands at the telomeric region can inhibit the telomerase activity. In turn, the ligands can be used to down regulate oncogene expression making G-quadruplex an attractive target for anticancer therapy. Many G-quadruplex ligands have been proposed with a planar core to facilitate the pi–pi stacking and electrostatic interactions with the G-quartets. However, many drug candidates are impossibilitated to discriminate a G-quadruplex from a double helix DNA structure. In this context, it is important to investigate the site topology for the interaction of a G-quadruplex with a ligand. In this work, we determine the free energy surface of a G-quadruplex-ligand to study the binding modes of the G-quadruplex (TG4T) with the daunomycin (DM) drug. The complex TG4T-DM is studied using classical molecular dynamics in combination with metadynamics simulations. The metadynamics simulations permit an enhanced sampling of the conformational space with a modest computational cost and obtain free energy surfaces in terms of the collective variables (CV). The free energy surfaces of TG4T-DM exhibit other local minima, indicating the presence of additional binding modes of daunomycin that are not observed in short MD simulations without the metadynamics approach. The results are compared with similar calculations on a different structure (the mutated mu-G4T-DM where the 5' thymines on TG4T-DM have been deleted). The results should be of help to design new G-quadruplex drugs, and understand the differences in the recognition topology sites of the duplex and quadruplex DNA structures in their interaction with ligands.

Keywords: g-quadruplex, cancer, molecular dynamics, metadynamics

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Authors: Imen Salhi, Salah Bouhlel, Bernrd Lehmann

Abstract:

The Kebbouch South Pb-Zn deposit is located 20 km to the east of El Kef (NW) in the southeastern part of the Triassic diapir belt in the Tunisian Atlas. The deposit is composed of sulfide and non-sulfide zinc-lead ore bodies. The aim of this study is to provide petrographic results, mineralogy, as well as fluid inclusion data of the carbonate-hosted Pb-Zn Kebbouch South deposit. Mineralization forms two major ore types: (1) lenticular dolostones and clay breccias in the contact zone between Triassic and Upper Cretaceous strata;, it consists of small-scale lenticular, strata-or fault-controlled mineralization mainly composed of marcasite, galena, sphalerite, pyrite, and (2) stratiform mineralization in the Bahloul Formation (Upper Cenomanian-Lower Turonian) consisting of framboidal and cubic pyrite, disseminated sphalerite and galena. Non-metalliferous and/or gangue minerals are represented by dolomite, calcite, celestite and quartz. Fluid inclusion petrography study has been carried out on calcite and celestite. Fluid inclusions hosted in celestite are less than 20 µm large and show two types of aqueous inclusions: monophase liquid aqueous inclusions (L), abundant and very small, generally less than 15 µm and liquid-rich two phase inclusions (L+V). The gas phase forms a mobile vapor bubble. Microthermometric analyses of (L+V) fluid inclusions for celestite indicate that the homogenization temperature ranges from 121 to 156°C, and final ice melting temperatures are in the range of – 19 to -9°C corresponding to salinities of 12 to 21 wt% NaCl eq. (L+V) fluid inclusions from calcite are frequently localized along the growth zones; their homogenization temperature ranges from 96 to 164°C with final ice melting temperatures between -16 and -7°C corresponding to salinities of 9 to 19 wt% NaCl eq. According to mineralogical and fluid inclusion studies, mineralization in the Pb – Zn Kebbouch South deposit formed between 96 to 164°C with salinities ranging from 9 to 21 wt% NaCl eq. A contribution of basinal brines in the ore formation of the kebbouch South Pb–Zn deposit is likely. The deposit is part of the family of MVT deposits associated with the salt diapir environment.

Keywords: fluid inclusion, Kebbouch South, mineralogy, MVT deposits, Pb-Zn

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