Search results for: molecular mechanics.

Authors: Arkady Bolotin

Abstract:

One-way functions are functions that are easy to compute but hard to invert. Their existence is an open conjecture; it would imply the existence of intractable problems (i.e. NP-problems which are not in the P complexity class). If true, the existence of one-way functions would have an impact on the theoretical framework of physics, in particularly, quantum mechanics. Such aspect of one-way functions has never been shown before. In the present work, we put forward the following. We can calculate the microscopic state (say, the particle spin in the z direction) of a macroscopic system (a measuring apparatus registering the particle z-spin) by the system macroscopic state (the apparatus output); let us call this association the function F. The question is: can we compute the function F in the inverse direction? In other words, can we compute the macroscopic state of the system through its microscopic state (the preimage F -1)? In the paper, we assume that the function F is a one-way function. The assumption implies that at the macroscopic level the Schrödinger equation becomes unfeasible to compute. This unfeasibility plays a role of limit of the validity of the linear Schrödinger equation.

Keywords: One-way functions, P versus NP problem, quantummeasurements.

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Authors: Chung-Chun Hsiao, Yu-Kai, Ting, Kai-Yuan Liu, Pang-Wei Yen, Jia-Ying Tu

Abstract:

In this paper, a new design of spherical robotic system based on the concepts of gimbal structure and gyro dynamics is presented. Robots equipped with multiple wheels and complex steering mechanics may increase the weight and degrade the energy transmission efficiency. In addition, the wheeled and legged robots are relatively vulnerable to lateral impact and lack of lateral mobility. Therefore, the proposed robotic design uses a spherical shell as the main body for ground locomotion, instead of using wheel devices. Three spherical shells are structured in a similar way to a gimbal device and rotate like a gyro system. The design and mechanism of the proposed robotic system is introduced. In addition, preliminary results of the dynamic model based on the principles of planar rigid body kinematics and Lagrangian equation are included. Simulation results and rig construction are presented to verify the concepts.

Keywords: Gyro, gimbal, Lagrange equation, spherical robots.

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Authors: Jing-Gang Xie

Abstract:

The research, in this case, considers the integration of the Quantum Field Theory and the General Relativity Theory. As two successful models in explaining behaviors of particles, they are incompatible since they work at different masses and scales of energy, with the evidence that regards the description of black holes and universe formation. It is so considering previous efforts in merging the two theories, including the likes of the String Theory, Quantum Gravity models, and others. In a bid to prove an actionable experiment, the paper’s approach starts with the derivations of the existing theories at present. It goes on to test the derivations by applying the same initial assumptions, coupled with several deviations. The resulting equations get similar results to those of classical Newton model, quantum mechanics, and general relativity as long as conditions are normal. However, outcomes are different when conditions are extreme, specifically with no breakdowns even for less than Schwarzschild radius, or at Planck length cases. Even so, it proves the possibilities of integrating the two theories.

Keywords: General relativity theory, particles, photons, quantum gravity model, gravitational frequency shift.

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Authors: Keny Ordaz-Hernandez, Xavier Fischer, Fouad Bennis

Abstract:

In a particular case of behavioural model reduction by ANNs, a validity domain shortening has been found. In mechanics, as in other domains, the notion of validity domain allows the engineer to choose a valid model for a particular analysis or simulation. In the study of mechanical behaviour for a cantilever beam (using linear and non-linear models), Multi-Layer Perceptron (MLP) Backpropagation (BP) networks have been applied as model reduction technique. This reduced model is constructed to be more efficient than the non-reduced model. Within a less extended domain, the ANN reduced model estimates correctly the non-linear response, with a lower computational cost. It has been found that the neural network model is not able to approximate the linear behaviour while it does approximate the non-linear behaviour very well. The details of the case are provided with an example of the cantilever beam behaviour modelling.

Keywords: artificial neural network, validity domain, cantileverbeam, non-linear behaviour, model reduction.

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Authors: V. Barbakadze, L. Gogilashvili, L. Amiranashvili, M. Merlani, K. Mulkijanyan

Abstract:

The high-molecular water-soluble preparations from several species of two genera (Symphytum and Anchusa) of Boraginaceae family Symphytum asperum, S. caucasicum, S.officinale and Anchusa italica were isolated. According to IR, 13C and 1H NMR, APT, 1D NOE, 2D heteronuclear 1H/13C HSQC and 2D DOSY experiments, the main chemical constituent of these preparations was found to be caffeic acid-derived polyether, namely poly[3-(3,4-dihydroxyphenyl)glyceric acid] (PDPGA) or poly[oxy-1- carboxy-2-(3,4-dihydroxyphenyl)ethylene]. Most carboxylic groups of this caffeic acid-derived polymer of A. italica are methylated.

Keywords: Anchusa, poly[3-(3, 4-dihydroxyphenyl)glyceric acid], poly[oxy-1-carboxy-2-(3, 4-dihydroxyphenyl)ethylene], Symphytum.

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Authors: Atamas N. A., Atamas A. A.

Abstract:

Energetic and structural results for ethanol-water mixtures as a function of the mole fraction were calculated using Monte Carlo methodology. Energy partitioning results obtained for equimolar water-ethanol mixture and ether organic liquids are compared. It has been shown that at xet=0.22 the RDFs for waterethanol and ethanol-ethanol interactions indicated strong hydrophobic interactions between ethanol molecules and the local structure of solution is less structured at this concentration as at ether ones. Results obtained for ethanol-water mixture as a function of concentration are in good agreement with the experimental data.

Keywords: Ethanol, molecular liquids, Monte Carlo, water, thermodynamics.

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Authors: Kazutoshi Shishido, Sanehiro Muromachi, Ryo Ohmura

Abstract:

This paper reports the three-phase (gas + liquid + hydrate) equilibrium pressure versus temperature data for a (O3 + O2 + CO2 + H2O) system for developing the hydrate-based technology to preserve ozone, a chemically unstable substance, for various industrial, medical and consumer uses. These data cover the temperature range from 272 K to 277 K, corresponding to pressures from 1.6 MPa to 3.1 MPa, for each of the three different (O3 + O2)-to-CO2 or O2-to-CO2 molar ratios in the gas phase, which are approximately 4 : 6, 5 : 5, respectively. The mole fraction of ozone in the gas phase was ~0.03 , which are the densest ozone fraction to artificially form O3 containing hydrate ever reported in the literature. Based on these data, the formation of hydrate containing high-concentration ozone, as high as 1 mass %, will be expected.

Keywords: Clathrate hydrate, Ozone, Molecule storage, Sterilization.

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Authors: A. Armin, R. Fotouhi, W. Szyszkowski

Abstract:

In this paper a 3-D finite element (FE) investigation of soil-blade interaction is described. The effects of blade’s shape and rake angle are examined both numerically and experimentally. The soil is considered as an elastic-plastic granular material with non-associated Drucker-Prager material model. Contact elements with different properties are used to mimic soil-blade sliding and soil-soil cutting phenomena. A separation criterion is presented and a procedure to evaluate the forces acting on the blade is given and discussed in detail. Experimental results were derived from tests using soil bin facility and instruments at the University of Saskatchewan. During motion of the blade, load cells collect data and send them to a computer. The measured forces using load cells had noisy signals which are needed to be filtered. The FE results are compared with experimental results for verification. This technique can be used in blade shape optimization and design of more complicated blade’s shape.

Keywords: Finite element analysis, soil-blade contact modeling, blade force, experimental results.

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Authors: Osama A. Terfas

Abstract:

The development of shape and size of a crack in a pressure vessel under uniaxial and biaxial loadings is important in fitness-for-service evaluations such as leak-before-break. In this work finite element modelling was used to evaluate the mean stress and the J-integral around a front of a surface-breaking crack. A procedure on the basis of ductile tearing resistance curves of high and low constrained fracture mechanics geometries was developed to estimate the amount of ductile crack extension for surface-breaking cracks and to show the evolution of the initial crack shape. The results showed non-uniform constraint levels and crack driving forces around the crack front at large deformation levels. It was also shown that initially semi-elliptical surface cracks under biaxial load developed higher constraint levels around the crack front than in uniaxial tension. However similar crack shapes were observed with more extensions associated with cracks under biaxial loading.

Keywords: biaxial load, crack shape, fracture toughness, surface crack, uniaxial load.

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Authors: J. Baskar Babujee, J. Senbagamalar,

Abstract:

The topological distance between a pair of vertices i and j, which is denoted by d(vi, vj), is the number of edges of the shortest path joining i and j. The Wiener index W(G) is the sum of distances between all pairs of vertices of a graph G. W(G) = i

Keywords: Graph, Degree, Distance, Pendent vertex, Wiener index, Tree.

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Authors: S. Daneshmand, C. Aghanajafi, A. Bahrami

Abstract:

In this paper the supersonic ejectors are experimentally and analytically studied. Ejector is a device that uses the energy of a fluid to move another fluid. This device works like a vacuum pump without usage of piston, rotor or any other moving component. An ejector contains an active nozzle, a passive nozzle, a mixing chamber and a diffuser. Since the fluid viscosity is large, and the flow is turbulent and three dimensional in the mixing chamber, the numerical methods consume long time and high cost to analyze the flow in ejectors. Therefore this paper presents a simple analytical method that is based on the precise governing equations in fluid mechanics. According to achieved analytical relations, a computer code has been prepared to analyze the flow in different components of the ejector. An experiment has been performed in supersonic regime 1.5Keywords: Ejector, Wind Tunnel, Supersonic, Diffuser, Machnumber, Mixing Chamber

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Authors: M. Nikbakht, N. Choupani

Abstract:

In this study the behavior of interlaminar fracture of carbon-epoxy thermoplastic laminated composite is investigated numerically and experimentally. Tests are performed with Arcan specimens. Testing with Arcan specimen gives the opportunity of utilizing just one kind of specimen for extracting fracture properties for mode I, mode II and different mixed mode ratios of materials with exerting load via different loading angles. Variation of loading angles in range of 0-90° made possible to achieve different mixed mode ratios. Correction factors for various conditions are obtained from ABAQUS 2D finite element models which demonstrate the finite shape of Arcan specimens used in this study. Finally, applying the correction factors to critical loads obtained experimentally, critical interlaminar fracture toughness of this type of carbon- epoxy composite has been attained.

Keywords: Fracture Mechanics, Mixed Mode, Arcan Specimen, Finite Element.

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Authors: J. Gazzola, I. M. Dal Fabbro, J. Soriano, M. V. G. Silva, S. Rodrigues

Abstract:

Application of wood in rural construction is diffused all around the world since remote times. However, its inclusion in structural design deserves strong support from broad knowledge of material properties. The pertinent literature reveals the application of optical methods in determining the complete field displacement on bodies exhibiting regular as well as irregular surfaces. The use of moiré techniques in experimental mechanics consists in analyzing the patterns generated on the body surface before and after deformation. The objective of this research work is to study the qualitative deformation behavior of wooden testing specimens under specific loading situations. The experiment setup follows the literature description of shadow moiré methods. Results indicate strong anisotropy influence of the generated displacement field. Important qualitative as well as quantitative stress and strain distribution were obtained wooden members which are applicable to rural constructions.

Keywords: Moiré methods, wooden structural material, rural constructions.

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Authors: I. Restrepo, S. Solorzano

Abstract:

This work was focused in to study the compatibility, dispersion and exfoliation of modified nanoclays in biodegradable polymers and evaluate its effect on the physical, mechanical and thermal properties on the biodegradable matrix used. The formulations have been developed with polylactic acid (PLA) and organically modified montmorillonite-type commercial nanoclays (Cloisite 15, Cloisite 20, and Cloisite 30B) in the presence of a plasticizer agent, specifically Polyethylene Glycol of low molecular weight. Different compositions were evaluated, in order to identify the influence of each nanoclayin the polymeric matrix. The mixtures were characterized by thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), X-ray diffraction (DRX), transmission electron microscopy (TEM) and Tensile Test. These tests have allowed understanding the behavior of each of the mixtures developed.

Keywords: Biopolymers, Nanoclays, polylacticacid (PLA), polymer blends.

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Authors: Tian Hai, Yang Shengsheng, Jr., Wang Yi

Abstract:

Based on an analysis of the mechanism of degradation of optical characteristics of the ZnO-pigmented white paint by electron irradiation, a model of single molecular color centers is built. An equation that explains the relationship between the changes of variation of the ZnO-pigmented white paint-s spectrum absorptance and electron fluence is derived. The uncertain parameters in the equation can be calculated using the curve fitting by experimental data. The result indicates that the model can be applied to predict the degradation of optical characteristics of ZnO-pigmented white paint by electron radiation.

Keywords: ZnO-pigmented white pain, effects of electron radiation, optical characteristics degradation, prediction model.

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Authors: Wisuwat Plodpradista

Abstract:

Tubular linear induction motor (TLIM) can be used as a capsule pump in a large pneumatic capsule pipeline (PCP) system. Parametric performance evaluation of the designed 1-meter diameter PCP-TLIM system yields encouraging results for practical implementation. The capsule thrust and speed inside the TLIM pump can be calculated from the combination of the PCP fluid mechanics and the TLIM equations. The TLIM equivalent circuits derived from those of the conventional three-phase induction motor are used as a model to predict the static test results of a small-scale PCP-TLIM system. In this paper, additional dynamic tests are performed on the same small-scale PCP-TLIM system with two capsules of different diameters. The behaviors of the capsule inside the pump are observed and analyzed. The dynamic performances from the dynamic tests are compared with the theoretical predictions based on the TLIM equivalent circuit model.

Keywords: Pneumatic capsule pipeline, Tubular linear induction motor

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Authors: C. De Lazzari, E. Del Prete, I. Genuini, F. Fedele

Abstract:

Cardiovascular human simulator can be a useful tool in understanding complex physiopathological process in cardiocirculatory system. It can also be a useful tool in order to investigate the effects of different drugs on hemodynamic parameters. The aim of this work is to test the potentiality of our cardiovascular numerical simulator CARDIOSIM© in reproducing flow/pressure coronary waveforms in presence of two different drugs: Amlodipine (AMLO) and Adenosine (ADO). In particular a time-varying intramyocardial compression, assumed to be proportional to the left ventricular pressure, was related to the venous coronary compliances in order to study its effects on the coronary blood flow and the flow/pressure loop. Considering that coronary circulation dynamics is strongly interrelated with the mechanics of the left ventricular contraction, relaxation, and filling, the numerical model allowed to analyze the effects induced by the left ventricular pressure on the coronary flow.

Keywords: Cardiovascular system, Coronary blood flow, Hemodynamic, Numerical simulation.

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Authors: K. Sudprasert, M. Precharattana, N. Nuttavut, D. Triampo, B. Pattanasiri, Y. Lenbury, W. Triampo

Abstract:

The study of non-equilibrium systems has attracted increasing interest in recent years, mainly due to the lack of theoretical frameworks, unlike their equilibrium counterparts. Studying the steady state and/or simple systems is thus one of the main interests. Hence in this work we have focused our attention on the driven lattice gas model (DLG model) consisting of interacting particles subject to an external field E. The dynamics of the system are given by hopping of particles to nearby empty sites with rates biased for jumps in the direction of E. Having used small two dimensional systems of DLG model, the stochastic properties at nonequilibrium steady state were analytically studied. To understand the non-equilibrium phenomena, we have applied the analytic approach via master equation to calculate probability function and analyze violation of detailed balance in term of the fluctuation-dissipation theorem. Monte Carlo simulations have been performed to validate the analytic results.

Keywords: Non-equilibrium, lattice gas, stochastic process

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Authors: Cândida M. Pereira, Amílcar L. Ramalho, Jorge A. Ambrósio

Abstract:

In the numerical solution of the forward dynamics of a multibody system, the positions and velocities of the bodies in the system are obtained first. With the information of the system state variables at each time step, the internal and external forces acting on the system are obtained by appropriate contact force models if the continuous contact method is used instead of a discrete contact method. The local deformation of the bodies in contact, represented by penetration, is used to compute the contact force. The ability and suitability with current cylindrical contact force models to describe the contact between bodies with cylindrical geometries with particular focus on internal contacting geometries involving low clearances and high loads simultaneously is discussed in this paper. A comparative assessment of the performance of each model under analysis for different contact conditions, in particular for very different penetration and clearance values, is presented. It is demonstrated that some models represent a rough approximation to describe the conformal contact between cylindrical geometries because contact forces are underestimated.

Keywords: Clearance joints, Contact mechanics, Contact dynamics, Internal cylindrical contact, Multibody dynamics.

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Authors: M. Adeel

Abstract:

The damage tolerance behavior of integrally and conventional stiffened panel is investigated based on the fracture mechanics and finite element analysis. The load bearing capability and crack growth characteristic of both types of the stiffened panels having same configuration subjected to distributed tensile load is examined in this paper. A fourteen-stringer stiffened panel is analyzed for a central skin crack propagating towards the adjacent stringers. Stress intensity factors and fatigue crack propagation rates of both types of the stiffened panels are then compared. The analysis results show that integral stiffening causes higher stress intensity factor than conventional stiffened panel as the crack tip passes through the stringer and the integrally stiffened panel has less load bearing capability than the riveted stiffened panel.

Keywords: Conventional Stiffened Structure, Damage Tolerance, Finite Element Analysis, Integrally Stiffened Structure, Stress Intensity Factor.

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Authors: Mahmoud Z. Iskandarani, Nidal F. Shilbayeh

Abstract:

The voltage/current characteristics and the effect of NO2 gas on the electrical conductivity of a PbPc gas sensor array is investigated. The gas sensor is manufactured using vacuum deposition of gold electrodes on sapphire substrate with the leadphathalocyanine vacuum sublimed on the top of the gold electrodes. Two versions of the PbPc gas sensor array are investigated. The tested types differ in the gap sizes between the deposited gold electrodes. The sensors are tested at different temperatures to account for conductivity changes as the molecular adsorption/desorption rate is affected by heat. The obtained results found to be encouraging as the sensors shoed stability and sensitivity towards low concentration of applied NO2 gas.

Keywords: Intelligent System, PbPc, Gas Sensor, Hardware, Software, Neural.

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Authors: P.G. Jayathilake, B.C. Khoo, Zhijun Tan

Abstract:

A two-dimensional thin-walled capsule of a flexible semi-permeable membrane is adhered onto a rigid planar substrate under adhesive forces (derived from a potential function) in the presence of osmosis across the membrane. The capsule is immersed in a hypotonic and diluted binary solution of a non-electrolyte solute. The Stokes flow problem is solved by the immersed interface method (IIM) with equal viscosities for the enclosed and surrounding fluid of the capsule. The numerical results obtained are verified against two simplified theoretical solutions and the agreements are good. The osmotic inflation of the adhered capsule is studied as a function of the solute concentration field, hydraulic conductivity, and the initial capsule shape. Our findings indicate that the contact length shrinks in dimension as capsule inflates in the hypotonic medium, and the equilibrium contact length does not depend on the hydraulic conductivity of the membrane and the initial shape of the capsule.

Keywords: Capsule-substrate adhesion, Fluid mechanics, Immersed interface method, Osmosis, Mass transfer.

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Authors: Mahesh Chudasama, Harit Raval

Abstract:

Conical sections and shells made from metal plates are widely used in various industrial applications. 3-roller conical bending process is preferably used to produce such conical sections and shells. Bending mechanics involved in the process is complex and little work is done in this area. In the present paper an analytical model is developed to predict bending force which will be acting during 3-roller conical bending process. To verify the developed model, conical bending experiments are performed. Analytical results and experimental results were compared. Force predicted by analytical model is in close proximity of the experimental results. The error in the prediction is ±10%. Hence the model gives quite satisfactory results. Present model is also compared with the previously published bending force prediction model and it is found that the present model gives better results. The developed model can be used to estimate the bending force during 3-roller bending process and can be useful to the designers for designing the 3-roller conical bending machine.

Keywords: Bending-force, Experimental-verification, Internal-moment, Roll-bending.

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Authors: U. Kairov, T. Karpenyuk, E. Ramanculov, A. Zinovyev

Abstract:

The most common result of analysis of highthroughput data in molecular biology represents a global list of genes, ranked accordingly to a certain score. The score can be a measure of differential expression. Recent work proposed a new method for selecting a number of genes in a ranked gene list from microarray gene expression data such that this set forms the Optimally Functionally Enriched Network (OFTEN), formed by known physical interactions between genes or their products. Here we present calculation results of relative connectivity of genes from META-OFTEN network and tentative biological interpretation of the most reproducible signal. The relative connectivity and inbetweenness values of genes from META-OFTEN network were estimated.

Keywords: Microarray, META-OFTEN, gene network.

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Authors: Jun Yop An, Kyoung Ryoung Park, Jung-Gyu Lee, Hyung-Seop Youn, Jung-Yeon Kang, Gil Bu Kang, Soo Hyun Eom

Abstract:

MinC plays an important role in bacterial cell division system by inhibiting FtsZ assembly. However, the molecular mechanism of the action is poorly understood. E. coli MinC Nterminus domain was purified and crystallized using 1.4 M sodium citrate pH 6.5 as a precipitant. X-ray diffraction data was collected and processed to 2.3 Å from a native crystal. The crystal belonged to space group P212121, with the unit cell parameters a = 52.7, b = 54.0, c = 64.7 Å. Assuming the presence of two molecules in the asymmetric unit, the Matthews coefficient value is 1.94 Å3 Da-1, which corresponds to a solvent content of 36.5%. The overall structure of MinCN is observed as a dimer form through anti-parallel ß-strand interaction.

Keywords: MinC, Cell division, Crystallization.

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Authors: Alexander Breitholz, Wolfgang Arlt, Ki-Pung Yoo

Abstract:

Group contribution based models are widely used in industrial applications for its convenience and flexibility. Although a number of group contribution models have been proposed, there were certain limitations inherent to those models. Models based on group contribution excess Gibbs free energy are limited to low pressures and models based on equation of state (EOS) cannot properly describe highly nonideal mixtures including acids without introducing additional modification such as chemical theory. In the present study new a new approach derived from quantum chemistry have been used to calculate necessary EOS group interaction parameters. The COSMO-RS method, based on quantum mechanics, provides a reliable tool for fluid phase thermodynamics. Benefits of the group contribution EOS are the consistent extension to hydrogen-bonded mixtures and the capability to predict polymer-solvent equilibria up to high pressures. The authors are confident that with a sufficient parameter matrix the performance of the lattice EOS can be improved significantly.

Keywords: COSMO-RS, Equation of State, Group contribution, Lattice Fluid, Phase equilibria.

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Authors: Pattrarat Teamkao, Paitip Thiravetyan

Abstract:

The aim of this work was to investigate the potential of soil microorganisms and the burhead plant, as well as the combination of soil microorganisms and plants to remediate monoethylene glycol (MEG), diethylene glycol (DEG), and triethylene glycol (TEG) in synthetic wastewater. The result showed that a system containing both burhead plant and soil microorganisms had the highest efficiency in EGs removal. Around 100% of MEG and DEG and 85% of TEG were removed within 15 days of the experiments. However, the burhead plant had higher removal efficiency than soil microorganisms for MEG and DEG but the same for TEG in the study systems. The removal rate of EGs in the study system related to the molecular weight of the compounds and MEG, the smallest glycol, was removed faster than DEG and TEG by both the burhead plant and soil microorganisms in the study system.

Keywords: Ethylene glycol, burhead plant, soil microorganisms, phytoremediation

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Authors: Malik I. Al-Amayreh, Mohammad I. Kilani, Ahmed S. Al-Salaymeh

Abstract:

This work presents a Computational Fluid Dynamics (CFD) simulation of a butterfly valve used to control the flow of combustible gas mixture in an industrial process setting.The work uses CFD simulation to analyze the flow characteristics in the vicinity of the valve, including the pressure distributions and Frequency spectrum of the pressure pulsations downstream the valves and the vortex shedding allow predicting the torque fluctuations acting on the valve shaft and the possibility of generating mechanical vibration and resonance.These fluctuations are due to aerodynamic torque resulting from fluid turbulence and vortex shedding in the valve vicinity. The valve analyzed is located in a pipeline between two opposing 90o elbows, which exposes the valve and the surrounding structure to the turbulence generated upstream and downstream the elbows at either end of the pipe.CFD simulations show that the best location for the valve from a vibration point of view is in the middle of the pipe joining the elbows.

Keywords: Butterfly Valve Vibration Analysis, Computational Fluid Dynamics, Fluid Flow Circuit Design, Fluid Mechanics.

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Authors: M. Azizur Rahman, Tamotsu Oomori

Abstract:

Calcite aCalcite and aragonite are the two common polymorphs of CaCO3 observed as biominerals. It is universal that the sea water contents a high Mg2+ (50mM) relative to Ca2+ (10mM). In vivo crystallization, Mg2+ inhibits calcite formation. For this reason, stony corals skeleton may be formed only aragonite crystals in the biocalcification. It is special in case of soft corals of which formed only calcite crystal; however, this interesting phenomenon, still uncharacterized in the marine environment, has been explored in this study using newly purified cell-free proteins isolated from the endoskeletal sclerites of soft coral. By recording the decline of pH in vitro, the control of CaCO3 nucleation and crystal growth by the cellfree proteins was revealed. Using Atomic Force Microscope, here we find that these endoskeletal cell-free proteins significantly design the morphological shape in the molecular-scale kinetics of crystal formation and those proteins act as surfactants to promote ion attachment at calcite steps.nd aragonite are the two common polymorphs of CaCO3 observed as biominerals. It is universal that the sea water contents a high Mg2+ (50mM) relative to Ca2+ (10mM). In vivo crystallization, Mg2+ inhibits calcite formation. For this reason, stony corals skeleton may be formed only aragonite crystals in the biocalcification. It is special in case of soft corals of which formed only calcite crystal; however, this interesting phenomenon, still uncharacterized in the marine environment, has been explored in this study using newly purified cell-free proteins isolated from the endoskeletal sclerites of soft coral. By recording the decline of pH in vitro, the control of CaCO3 nucleation and crystal growth by the cell-free proteins was revealed. Using Atomic Force Microscope, here we find that these endoskeletal cell-free proteins significantly design the morphological shape in the molecular-scale kinetics of crystal formation and those proteins act as surfactants to promote ion attachment at calcite steps. KeywordsBiomineralization, Calcite, Cell-free protein, Soft coral

Keywords: Biomineralization, Calcite, Cell-free protein, Soft coral

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Authors: Agnieszka Danek, Rafał Pokrzywa

Abstract:

Approximate tandem repeats in a genomic sequence are two or more contiguous, similar copies of a pattern of nucleotides. They are used in DNA mapping, studying molecular evolution mechanisms, forensic analysis and research in diagnosis of inherited diseases. All their functions are still investigated and not well defined, but increasing biological databases together with tools for identification of these repeats may lead to discovery of their specific role or correlation with particular features. This paper presents a new approach for finding approximate tandem repeats in a given sequence, where the similarity between consecutive repeats is measured using the Hamming distance. It is an enhancement of a method for finding exact tandem repeats in DNA sequences based on the Burrows- Wheeler transform.

Keywords: approximate tandem repeats, Burrows-Wheeler transform, Hamming distance, suffix array

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