Search results for: Molecular Interaction
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 1322

Search results for: Molecular Interaction

1172 SENSE-SEAT: Improving Creativity and Productivity through the Redesign of a Multisensory Technological Office Chair

Authors: Fernando Miguel Campos, Carlos Ferreira, João Pestana, Pedro Campos, Nils Ehrenberg, Wojciech Hydzik

Abstract:

The current trend of organizations offering their workers open-office spaces and co-working offices has been primed for stimulating teamwork and collaboration. However, this is not always valid as these kinds of spaces bring other types of challenges that compromise workers productivity and creativity. We present an approach for improving creativity and productivity at the workspace by redesigning an office chair that incorporates subtle technological elements that help users focus, relax and being more productive and creative. This sheds light on how we can better design interactive furniture for such popular contexts, as we develop this new chair through a multidisciplinary approach using ergonomics, interior design, interaction design, hardware and software engineering and psychology.

Keywords: Creativity, co-working, ergonomics, human-computer interaction, interaction, interactive furniture, productivity.

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1171 Gas-Liquid Interaction on Perforated Plates

Authors: M.O. Balabekova, O.S. Balabekov

Abstract:

The paper deals with hydrodynamics of liquid-gas layers under gas streaming through liquid layer on perforated plates in column apparatuses. The plates with large apertures have been investigated especially. It was shown that hydrodynamic regularities for these plates are essentially different from known laws for foam forming on fine-perforated plates. Main regularities of liquid-gas interaction on plates with large apertures have been established.

Keywords: column apparatus, large aperture, liquid-gas layer, perforated plate.

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1170 Vision Based Hand Gesture Recognition

Authors: Pragati Garg, Naveen Aggarwal, Sanjeev Sofat

Abstract:

With the development of ubiquitous computing, current user interaction approaches with keyboard, mouse and pen are not sufficient. Due to the limitation of these devices the useable command set is also limited. Direct use of hands as an input device is an attractive method for providing natural Human Computer Interaction which has evolved from text-based interfaces through 2D graphical-based interfaces, multimedia-supported interfaces, to fully fledged multi-participant Virtual Environment (VE) systems. Imagine the human-computer interaction of the future: A 3Dapplication where you can move and rotate objects simply by moving and rotating your hand - all without touching any input device. In this paper a review of vision based hand gesture recognition is presented. The existing approaches are categorized into 3D model based approaches and appearance based approaches, highlighting their advantages and shortcomings and identifying the open issues.

Keywords: Computer Vision, Hand Gesture, Hand Posture, Human Computer Interface.

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1169 Incident Shock Wave Interaction with an Axisymmetric Cone Body Placed in Shock Tube

Authors: Rabah Haoui

Abstract:

This work presents a numerical simulation of the interaction of an incident shock wave propagates from the left to the right with a cone placed in a tube at shock. The Mathematical model is based on a non stationary, viscous and axisymmetric flow. The Discretization of the Navier-stokes equations is carried out by the finite volume method in the integral form along with the Flux Vector Splitting method of Van Leer. Here, adequate combination of time stepping parameter, CFL coefficient and mesh size level is selected to ensure numerical convergence. The numerical simulation considers a shock tube filled with air. The incident shock wave propagates to the right with a determined Mach number and crosses the cone by leaving behind it a stationary detached shock wave in front of the nose cone. This type of interaction is observed according to the time of flow.

Keywords: Supersonic flow, viscous flow, finite volume, cone body

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1168 Spin Coherent State Path Integral for the Interaction of Two-Level System with Time Dependent Non-Uniform Magnetic Field

Authors: Rekik Rima, Aouachria Mekki

Abstract:

We study the movement of a two-level atom in interaction with time dependent nonuniform magnetic filed using the path integral formalism. The propagator is first written in the standard form by replacing the spin by a unit vector aligned along the polar and azimuthal directions. Then it is determined exactly using perturbation methods. Thus the Rabi formula of the system are deduced.

Keywords: Path integral, Formalism, Propagator, Transition probability.

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1167 On Adaptive, Auto-Configurable Apps

Authors: Prisa Damrongsiri, Kittinan Pongpianskul, Mario Kubek, Herwig Unger

Abstract:

Apps are today the most important possibility to adapt mobile phones and computers to fulfill the special needs of their users. Location- and context-sensitive programs are hereby the key to support the interaction of the user with his/her environment and also to avoid an overload with a plenty of dispensable information. The contribution shows, how a trusted, secure and really bi-directional communication and interaction among users and their environment can be established and used, e.g. in the field of home automation.

Keywords: Apps, context-sensitive, location-sensitive, selfconfiguration, mobile computing, smart home.

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1166 Seismic Soil-Pile Interaction Considering Nonlinear Soil Column Behavior in Saturated and Dry Soil Conditions

Authors: Mohammad Moeini, Mehrdad Ghyabi, Kiarash Mohtasham Dolatshahi

Abstract:

This paper investigates seismic soil-pile interaction using the Beam on Nonlinear Winkler Foundation (BNWF) approach. Three soil types are considered to cover all the possible responses, as well as nonlinear site response analysis using finite element method in OpenSees platform. Excitations at each elevation that are output of the site response analysis are used as the input excitation to the soil pile system implementing multi-support excitation method. Spectral intensities of acceleration show that the extent of the response in sand is more severe than that of clay, in addition, increasing the PGA of ground strong motion will affect the sandy soil more, in comparison with clayey medium, which is an indicator of the sensitivity of soil-pile systems in sandy soil.

Keywords: Beam on nonlinear Winkler foundation method, multi-support excitation, nonlinear site response analysis, seismic soil-pile interaction.

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1165 Molecular Dynamics Study on Mechanical Responses of Circular Graphene Nanoflake under Nanoindentation

Authors: Jeong-Won Kang

Abstract:

Graphene, a single-atom sheet, has been considered as the most promising material for making future nanoelectromechanical systems as well as purely electrical switching with graphene transistors. Graphene-based devices have advantages in scaled-up device fabrication due to the recent progress in large area graphene growth and lithographic patterning of graphene nanostructures. Here we investigated its mechanical responses of circular graphene nanoflake under the nanoindentation using classical molecular dynamics simulations. A correlation between the load and the indentation depth was constructed. The nanoindented force in this work was applied to the center point of the circular graphene nanoflake and then, the resonance frequency could be tuned by a nanoindented depth. We found the hardening or the softening of the graphene nanoflake during its nanoindented-deflections, and such properties were recognized by the shift of the resonance frequency. The calculated mechanical parameters in the force-vs-deflection plot were in good agreement with previous experimental and theoretical works. This proposed schematics can detect the pressure via the deflection change or/and the resonance frequency shift, and also have great potential for versatile applications in nanoelectromechanical systems.

Keywords: Graphene, pressure sensor, circular graphene nanoflake, molecular dynamics.

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1164 An Index based Forward Backward Multiple Pattern Matching Algorithm

Authors: Raju Bhukya, DVLN Somayajulu

Abstract:

Pattern matching is one of the fundamental applications in molecular biology. Searching DNA related data is a common activity for molecular biologists. In this paper we explore the applicability of a new pattern matching technique called Index based Forward Backward Multiple Pattern Matching algorithm(IFBMPM), for DNA Sequences. Our approach avoids unnecessary comparisons in the DNA Sequence due to this; the number of comparisons of the proposed algorithm is very less compared to other existing popular methods. The number of comparisons rapidly decreases and execution time decreases accordingly and shows better performance.

Keywords: Comparisons, DNA Sequence, Index.

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1163 Implicit Eulerian Fluid-Structure Interaction Method for the Modeling of Highly Deformable Elastic Membranes

Authors: Aymen Laadhari, Gábor Székely

Abstract:

This paper is concerned with the development of a fully implicit and purely Eulerian fluid-structure interaction method tailored for the modeling of the large deformations of elastic membranes in a surrounding Newtonian fluid. We consider a simplified model for the mechanical properties of the membrane, in which the surface strain energy depends on the membrane stretching. The fully Eulerian description is based on the advection of a modified surface tension tensor, and the deformations of the membrane are tracked using a level set strategy. The resulting nonlinear problem is solved by a Newton-Raphson method, featuring a quadratic convergence behavior. A monolithic solver is implemented, and we report several numerical experiments aimed at model validation and illustrating the accuracy of the presented method. We show that stability is maintained for significantly larger time steps.

Keywords: Fluid-membrane interaction, stretching, Eulerian, finite element method, Newton, implicit.

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1162 Definition of Cognitive Infocommunications and an Architectural Implementation of Cognitive Infocommunications Systems

Authors: Peter Baranyi, Gyorgy Persa, Adam Csapo

Abstract:

Cognitive Infocommunications (CogInfoCom) is a new research direction which has emerged as the synergic convergence of infocommunications and the cognitive sciences. In this paper, we provide the definition of CogInfoCom, and propose an architectural framework for the interaction-oriented design of CogInfoCom systems. We provide the outlines of an application example of the interaction-oriented architecture, and briefly discuss its main characteristics.

Keywords: Cognitive infocommunications, CogInfoCom, Cognitive Infocommunication Channels, CogInfoCom channels

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1161 Influence of Inter-tube Connections on the Stress-Strain Behavior of Nanotube-Polymer Composites: Molecular Dynamics

Authors: Jianwei Zhang, Dazhi Jiang, Huaxin Peng, Chunqi Wang

Abstract:

Stress-strain curve of inter-tube connected carbon nanotube (CNT) reinforced polymer composite under axial loading generated from molecular dynamics simulation is presented. Comparison of the response to axial mechanical loading between this composite system with composite systems reinforced by long, continuous CNTs (replicated via periodic boundary conditions) and short, discontinuous CNTs has been made. Simulation results showed that the inter-tube connection improved the mechanical properties of short discontinuous CNTs dramatically. Though still weaker than long CNT/polymer composite, more remarkable increase in the stiffness relative to the polymer was observed in the inter-tube connected CNT/polymer composite than in the discontinuous CNT/polymer composite. The manually introduced bridge break process resulted in a stress-strain curve of ductile fracture mode, which is consistent with the experimental result.

Keywords: Carbon nanotube, inter-tube connection, molecular dynamics, stress-strain curve

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1160 A New Approach In Protein Folding Studies Revealed The Potential Site For Nucleation Center

Authors: Nurul Bahiyah Ahmad Khairudin, Habibah A Wahab

Abstract:

A new approach to predict the 3D structures of proteins by combining the knowledge-based method and Molecular Dynamics Simulation is presented on the chicken villin headpiece subdomain (HP-36). Comparative modeling is employed as the knowledge-based method to predict the core region (Ala9-Asn28) of the protein while the remaining residues are built as extended regions (Met1-Lys8; Leu29-Phe36) which then further refined using Molecular Dynamics Simulation for 120 ns. Since the core region is built based on a high sequence identity to the template (65%) resulting in RMSD of 1.39 Å from the native, it is believed that this well-developed core region can act as a 'nucleation center' for subsequent rapid downhill folding. Results also demonstrate that the formation of the non-native contact which tends to hamper folding rate can be avoided. The best 3D model that exhibits most of the native characteristics is identified using clustering method which then further ranked based on the conformational free energies. It is found that the backbone RMSD of the best model compared to the NMR-MDavg is 1.01 Å and 3.53 Å, for the core region and the complete protein, respectively. In addition to this, the conformational free energy of the best model is lower by 5.85 kcal/mol as compared to the NMR-MDavg. This structure prediction protocol is shown to be effective in predicting the 3D structure of small globular protein with a considerable accuracy in much shorter time compared to the conventional Molecular Dynamics simulation alone.

Keywords: 3D model, Chicken villin headpiece subdomain, Molecular dynamic simulation NMR-MDavg, RMSD.

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1159 Breaking of Charge Independence of Nucleon-Nucleon Interaction Using Phase Shift Calculations

Authors: B. Rezaei, N. Amiri, N. Azizi

Abstract:

Using calculated phase- shift values, for pp, nn, and np elastic scattering in the energy range 1MeV to 350MeV, the charge independence breaking of nucleon-nucleon interaction is investigated. We have used Darboux transformation to calculate phase-shift for the first three values of

Keywords: Phase-shift, charge independence breaking, Darboux transformation.

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1158 Richtmyer-Meshkov Instability and Gas-Particle Interaction of Contoured Shock-Tube Flows: A Numerical Study

Authors: Yi Liu

Abstract:

In this paper, computational fluid dynamics (CFD) is utilized to characterize a prototype biolistic delivery system, the biomedical device based on the contoured-shock-tube design (CST), with the aim at investigating shocks induced flow instabilities within the contoured shock tube. The shock/interface interactions, the growth of perturbation at an interface between two fluids of different density are interrogated. The key features of the gas dynamics and gas-particle interaction are discussed

Keywords: Simulation, Shock wave, Particle, Interface, Supersonic, Richtmyer-Meshkov Instability

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1157 Fluid Structure Interaction Induced by Liquid Slosh in Partly Filled Road Tankers

Authors: Guorong Yan, Subhash Rakheja

Abstract:

The liquid cargo contained in a partly-filled road tank vehicle is prone to dynamic slosh movement when subjected to external disturbances. The slosh behavior has been identified as a significant factor impairing the safety of liquid cargo transportation. The laboratory experiments have been conducted for analyzing fluid slosh in partly filled tanks. The experiment results measured under forced harmonic excitations reveal the three-dimensional nature of the fluid motion and coupling between the lateral and longitudinal fluid slosh at resonance. Several spectral components are observed for the transient slosh forces, which can be associated with the excitation, resonance, and beat frequencies. The peak slosh forces and moments in the vicinity of resonance are significantly larger than those of the equivalent rigid mass. Due to the nature of coupling between sloshing fluid and vehicle body, the issue of the dynamic fluid-structure interaction is essential in the analysis of tank-vehicle dynamics. A dynamic pitch plane model of a Tridem truck incorporated the fluid slosh dynamics is developed to analyze the fluid-vehicle interaction under the straight-line braking maneuvers. The results show that the vehicle responses are highly associated with the characteristics of fluid slosh force and moment.

Keywords: Braking performance, fluid induced vibration, fluidslosh, fluid structure interaction, tank trucks, vehicle dynamics.

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1156 Catalytic Aquathermolysis of Egyptian Heavy Crude Oil

Authors: S. Desouky, A. Al sabagh , M. Betiha, A. Badawi, A. Ghanem, S. Khalil

Abstract:

Two Amphiphilic catalysts, iron (III) dodecylbenzene sulfonate and nickel (II) dodecylbenzene sulfonate, were synthesized and used in the catalytic aquathermolysis of heavy crude oil to reduce its viscosity. The prepared catalysts exhibited good performance in the aquathermolysis and the viscosity is reduced by ~ 78.9 % for Egyptian heavy crude oil. The chemical and physical properties of heavy oil both before and after reaction were investigated by FT-IR, dynamic viscosity, molecular weight and SARA analysis. The results indicated that the content of resin, asphaltene, average molecular weight and sulfur content of heavy oil is reduced after the catalytic aquathermolysis.

Keywords: Amphiphilic catalyst, Aquathermolysis, Heavy oil, Viscosity reduction.

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1155 Comparison of Numerical and Laboratory Results of Pull-out Test on Soil–Geogrid Interactions

Authors: Parisa Ahmadi Oliaei, Seyed Abolhassan Naeini

Abstract:

The knowledge of soil–reinforcement interaction parameters is particularly important in the design of reinforced soil structures. The pull-out test is one of the most widely used tests in this regard. The results of tensile tests may be very sensitive to boundary conditions, and more research is needed for a better understanding of the pull-out response of reinforcement, so numerical analysis using the finite element method can be a useful tool for the understanding of the pull-out response of soil-geogrid interaction. The main objective of the present study is to compare the numerical and experimental results of a pull-out test on geogrid-reinforced sandy soils interactions. Plaxis 2D finite element software is used for simulation. In the present study, the pull-out test modeling has been done on sandy soil. The effect of geogrid hardness was also investigated by considering two different types of geogrids. The numerical results curve had a good agreement with the pull-out laboratory results.

Keywords: Plaxis, pull-out test, sand, soil-geogrid interaction.

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1154 Effects of Sea Water Level Fluctuations on Seismic Response of Jacket Type Offshore Platforms

Authors: M. Rad, M. Dolatshahi Pirooz, M. Esmayili

Abstract:

To understand the seismic behavior of the offshore structures, the dynamic interaction of the water-structure-soil should be assessed. In this regard the role of the water dynamic properties in magnifying or reducing of the effects of earthquake induced motions on offshore structures haven't been investigated in precise manner in available literature. In this paper the sea water level fluctuations effects on the seismic behavior of a sample of offshore structures has been investigated by emphasizing on the water-structure interaction phenomenon. For this purpose a two dimensional finite element model of offshore structures as well as surrounded water has been developed using ANSYS software. The effect of soil interaction with embedded pile foundation has been imposed by using a series of nonlinear springs in horizontal and vertical directions in soil-piles contact points. In the model, the earthquake induced motions have been applied on springs and consequently the motions propagated upward to the structure and surrounded water. As a result of numerical study, the horizontal deformations of the offshore deck as well as internal force and buckling coefficient in structural elements have been recorded and controlled with and without water presence. In part of study a parametric study has been accomplished on sea water level fluctuations and effect of this parameter has been studied on the aforementioned numerical results.

Keywords: Fluid-Structure Interaction, Jacket, Sea Water Level, Seismic Loading.

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1153 Energy-Level Structure of a Confined Electron-Positron Pair in Nanostructure

Authors: Tokuei Sako, Paul-Antoine Hervieux

Abstract:

The energy-level structure of a pair of electron and positron confined in a quasi-one-dimensional nano-scale potential well has been investigated focusing on its trend in the small limit of confinement strength ω, namely, the Wigner molecular regime. An anisotropic Gaussian-type basis functions supplemented by high angular momentum functions as large as l = 19 has been used to obtain reliable full configuration interaction (FCI) wave functions. The resultant energy spectrum shows a band structure characterized by ω for the large ω regime whereas for the small ω regime it shows an energy-level pattern dominated by excitation into the in-phase motion of the two particles. The observed trend has been rationalized on the basis of the nodal patterns of the FCI wave functions. 

Keywords: Confined systems, positron, wave function, Wigner molecule, quantum dots.

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1152 Alternative Splicingof an Arabidopsis Gene, At2g24600, Encoding Ankyrin-Repeat Protein

Authors: H. Sakamoto, S. Kurosawa, M. Suzuki, S. Oguri

Abstract:

In Arabidopsis, several genes encoding proteins with ankyrin repeats and transmembrane domains (AtANKTM) have been identified as mediators of biotic and abiotic stress responses. It has been known that the expression of an AtANKTM gene, At2g24600, is induced in response to abiotic stress and that there are four splicing variants derived from this locus. In this study, by RT-PCR and sequencing analysis, an unknown splicing variant of the At2g24600 transcript was identified. Based on differences in the predicted amino acid sequences, the five splicing variants are divided into three groups. The three predicted proteins are highly homologous, yet have different numbers of ankyrinrepeats and transmembrane domains. It is generally considered that ankyrin repeats mediate protein-protein interaction and that the number oftransmembrane domains affects membrane topology of proteins. The protein variants derived from the At2g24600 locus may have different molecular functions each other.

Keywords: Alternative splicing, ankyrin repeats, transmembrane domains, Arabidopsis.

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1151 Formation of Chemical Compound Layer at the Interface of Initial Substances A and B with Dominance of Diffusion of the A Atoms

Authors: Pavlo Selyshchev, Samuel Akintunde

Abstract:

A theoretical approach to consider formation of chemical compound layer at the interface between initial substances A and B due to the interfacial interaction and diffusion is developed. It is considered situation when speed of interfacial interaction is large enough and diffusion of A-atoms through AB-layer is much more then diffusion of B-atoms. Atoms from A-layer diffuse toward B-atoms and form AB-atoms on the surface of B-layer. B-atoms are assumed to be immobile. The growth kinetics of the AB-layer is described by two differential equations with non-linear coupling, producing a good fit to the experimental data. It is shown that growth of the thickness of the AB-layer determines by dependence of chemical reaction rate on reactants concentration. In special case the thickness of the AB-layer can grow linearly or parabolically depending on that which of processes (interaction or the diffusion) controls the growth. The thickness of AB-layer as function of time is obtained. The moment of time (transition point) at which the linear growth are changed by parabolic is found.

Keywords: Phase formation, Binary systems, Interfacial Reaction, Diffusion, Compound layers, Growth kinetics.

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1150 Blood Cell Dynamics in a Simple Shear Flow using an Implicit Fluid-Structure Interaction Method Based on the ALE Approach

Authors: Choeng-Ryul Choi, Chang-Nyung Kim, Tae-Hyub Hong

Abstract:

A numerical method is developed for simulating the motion of particles with arbitrary shapes in an effectively infinite or bounded viscous flow. The particle translational and angular motions are numerically investigated using a fluid-structure interaction (FSI) method based on the Arbitrary-Lagrangian-Eulerian (ALE) approach and the dynamic mesh method (smoothing and remeshing) in FLUENT ( ANSYS Inc., USA). Also, the effects of arbitrary shapes on the dynamics are studied using the FSI method which could be applied to the motions and deformations of a single blood cell and multiple blood cells, and the primary thrombogenesis caused by platelet aggregation. It is expected that, combined with a sophisticated large-scale computational technique, the simulation method will be useful for understanding the overall properties of blood flow from blood cellular level (microscopic) to the resulting rheological properties of blood as a mass (macroscopic).

Keywords: Blood Flow, Fluid-Structure Interaction (FSI), Micro-Channels, Arbitrary Shapes, Red Blood Cells (RBCs)

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1149 Nonlinear Mathematical Model of the Rotor Motion in a Thin Hydrodynamic Gap

Authors: Jaroslav Krutil, František Pochylý, Simona Fialová

Abstract:

The article presents two mathematical models of the interaction between a rotating shaft and an incompressible fluid. The mathematical model includes both the journal bearings and the axially traversed hydrodynamic sealing gaps of hydraulic machines. A method is shown for the identification of additional effects of the fluid acting on the rotor of the machine, both for a linear and a nonlinear model. The interaction is expressed by matrices of mass, stiffness and damping.

Keywords: CFD modeling, hydrodynamic gap, matrices of mass, stiffness and damping, nonlinear mathematical model.

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1148 Combining Molecular Statics with Heat Transfer Finite Difference Method for Analysis of Nanoscale Orthogonal Cutting of Single-Crystal Silicon Temperature Field

Authors: Zone-Ching Lin, Meng-Hua Lin, Ying-Chih Hsu

Abstract:

This paper uses quasi-steady molecular statics model and diamond tool to carry out simulation temperature rise of nanoscale orthogonal cutting single-crystal silicon. It further qualitatively analyzes temperature field of silicon workpiece without considering heat transfer and considering heat transfer. This paper supposes that the temperature rise of workpiece is mainly caused by two heat sources: plastic deformation heat and friction heat. Then, this paper develops a theoretical model about production of the plastic deformation heat and friction heat during nanoscale orthogonal cutting. After the increased temperature produced by these two heat sources are added up, the acquired total temperature rise at each atom of the workpiece is substituted in heat transfer finite difference equation to carry out heat transfer and calculates the temperature field in each step and makes related analysis.

Keywords: Quasi-steady molecular statics, Nanoscale orthogonal cutting, Finite difference, Temperature.

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1147 The Relationship between Adolescent Emotional Inhibition and Depression Disorder: The Moderate Effect of Gender

Authors: Jia-Ru Li, Chih-Hung Wang, Ching-Wen Lin

Abstract:

The association between emotional inhibition strategies linked to depression has been showed inconsistent among studies. Mild emotional inhibition maybe benefit for social interaction, especially for female among East Asian cultures. The present study aimed to examine whether the inhibition–depression relationship is dependent on level of emotion inhibition and gender context, given differing value of suppressing emotional displays. We hypothesized that the negative associations between inhibition and adolescent depression would not directly, in which affected by interaction between emotion inhibition and gender. To test this hypothesis, we asked 309 junior high school students which age range from 12 to14 years old to report on their use of emotion inhibition and depression syndrome. A multiple regressions analysis revealed that significant interaction that gender as a moderator to the relationships between emotion inhibition and adolescent depression. The group with the highest level of depression was girls with high levels of emotion inhibition, whose depression score was higher than that of boys with high levels of emotion inhibition. The result highlights that the importance of context in understanding the inhibition-depression relationship.

Keywords: Emotional inhibition strategies, gender, adolescent depression.

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1146 Seismic Investigation on the Effect of Surface Structures and Twin Tunnel on the Site Response in Urban Areas

Authors: Seyed Abolhasan Naeini, Saeideh Mohammadi

Abstract:

Site response has a profound effect on earthquake damages. Seismic interaction of urban tunnels with surface structures could also affect seismic site response. Here, we use FLAC 2D to investigate the interaction of a single tunnel and twin tunnels-surface structures on the site response. Soil stratification and properties are selected based on Line. No 7 of the Tehran subway. The effect of surface structure is considered in two ways: Equivalent surcharge and geometrical modeling of the structure. Comparison of the results shows that consideration of the structure geometry is vital in dynamic analysis and leads to the changes in the magnitude of displacements, accelerations and response spectrum. Therefore it is necessary for the surface structures to be wholly modeled and not just considered as a surcharge in dynamic analysis. The use of twin tunnel also leads to the reduction of dynamic residual settlement.

Keywords: Superstructure, tunnel, site response, surcharge, interaction.

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1145 Molecular Docking on Recomposed versus Crystallographic Structures of Zn-Dependent Enzymes and their Natural Inhibitors

Authors: Tudor Petreuş, Andrei Neamţu, Cristina Dascălu, Paul Dan Sîrbu, Carmen E. Cotrutz

Abstract:

Matrix metalloproteinases (MMP) are a class of structural and functional related enzymes involved in altering the natural elements of the extracellular matrix. Most of the MMP structures are cristalographycally determined and published in WorldWide ProteinDataBank, isolated, in full structure or bound to natural or synthetic inhibitors. This study proposes an algorithm to replace missing crystallographic structures in PDB database. We have compared the results of a chosen docking algorithm with a known crystallographic structure in order to validate enzyme sites reconstruction there where crystallographic data are missing.

Keywords: matrix metalloproteinases, molecular docking, structure superposition, surface complementarity.

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1144 Optical and Double Folding Model Analysis for Alpha Particles Elastically Scattered from 9Be and 11B Nuclei at Different Energies

Authors: Ahmed H. Amer, A. Amar, Sh. Hamada, I. I. Bondouk, F. A. El-Hussiny

Abstract:

Elastic scattering of α-particles from 9Be and 11B nuclei at different alpha energies have been analyzed. Optical model parameters (OMPs) of α-particles elastic scattering by these nuclei at different energies have been obtained. In the present calculations, the real part of the optical potential are derived by folding of nucleonnucleon (NN) interaction into nuclear matter density distribution of the projectile and target nuclei using computer code FRESCO. A density-dependent version of the M3Y interaction (CDM3Y6), which is based on the G-matrix elements of the Paris NN potential, has been used. Volumetric integrals of the real and imaginary potential depth (JR, JW) have been calculated and found to be energy dependent. Good agreement between the experimental data and the theoretical predictions in the whole angular range. In double folding (DF) calculations, the obtained normalization coefficient Nr is in the range 0.70–1.32.

Keywords: Elastic scattering of α-particles, optical model parameters, double folding model, nucleon-nucleon interaction.

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1143 Wasp Venom Peptides may play a role in the Pathogenesis of Acute Disseminated Encephalomyelitis in Humans: A Structural Similarity Analysis

Authors: Permphan Dharmasaroja

Abstract:

Acute disseminated encephalomyelitis (ADEM) has been reported to develop after a hymenoptera sting, but its pathogenesis is not known in detail. Myelin basic protein (MBP)- specific T cells have been detected in the blood of patients with ADEM, and a proportion of these patients develop multiple sclerosis (MS). In an attempt to understand the mechanisms underlying ADEM, molecular mimicry between hymenoptera venom peptides and the human immunodominant MBP peptide was scrutinized, based on the sequence and structural similarities, whether it was the root of the disease. The results suggest that the three wasp venom peptides have low sequence homology with the human immunodominant MBP residues 85-99. Structural similarity analysis among the three venom peptides and the MS-related HLA-DR2b (DRA, DRB1*1501)-associated immunodominant MHC binding/TCR contact residues 88-93, VVHFFK showed that hyaluronidase residues 7-12, phospholipase A1 residues 98-103, and antigen 5 residues 109-114 showed a high degree of similarity 83.3%, 100%, and 83.3% respectively. In conclusion, some wasp venom peptides, particularly phospholipase A1, may potentially act as the molecular motifs of the human 3HLA-DR2b-associated immunodominant MBP88-93, and possibly present a mechanism for induction of wasp sting-associated ADEM.

Keywords: central nervous system, Hymenoptera, myelin basicprotein, molecular mimicry.

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