Search results for: Minimum Force.
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 1688

Search results for: Minimum Force.

1148 Routing Algorithm for a Clustered Network

Authors: Hemanth KumarA.R, Sudhakara G., Satyanarayana B.S.

Abstract:

The Cluster Dimension of a network is defined as, which is the minimum cardinality of a subset S of the set of nodes having the property that for any two distinct nodes x and y, there exist the node Si, s2 (need not be distinct) in S such that ld(x,s1) — d(y, s1)1 > 1 and d(x,s2) < d(x,$) for all s E S — {s2}. In this paper, strictly non overlap¬ping clusters are constructed. The concept of LandMarks for Unique Addressing and Clustering (LMUAC) routing scheme is developed. With the help of LMUAC routing scheme, It is shown that path length (upper bound)PLN,d < PLD, Maximum memory space requirement for the networkMSLmuAc(Az) < MSEmuAc < MSH3L < MSric and Maximum Link utilization factor MLLMUAC(i=3) < MLLMUAC(z03) < M Lc

Keywords: Metric dimension, Cluster dimension, Cluster.

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1147 Numerical Simulation for Self-Loosening Phenomenon Analysis of Bolt Joint under Vibration

Authors: Long Kim Vu, Ban Dang Nguyen

Abstract:

In this paper, the finite element method (FEM) is utilized to simulate the comprehensive process including tightening, releasing and self-loosening of a bolt joint under transverse vibration. Following to the accurate geometry of helical threads, an absolutely hexahedral meshing is implemented. The accuracy of simulation process is verified and validated by comparison with the experimental results on clamping force-vibration relationship, which shows the sufficient correlation. Further analysis with different amplitude and frequency of transverse vibration is done to determine the dominant factor inducing the failure.

Keywords: Bolt self-loosening, contact state, FEM, transverse vibration.

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1146 An Approach on the Design of a Solar Cell Characterization Device

Authors: Christoph Mayer, Dominik Holzmann

Abstract:

This paper presents the development of a compact, portable and easy to handle solar cell characterization device. The presented device reduces the effort and cost of single solar cell characterization to a minimum. It enables realistic characterization of cells under sunlight within minutes. In the field of photovoltaic research the common way to characterize a single solar cell or a module is, to measure the current voltage curve. With this characteristic the performance and the degradation rate can be defined which are important for the consumer or developer. The paper consists of the system design description, a summary of the measurement results and an outline for further developments.

Keywords: Solar cell, photovoltaics, PV, characterization.

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1145 Dominant Correlation Effects in Atomic Spectra

Authors: Hubert Klar

Abstract:

High double excitation of two-electron atoms has been investigated using hyperpherical coordinates within a modified adiabatic expansion technique. This modification creates a novel fictitious force leading to a spontaneous exchange symmetry breaking at high double excitation. The Pauli principle must therefore be regarded as approximation valid only at low excitation energy. Threshold electron scattering from high Rydberg states shows an unexpected time reversal symmetry breaking. At threshold for double escape we discover a broad (few eV) Cooper pair.

Keywords: Correlation, resonances, threshold ionization, Cooper pair.

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1144 An Overview of Some High Order and Multi-Level Finite Difference Schemes in Computational Aeroacoustics

Authors: Appanah Rao Appadu, Muhammad Zaid Dauhoo

Abstract:

In this paper, we have combined some spatial derivatives with the optimised time derivative proposed by Tam and Webb in order to approximate the linear advection equation which is given by = 0. Ôêé Ôêé + Ôêé Ôêé x f t u These spatial derivatives are as follows: a standard 7-point 6 th -order central difference scheme (ST7), a standard 9-point 8 th -order central difference scheme (ST9) and optimised schemes designed by Tam and Webb, Lockard et al., Zingg et al., Zhuang and Chen, Bogey and Bailly. Thus, these seven different spatial derivatives have been coupled with the optimised time derivative to obtain seven different finite-difference schemes to approximate the linear advection equation. We have analysed the variation of the modified wavenumber and group velocity, both with respect to the exact wavenumber for each spatial derivative. The problems considered are the 1-D propagation of a Boxcar function, propagation of an initial disturbance consisting of a sine and Gaussian function and the propagation of a Gaussian profile. It is known that the choice of the cfl number affects the quality of results in terms of dissipation and dispersion characteristics. Based on the numerical experiments solved and numerical methods used to approximate the linear advection equation, it is observed in this work, that the quality of results is dependent on the choice of the cfl number, even for optimised numerical methods. The errors from the numerical results have been quantified into dispersion and dissipation using a technique devised by Takacs. Also, the quantity, Exponential Error for Low Dispersion and Low Dissipation, eeldld has been computed from the numerical results. Moreover, based on this work, it has been found that when the quantity, eeldld can be used as a measure of the total error. In particular, the total error is a minimum when the eeldld is a minimum.

Keywords: Optimised time derivative, dissipation, dispersion, cfl number, Nomenclature: k : time step, h : spatial step, β :advection velocity, r: cfl/Courant number, hkrβ= , w =θ, h : exact wave number, n :time level, RPE : Relative phase error per unit time step, AFM :modulus of amplification factor

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1143 A Supervised Text-Independent Speaker Recognition Approach

Authors: Tudor Barbu

Abstract:

We provide a supervised speech-independent voice recognition technique in this paper. In the feature extraction stage we propose a mel-cepstral based approach. Our feature vector classification method uses a special nonlinear metric, derived from the Hausdorff distance for sets, and a minimum mean distance classifier.

Keywords: Text-independent speaker recognition, mel cepstral analysis, speech feature vector, Hausdorff-based metric, supervised classification.

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1142 Induced Acyclic Graphoidal Covers in a Graph

Authors: K. Ratan Singh, P. K. Das

Abstract:

An induced acyclic graphoidal cover of a graph G is a collection ψ of open paths in G such that every path in ψ has atleast two vertices, every vertex of G is an internal vertex of at most one path in ψ, every edge of G is in exactly one path in ψ and every member of ψ is an induced path. The minimum cardinality of an induced acyclic graphoidal cover of G is called the induced acyclic graphoidal covering number of G and is denoted by ηia(G) or ηia. Here we find induced acyclic graphoidal cover for some classes of graphs.

Keywords: Graphoidal cover, Induced acyclic graphoidal cover, Induced acyclic graphoidal covering number.

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1141 Effect of Impact Location upon Sub-Impacts between Beam and Block

Authors: T. F. Jin, X. C. Yin, P. B. Qian

Abstract:

The present investigation is concerned with sub-impacts taken placed when a rigid hemispherical-head block transversely impacts against a beam at different locations. Dynamic substructure technique for elastic-plastic impact is applied to solve numerically this problem. The time history of impact force and energy exchange between block and beam are obtained. The process of sub-impacts is analyzed from the energy exchange point of view. The results verify the influences of the impact location on impact duration, the first sub-impact and energy exchange between the beam and the block.

Keywords: Beam, sub-impact, substructure, elastic-plasticity.

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1140 Simulation Studies on Concentrating Type Solar Cookers

Authors: V. K. Krishnan, T. Balusamy

Abstract:

A solar dish collector has been designed, fabricated and tested for its performance on 10-03-2015 in Salem, Tamilnadu, India. The experiments on cooking vessels of coated and un-coated with 5 Liters capacity have been used for cooking Rice. The results are shown in graphs. The solar cooker is always capable of cooking food within the expected length of time and based on the solar radiation levels. With minimum cooking power, the coated pressure cooker of 5 Liters capacity cooks the food at faster manner. This is due to the conductivity of the coating material provided in the cooker.

Keywords: Solar cooker, solar concentrator type, thermal performance, simulation.

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1139 Time Map

Authors: A. Peveri

Abstract:

The interaction of mass will determine the curvature of space-time, may determine that events proceed at different rates of time at each point in space, so each has a corresponding gravitational potential time. So we can find different values ​​of gravity (g), corresponding to different times (t), thus making a "map of time in space." The space-time is curved by present mass, causing a force of attraction towards the body, but if you invest the curvature of space-time, we find that this field is repulsive: Obtaining negative gravitational forces and positive gravitational forces respectively.

Keywords: Space-time, time, positive gravitation, negative gravitation.

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1138 A Methodology for Definition of Road Networks in Rural Areas of Nepal

Authors: J. K. Shrestha, A. Benta, R. B. Lopes, N. Lopes

Abstract:

This work provides a practical method for the development of rural road networks in rural areas of developing countries. The proposed methodology enables to determine obligatory points in the rural road network maximizing the number of settlements that have access to basic services within a given maximum distance. The proposed methodology is simple and practical, hence, highly applicable to real-world scenarios, as demonstrated in the definition of the road network for the rural areas of Nepal.

Keywords: Minimum spanning tree, nodal points, rural road network.

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1137 A Frame Work for the Development of a Suitable Method to Find Shoot Length at Maturity of Mustard Plant Using Soft Computing Model

Authors: Satyendra Nath Mandal, J. Pal Choudhury, Dilip De, S. R. Bhadra Chaudhuri

Abstract:

The production of a plant can be measured in terms of seeds. The generation of seeds plays a critical role in our social and daily life. The fruit production which generates seeds, depends on the various parameters of the plant, such as shoot length, leaf number, root length, root number, etc When the plant is growing, some leaves may be lost and some new leaves may appear. It is very difficult to use the number of leaves of the tree to calculate the growth of the plant.. It is also cumbersome to measure the number of roots and length of growth of root in several time instances continuously after certain initial period of time, because roots grow deeper and deeper under ground in course of time. On the contrary, the shoot length of the tree grows in course of time which can be measured in different time instances. So the growth of the plant can be measured using the data of shoot length which are measured at different time instances after plantation. The environmental parameters like temperature, rain fall, humidity and pollution are also play some role in production of yield. The soil, crop and distance management are taken care to produce maximum amount of yields of plant. The data of the growth of shoot length of some mustard plant at the initial stage (7,14,21 & 28 days after plantation) is available from the statistical survey by a group of scientists under the supervision of Prof. Dilip De. In this paper, initial shoot length of Ken( one type of mustard plant) has been used as an initial data. The statistical models, the methods of fuzzy logic and neural network have been tested on this mustard plant and based on error analysis (calculation of average error) that model with minimum error has been selected and can be used for the assessment of shoot length at maturity. Finally, all these methods have been tested with other type of mustard plants and the particular soft computing model with the minimum error of all types has been selected for calculating the predicted data of growth of shoot length. The shoot length at the stage of maturity of all types of mustard plants has been calculated using the statistical method on the predicted data of shoot length.

Keywords: Fuzzy time series, neural network, forecasting error, average error.

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1136 Solving the Economic Dispatch Problem by Using Differential Evolution

Authors: S. Khamsawang, S. Jiriwibhakorn

Abstract:

This paper proposes an application of the differential evolution (DE) algorithm for solving the economic dispatch problem (ED). Furthermore, the regenerating population procedure added to the conventional DE in order to improve escaping the local minimum solution. To test performance of DE algorithm, three thermal generating units with valve-point loading effects is used for testing. Moreover, investigating the DE parameters is presented. The simulation results show that the DE algorithm, which had been adjusted parameters, is better convergent time than other optimization methods.

Keywords: Differential evolution, Economic dispatch problem, Valve-point loading effect, Optimization method.

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1135 New Efficient Iterative Optimization Algorithm to Design the Two Channel QMF Bank

Authors: Ram Kumar Soni, Alok Jain, Rajiv Saxena

Abstract:

This paper proposes an efficient method for the design of two channel quadrature mirror filter (QMF) bank. To achieve minimum value of reconstruction error near to perfect reconstruction, a linear optimization process has been proposed. Prototype low pass filter has been designed using Kaiser window function. The modified algorithm has been developed to optimize the reconstruction error using linear objective function through iteration method. The result obtained, show that the performance of the proposed algorithm is better than that of the already exists methods.

Keywords: Filterbank, near perfect reconstruction, Kaiserwindow, QMF.

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1134 A new Cellular Automata Model of Cardiac Action Potential Propagation based on Summation of Excited Neighbors

Authors: F. Pourhasanzade, S. H. Sabzpoushan

Abstract:

The heart tissue is an excitable media. A Cellular Automata is a type of model that can be used to model cardiac action potential propagation. One of the advantages of this approach against the methods based on differential equations is its high speed in large scale simulations. Recent cellular automata models are not able to avoid flat edges in the result patterns or have large neighborhoods. In this paper, we present a new model to eliminate flat edges by minimum number of neighbors.

Keywords: Cellular Automata, Action Potential Simulation, Isotropic Pattern.

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1133 Induction of Expressive Rules using the Binary Coding Method

Authors: Seyed R Mousavi

Abstract:

In most rule-induction algorithms, the only operator used against nominal attributes is the equality operator =. In this paper, we first propose the use of the inequality operator, , in addition to the equality operator, to increase the expressiveness of induced rules. Then, we present a new method, Binary Coding, which can be used along with an arbitrary rule-induction algorithm to make use of the inequality operator without any need to change the algorithm. Experimental results suggest that the Binary Coding method is promising enough for further investigation, especially in cases where the minimum number of rules is desirable.

Keywords: Data mining, Inequality operator, Number of rules, Rule-induction.

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1132 New Design Constraints of FIR Filter on Magnitude and Phase of Error Function

Authors: Raghvendra Kumar, Lillie Dewan

Abstract:

Exchange algorithm with constraints on magnitude and phase error separately in new way is presented in this paper. An important feature of the algorithms presented in this paper is that they allow for design constraints which often arise in practical filter design problems. Meeting required minimum stopband attenuation or a maximum deviation from the desired magnitude and phase responses in the passbands are common design constraints that can be handled by the methods proposed here. This new algorithm may have important advantages over existing technique, with respect to the speed and stability of convergence, memory requirement and low ripples.

Keywords: Least square estimation, Constraints, Exchange algorithm.

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1131 The Finite Difference Scheme for the Suspended String Equation with the Nonlinear External Forces

Authors: Jaipong Kasemsuwan

Abstract:

This paper presents the finite difference scheme and the numerical simulation of suspended string. The vibration solutions when the various external forces are taken into account are obtained and compared with the solutions without external force. In addition, we also investigate how the external forces and their powers and coefficients affect the amplitude of vibration.

Keywords: Nonlinear external forces, Numerical simulation, Suspended string equation.

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1130 The Sign in the Communication Process

Authors: S. Pesina, T. Solonchak

Abstract:

In the process of information transmission (concept verbalization) we deal mostly with the substance (contents), and then pay attention to the form. Recalling events from the remote past, often we cannot exactly reproduce specific heard or pronounced words, as well as the syntactic structures. We remember events, feelings, images; we recall the general contents of the discourse. The thought gets a specific language form only during the concept verbalization phase. With minimum time for pondering, depending on the language competence level, the grammar and syntactic shaping often occurs automatically with the use of famous models and stereotypes. This means that the language form adapts itself to the consciousness, and not vice versa.

Keywords: Lexical eidos, phenomenology, noema, polysemantic word, semantic core.

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1129 A Compact Pi Network for Reducing Bit Error Rate in Dispersive FIR Channel Noise Model

Authors: Kavita Burse, R.N. Yadav, S.C. Shrivastava, Vishnu Pratap Singh Kirar

Abstract:

During signal transmission, the combined effect of the transmitter filter, the transmission medium, and additive white Gaussian noise (AWGN) are included in the channel which distort and add noise to the signal. This causes the well defined signal constellation to spread causing errors in bit detection. A compact pi neural network with minimum number of nodes is proposed. The replacement of summation at each node by multiplication results in more powerful mapping. The resultant pi network is tested on six different channels.

Keywords: Additive white Gaussian noise, digitalcommunication system, multiplicative neuron, Pi neural network.

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1128 Modeling of Sensitivity for SPR Biosensors- New Aspects

Authors: Volodymyr Chegel

Abstract:

The computer modeling is carried out for parameter of sensitivity of optoelectronic chemical and biosensors, using phenomena of surface plasmon resonance (SPR). The physical model of SPR-sensor-s is described with (or without) of modifications of sensitive gold film surface by a dielectric layer. The variants of increasing of sensitivity for SPR-biosensors, constructed on the principle gold – dielectric – biomolecular layer are considered. Two methods of mathematical treatment of SPR-curve are compared – traditional, with estimation of sensor-s response as shift of the SPRcurve minimum and proposed, for system with dielectric layer, using calculating of the derivative in the point of SPR-curve half-width.

Keywords: Surface Plasmon Resonance, modeling, sensitivity, biosensor

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1127 Power Minimization in Decode-and-XOR-Forward Two-Way Relay Networks

Authors: Dong-Woo Lim, Chang-Jae Chun, Hyung-Myung Kim

Abstract:

We consider a two-way relay network where two sources exchange information. A relay helps the two sources exchange information using the decode-and-XOR-forward protocol. We investigate the power minimization problem with minimum rate constraints. The system needs two time slots and in each time slot the required rate pair should be achievable. The power consumption is minimized in each time slot and we obtained the closed form solution. The simulation results confirm that the proposed power allocation scheme consumes lower total power than the conventional schemes.

Keywords: Decode-and-XOR-forward, power minimization, two-way relay

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1126 An Efficient Iterative Updating Method for Damped Structural Systems

Authors: Jiashang Jiang

Abstract:

Model updating is an inverse eigenvalue problem which concerns the modification of an existing but inaccurate model with measured modal data. In this paper, an efficient gradient based iterative method for updating the mass, damping and stiffness matrices simultaneously using a few of complex measured modal data is developed. Convergence analysis indicates that the iterative solutions always converge to the unique minimum Frobenius norm symmetric solution of the model updating problem by choosing a special kind of initial matrices.

Keywords: Model updating, iterative algorithm, damped structural system, optimal approximation.

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1125 Parametric Non-Linear Analysis of Reinforced Concrete Frames with Supplemental Damping Systems

Authors: Daniele Losanno, Giorgio Serino

Abstract:

This paper focuses on parametric analysis of reinforced concrete structures equipped with supplemental damping braces. Practitioners still luck sufficient data for current design of damper added structures and often reduce the real model to a pure damper braced structure even if this assumption is neither realistic nor conservative. In the present study, the damping brace is modelled as made by a linear supporting brace connected in series with the viscous/hysteretic damper. Deformation capacity of existing structures is usually not adequate to undergo the design earthquake. In spite of this, additional dampers could be introduced strongly limiting structural damage to acceptable values, or in some cases, reducing frame response to elastic behavior. This work is aimed at providing useful considerations for retrofit of existing buildings by means of supplemental damping braces. The study explicitly takes into consideration variability of (a) relative frame to supporting brace stiffness, (b) dampers’ coefficient (viscous coefficient or yielding force) and (c) non-linear frame behavior. Non-linear time history analysis has been run to account for both dampers’ behavior and non-linear plastic hinges modelled by Pivot hysteretic type. Parametric analysis based on previous studies on SDOF or MDOF linear frames provide reference values for nearly optimal damping systems design. With respect to bare frame configuration, seismic response of the damper-added frame is strongly improved, limiting deformations to acceptable values far below ultimate capacity. Results of the analysis also demonstrated the beneficial effect of stiffer supporting braces, thus highlighting inadequacy of simplified pure damper models. At the same time, the effect of variable damping coefficient and yielding force has to be treated as an optimization problem.

Keywords: Brace stiffness, dissipative braces, non-linear analysis, plastic hinges, reinforced concrete.

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1124 Aerodynamic Interaction between Two Speed Skaters Measured in a Closed Wind Tunnel

Authors: Ola Elfmark, Lars M. Bardal, Luca Oggiano, H˚avard Myklebust

Abstract:

Team pursuit is a relatively new event in international long track speed skating. For a single speed skater the aerodynamic drag will account for up to 80% of the braking force, thus reducing the drag can greatly improve the performance. In a team pursuit the interactions between athletes in near proximity will also be essential, but is not well studied. In this study, systematic measurements of the aerodynamic drag, body posture and relative positioning of speed skaters have been performed in the low speed wind tunnel at the Norwegian University of Science and Technology, in order to investigate the aerodynamic interaction between two speed skaters. Drag measurements of static speed skaters drafting, leading, side-by-side, and dynamic drag measurements in a synchronized and unsynchronized movement at different distances, were performed. The projected frontal area was measured for all postures and movements and a blockage correction was performed, as the blockage ratio ranged from 5-15% in the different setups. The static drag measurements where performed on two test subjects in two different postures, a low posture and a high posture, and two different distances between the test subjects 1.5T and 3T where T being the length of the torso (T=0.63m). A drag reduction was observed for all distances and configurations, from 39% to 11.4%, for the drafting test subject. The drag of the leading test subject was only influenced at -1.5T, with the biggest drag reduction of 5.6%. An increase in drag was seen for all side-by-side measurements, the biggest increase was observed to be 25.7%, at the closest distance between the test subjects, and the lowest at 2.7% with ∼ 0.7 m between the test subjects. A clear aerodynamic interaction between the test subjects and their postures was observed for most measurements during static measurements, with results corresponding well to recent studies. For the dynamic measurements, the leading test subject had a drag reduction of 3% even at -3T. The drafting showed a drag reduction of 15% when being in a synchronized (sync) motion with the leading test subject at 4.5T. The maximal drag reduction for both the leading and the drafting test subject were observed when being as close as possible in sync, with a drag reduction of 8.5% and 25.7% respectively. This study emphasize the importance of keeping a synchronized movement by showing that the maximal gain for the leading and drafting dropped to 3.2% and 3.3% respectively when the skaters are in opposite phase. Individual differences in technique also appear to influence the drag of the other test subject.

Keywords: Aerodynamic interaction, drag cycle, drag force, frontal area, speed skating.

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1123 Dynamic Analyze of Snake Robot

Authors: Seif Dalilsafaei

Abstract:

Crawling movement as a motive mode seen in nature of some animals such as snakes possesses a specific syntactic and dynamic analysis. Serpentine robot designed by inspiration from nature and snake-s crawling motion, is regarded as a crawling robot. In this paper, a serpentine robot with spiral motion model will be analyzed. The purpose of this analysis is to calculate the vertical and tangential forces along snake-s body and to determine the parameters affecting on these forces. Two types of serpentine robots have been designed in order to examine the achieved relations explained below.

Keywords: Force, Dynamic analyze, Joint and Snake robot.

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1122 The Adsorption of SDS on Ferro-Precipitates

Authors: R.Marsalek

Abstract:

This paper present a new way to find the aerodynamic characteristic equation of missile for the numerical trajectories prediction more accurate. The goal is to obtain the polynomial equation based on two missile characteristic parameters, angle of attack (α ) and flight speed (ν ). First, the understudied missile is modeled and used for flow computational model to compute aerodynamic force and moment. Assume that performance range of understudied missile where range -10< α <10 and 0< ν <200. After completely obtained results of all cases, the data are fit by polynomial interpolation to create equation of each case and then combine all equations to form aerodynamic characteristic equation, which will be used for trajectories simulation.

Keywords: ferro-precipitate, adsorption, SDS, zeta potential

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1121 Induced Acyclic Path Decomposition in Graphs

Authors: Abraham V. M., I. Sahul Hamid

Abstract:

A decomposition of a graph G is a collection ψ of graphs H1,H2, . . . , Hr of G such that every edge of G belongs to exactly one Hi. If each Hi is either an induced path in G, then ψ is called an induced acyclic path decomposition of G and if each Hi is a (induced) cycle in G then ψ is called a (induced) cycle decomposition of G. The minimum cardinality of an induced acyclic path decomposition of G is called the induced acyclic path decomposition number of G and is denoted by ¤Çia(G). Similarly the cyclic decomposition number ¤Çc(G) is defined. In this paper we begin an investigation of these parameters.

Keywords: Cycle decomposition, Induced acyclic path decomposition, Induced acyclic path decomposition number.

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1120 A New Method for Estimation of the Source Coherency Structure of Wideband Sources

Authors: Yong-jun Zhao, Heng-li Zhang, Zong-yun Hu

Abstract:

Based on the sources- smoothed rank profile (SRP) and modified minimum description length (MMDL) principle, a method for estimation of the source coherency structure (SCS) and the number of wideband sources is proposed in this paper. Instead of focusing, we first use a spatial smoothing technique to pre-process the array covariance matrix of each frequency for de-correlating the sources and then use smoothed rank profile to determine the SCS and the number of wideband sources. We demonstrate the availability of the method by numerical simulations.

Keywords: Wideband sources, source coherency structure (SCS), smoothed rank profile (SRP).

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1119 Electron Density Discrepancy Analysis of Energy Metabolism Coenzymes

Authors: Alan Luo, Hunter N. B. Moseley

Abstract:

Many macromolecular structure entries in the Protein Data Bank (PDB) have a range of regional (localized) quality issues, be it derived from X-ray crystallography, Nuclear Magnetic Resonance (NMR) spectroscopy, or other experimental approaches. However, most PDB entries are judged by global quality metrics like R-factor, R-free, and resolution for X-ray crystallography or backbone phi-psi distribution statistics and average restraint violations for NMR. Regional quality is often ignored when PDB entries are re-used for a variety of structurally based analyses. The binding of ligands, especially ligands involved in energy metabolism, is of particular interest in many structurally focused protein studies. Using a regional quality metric that provides chemically interpretable information from electron density maps, a significant number of outliers in regional structural quality was detected across X-ray crystallographic PDB entries for proteins bound to biochemically critical ligands. In this study, a series of analyses was performed to evaluate both specific and general potential factors that could promote these outliers. In particular, these potential factors were the minimum distance to a metal ion, the minimum distance to a crystal contact, and the isotropic atomic b-factor. To evaluate these potential factors, Fisher’s exact tests were performed, using regional quality criteria of outlier (top 1%, 2.5%, 5%, or 10%) versus non-outlier compared to a potential factor metric above versus below a certain outlier cutoff. The results revealed a consistent general effect from region-specific normalized b-factors but no specific effect from metal ion contact distances and only a very weak effect from crystal contact distance as compared to the b-factor results. These findings indicate that no single specific potential factor explains a majority of the outlier ligand-bound regions, implying that human error is likely as important as these other factors. Thus, all factors, including human error, should be considered when regions of low structural quality are detected. Also, the downstream re-use of protein structures for studying ligand-bound conformations should screen the regional quality of the binding sites. Doing so prevents misinterpretation due to the presence of structural uncertainty or flaws in regions of interest.

Keywords: Biomacromolecular structure, coenzyme, electron density discrepancy analysis, X-ray crystallography.

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