Search results for: Non-linear optical materials

Authors: Madiha Tariq, Hena Rabbani

Abstract:

Recently, cavity-optomechanics becomes an extensive research field that has manipulated the mechanical effects of light for coupling of the optical field with other physical objects specifically with regards to dynamical localization. We investigate the dynamical localization (both in momentum and position space) for a vibrational mirror in a Fabry-Pérot cavity driven by a single mode optical field and a transverse probe field. The weak probe field phenomenon results in classical chaos in phase space and spatio temporal dynamics in position |ψ(x)²| and momentum space |ψ(p)²| versus time show quantum localization in both momentum and position space. Also, we discuss the parametric dependencies of dynamical localization for a designated set of parameters to be experimentally feasible. Our work opens an avenue to manipulate the other optical phenomena and applicability of proposed work can be prolonged to turn-able laser sources in the future.

Keywords: Dynamical localization, cavity optomechanics, hamiltonian chaos, probe field.

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Authors: E. Batista, R. Mendes, A. Furtado, M. C. Ferreira, I. Godinho, J. A. Sousa, M. Alvares, R. Martins

Abstract:

Syringe pumps are commonly used for drug delivery in hospitals and clinical environments. These instruments are critical in neonatology and oncology, where any variation in the flow rate and drug dosing quantity can lead to severe incidents and even death of the patient. Therefore it is very important to determine the accuracy and precision of these devices using the suitable calibration methods. The Volume Laboratory of the Portuguese Institute for Quality (LVC/IPQ) uses two different methods to calibrate syringe pumps from 16 nL/min up to 20 mL/min. The Interferometric method uses an interferometer to monitor the distance travelled by a pusher block of the syringe pump in order to determine the flow rate. Therefore, knowing the internal diameter of the syringe with very high precision, the travelled distance, and the time needed for that travelled distance, it was possible to calculate the flow rate of the fluid inside the syringe and its uncertainty. As an alternative to the gravimetric and the interferometric method, a methodology based on the application of optical technology was also developed to measure flow rates. Mainly this method relies on measuring the increase of volume of a drop over time. The objective of this work is to compare the results of the calibration of two syringe pumps using the different methodologies described above. The obtained results were consistent for the three methods used. The uncertainties values were very similar for all the three methods, being higher for the optical drop method due to setup limitations.

Keywords: Calibration, interferometry, syringe pump, optical method, uncertainty.

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Authors: H. Mohammadiun, A. Kianifar, A. Kargar

Abstract:

Nowadays, there is little information, concerning the heat shield systems, and this information is not completely reliable to use in so many cases. for example, the precise calculation cannot be done for various materials. In addition, the real scale test has two disadvantages: high cost and low flexibility, and for each case we must perform a new test. Hence, using numerical modeling program that calculates the surface recession rate and interior temperature distribution is necessary. Also, numerical solution of governing equation for non-charring material ablation is presented in order to anticipate the recession rate and the heat response of non-charring heat shields. the governing equation is nonlinear and the Newton- Rafson method along with TDMA algorithm is used to solve this nonlinear equation system. Using Newton- Rafson method for solving the governing equation is one of the advantages of the solving method because this method is simple and it can be easily generalized to more difficult problems. The obtained results compared with reliable sources in order to examine the accuracy of compiling code.

Keywords: Ablation rate, surface recession, interior temperaturedistribution, non charring material ablation, Newton Rafson method.

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Authors: Daniela Elena Marinescu, Ioana Manafi, Dumitru Marin

Abstract:

We consider a Principal-Agent model with the Principal being a seller who does not know perfectly how much the buyer (the Agent) is willing to pay for the good. The buyer-s preferences are hence his private information. The model corresponds to the nonlinear pricing problem of Maskin and Riley. We assume there are three types of Agents. The model is solved using “informational rents" as variables. In the last section we present the main characteristics of the optimal contracts in asymmetric information and some possible extensions of the model.

Keywords: Adverse selection, asymmetric information, informational rent, nonlinear pricing, optimal contract

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Authors: M. A. Tayfun, M. A. Alkhalidi

Abstract:

The exact theoretical expression describing the probability distribution of nonlinear sea-surface elevations derived from the second-order narrowband model has a cumbersome form that requires numerical computations, not well-disposed to theoretical or practical applications. Here, the same narrowband model is reexamined to develop a simpler closed-form approximation suitable for theoretical and practical applications. The salient features of the approximate form are explored, and its relative validity is verified with comparisons to other readily available approximations, and oceanic data.

Keywords: Ocean waves, probability distributions, second-order nonlinearities, skewness coefficient, wave steepness.

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Authors: Fabrizio Logiurato

Abstract:

Light Polarization has many technological applications, and its discovery was crucial to reveal the transverse nature of the electromagnetic waves. However, despite its fundamental and practical importance, in high school, this property of light is often neglected. This is a pity not only for its conceptual relevance, but also because polarization gives the possibility to perform many brilliant experiments with low cost materials. Moreover, the treatment of this matter lends very well to an interdisciplinary approach between art, biology and technology, which usually makes things more interesting to students. For these reasons, we have developed, and in this work, we introduce a laboratory on light polarization for high school and undergraduate students. They can see beautiful pictures when birefringent materials are set between two crossed polarizing filters. Pupils are very fascinated and drawn into by what they observe. The colourful images remind them of those ones of abstract painting or alien landscapes. With this multidisciplinary teaching method, students are more engaged and participative, and also, the learning process of the respective physics concepts is more effective.

Keywords: Light polarization, optical activity, multidisciplinary education, science and art.

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Authors: József Valyon, Gábor Horváth

Abstract:

In comparison to the original SVM, which involves a quadratic programming task; LS–SVM simplifies the required computation, but unfortunately the sparseness of standard SVM is lost. Another problem is that LS-SVM is only optimal if the training samples are corrupted by Gaussian noise. In Least Squares SVM (LS–SVM), the nonlinear solution is obtained, by first mapping the input vector to a high dimensional kernel space in a nonlinear fashion, where the solution is calculated from a linear equation set. In this paper a geometric view of the kernel space is introduced, which enables us to develop a new formulation to achieve a sparse and robust estimate.

Keywords: Support Vector Machines, Least Squares SupportVector Machines, Regression, Sparse approximation.

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Authors: A. Elsayed Ahmed, A. Hafez, A. N. Ouda, H. Eldin Hussein Ahmed, H. Mohamed Abd-Elkader

Abstract:

Unmanned aircraft systems (UAS) are playing increasingly prominent roles in defense programs and defense strategies around the world. Technology advancements have enabled the development of it to do many excellent jobs as reconnaissance, surveillance, battle fighters, and communications relays. Simulating a small unmanned aerial vehicle (SUAV) dynamics and analyzing its behavior at the preflight stage is too important and more efficient. The first step in the UAV design is the mathematical modeling of the nonlinear equations of motion. . In this paper, a survey with a standard method to obtain the full non-linear equations of motion is utilized, and then the linearization of the equations according to a steady state flight condition (trimming) is derived. This modeling technique is applied to an Ultrastick-25e fixed wing UAV to obtain the valued linear longitudinal and lateral models. At the end the model is checked by matching between the behavior of the states of the nonlinear UAV and the resulted linear model with doublet at the control surfaces.

Keywords: Equations of motion, linearization, modeling, nonlinear model, UAV.

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Authors: Hoang Van Ngoc, Nguyen Vu Nhan, Nguyen Quang Bau

Abstract:

The light-effect in cylindrical quantum wire with an infinite potential for the case of electrons, optical phonon scattering, is studied based on the quantum kinetic equation. The density of the direct current in a cylindrical quantum wire by a linearly polarized electromagnetic wave, a DC electric field, and an intense laser field is calculated. Analytic expressions for the density of the direct current are studied as a function of the frequency of the laser radiation field, the frequency of the linearly polarized electromagnetic wave, the temperature of system, and the size of quantum wire. The density of the direct current in cylindrical quantum wire with an infinite potential for the case of electrons – optical phonon scattering is nonlinearly dependent on the frequency of the linearly polarized electromagnetic wave. The analytic expressions are numerically evaluated and plotted for a specific quantum wire, GaAs/GaAsAl.

Keywords: The light-effect, cylindrical quantum wire with an infinite potential, the density of the direct current, electrons - optical phonon scattering.

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Authors: Youngpo Lee, Jaewoo Lee, Seokho Yoon

Abstract:

This paper proposes a fast code acquisition scheme for optical code division multiple access (O-CDMA) systems. Unlike the conventional scheme, the proposed scheme employs multiple thresholds providing a shorter mean acquisition time (MAT) performance. The simulation results show that the MAT of the proposed scheme is shorter than that of the conventional scheme.

Keywords: Optical CDMA, acquisition, MAT, multiple-shift

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Authors: Mahdi Kiani, Hassan Salarieh, Aria Alasty, S. Mahdi Darbandi

Abstract:

The design and implementation of the hybrid control method for a three-pole active magnetic bearing (AMB) is proposed in this paper. The system is inherently nonlinear and conventional nonlinear controllers are a little complicated, while the proposed hybrid controller has a piecewise linear form, i.e. linear in each sub-region. A state-feedback hybrid controller is designed in this study, and the unmeasurable states are estimated by an observer. The gains of the hybrid controller are obtained by the Linear Quadratic Regulator (LQR) method in each sub-region. To evaluate the performance, the designed controller is implemented on an experimental setup in static mode. The experimental results show that the proposed method can efficiently stabilize the three-pole AMB system. The simplicity of design, domain of attraction, uncomplicated control law, and computational time are advantages of this method over other nonlinear control strategies in AMB systems.

Keywords: Active magnetic bearing, three pole AMB, hybrid control, Lyapunov function.

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Authors: F. Laaouad, M. Bouguerra, A. Hafaifa, A. Iratni

Abstract:

In this work, we treat the problems related to chemical and petrochemical plants of a certain complex process taking the centrifugal compressor as an example, a system being very complex by its physical structure as well as its behaviour (surge phenomenon). We propose to study the application possibilities of the recent control approaches to the compressor behaviour, and consequently evaluate their contribution in the practical and theoretical fields. Facing the studied industrial process complexity, we choose to make recourse to fuzzy logic for analysis and treatment of its control problem owing to the fact that these techniques constitute the only framework in which the types of imperfect knowledge can jointly be treated (uncertainties, inaccuracies, etc..) offering suitable tools to characterise them. In the particular case of the centrifugal compressor, these imperfections are interpreted by modelling errors, the neglected dynamics, no modelisable dynamics and the parametric variations. The purpose of this paper is to produce a total robust nonlinear controller design method to stabilize the compression process at its optimum steady state by manipulating the gas rate flow. In order to cope with both the parameter uncertainty and the structured non linearity of the plant, the proposed method consists of a linear steady state regulation that ensures robust optimal control and of a nonlinear compensation that achieves the exact input/output linearization.

Keywords: Compressor, Fuzzy logic, Surge control, Bilinearcontroller, Stability analysis, Nonlinear plant.

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Authors: C. Lodato, S. Lopes

Abstract:

The image segmentation method described in this paper has been developed as a pre-processing stage to be used in methodologies and tools for video/image indexing and retrieval by content. This method solves the problem of whole objects extraction from background and it produces images of single complete objects from videos or photos. The extracted images are used for calculating the object visual features necessary for both indexing and retrieval processes. The segmentation algorithm is based on the cooperation among an optical flow evaluation method, edge detection and region growing procedures. The optical flow estimator belongs to the class of differential methods. It permits to detect motions ranging from a fraction of a pixel to a few pixels per frame, achieving good results in presence of noise without the need of a filtering pre-processing stage and includes a specialised model for moving object detection. The first task of the presented method exploits the cues from motion analysis for moving areas detection. Objects and background are then refined using respectively edge detection and seeded region growing procedures. All the tasks are iteratively performed until objects and background are completely resolved. The method has been applied to a variety of indoor and outdoor scenes where objects of different type and shape are represented on variously textured background.

Keywords: Image Segmentation, Motion Detection, Object Extraction, Optical Flow

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Authors: E. Sobhani-Tehrani, K. Khorasani, N. Meskin

Abstract:

This paper presents a novel integrated hybrid approach for fault diagnosis (FD) of nonlinear systems. Unlike most FD techniques, the proposed solution simultaneously accomplishes fault detection, isolation, and identification (FDII) within a unified diagnostic module. At the core of this solution is a bank of adaptive neural parameter estimators (NPE) associated with a set of singleparameter fault models. The NPEs continuously estimate unknown fault parameters (FP) that are indicators of faults in the system. Two NPE structures including series-parallel and parallel are developed with their exclusive set of desirable attributes. The parallel scheme is extremely robust to measurement noise and possesses a simpler, yet more solid, fault isolation logic. On the contrary, the series-parallel scheme displays short FD delays and is robust to closed-loop system transients due to changes in control commands. Finally, a fault tolerant observer (FTO) is designed to extend the capability of the NPEs to systems with partial-state measurement.

Keywords: Hybrid fault diagnosis, Dynamic neural networks, Nonlinear systems.

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Authors: Abdulamgid.T. Bouzed, Suleiman. M. Elhamali

Abstract:

The technical realization of data transmission using glass fiber began after the development of diode laser in year 1962. The erbium doped fiber amplifiers (EDFA's) in high speed networks allow information to be transmitted over longer distances without using of signal amplification repeaters. These kinds of fibers are doped with erbium atoms which have energy levels in its atomic structure for amplifying light at 1550nm. When a carried signal wave at 1550nm enters the erbium fiber, the light stimulates the excited erbium atoms which pumped with laser beam at 980nm as additional light. The wavelength and intensity of the semiconductor lasers depend on the temperature of active zone and the injection current. The present paper shows the effect of the diode lasers temperature and injection current on the optical amplification. From the results of in- and output power one may calculate the max. optical gain by erbium doped fiber amplifier.

Keywords: Amplifier, erbium doped fiber, gain, lasers, temperature.

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Authors: Nicolò Vaiana, Giorgio Serino

Abstract:

In this paper, an advanced Nonlinear Exponential Model (NEM), able to simulate the uniaxial dynamic behavior of seismic isolators having a continuously decreasing tangent stiffness with increasing displacement in the relatively large displacements range and a hardening or softening behavior at large displacements, is presented. The mathematical model is validated by comparing the experimental force-displacement hysteresis loops obtained during cyclic tests, conducted on a helical wire rope isolator and a recycled rubber-fiber reinforced bearing, with those predicted analytically. Good agreement between the experimental and simulated results shows that the proposed model can be an effective numerical tool to predict the force-displacement relationship of seismic isolation devices within the large displacements range. Compared to the widely used Bouc-Wen model, unable to simulate the response of seismic isolators at large displacements, the proposed one allows to avoid the numerical solution of a first order nonlinear ordinary differential equation for each time step of a nonlinear time history analysis, thus reducing the computation effort. Furthermore, the proposed model can simulate the smooth transition of the hysteresis loops from small to large displacements by adopting only one set of five parameters determined from the experimental hysteresis loops having the largest amplitude.

Keywords: Base isolation, hardening behavior, nonlinear exponential model, seismic isolators, softening behavior.

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Authors: Rida B. Arieby, Hameed N. Hameed

Abstract:

In this work, tensile tests on high density polyethylene have been carried out under various constant strain rate and strain rate jump tests. The dependency of the true stress and specially the variation of volume strain have been investigated, the volume strain due to the phenomena of damage was determined in real time during the tests by an optical extensometer called Videotraction. A modified constitutive equations, including strain rate and damage effects, are proposed, such a model is based on a non-equilibrium thermodynamic approach called (DNLR). The ability of the model to predict the complex nonlinear response of this polymer is examined by comparing the model simulation with the available experimental data, which demonstrate that this model can represent the deformation behavior of the polymer reasonably well.

Keywords: Strain rate jump tests, Volume Strain, High Density Polyethylene, Large strain, Thermodynamics approach.

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Authors: Ekkaluk Eksook, Chutima Prommak

Abstract:

This paper address the network reliability optimization problem in the optical access network design for the 3G cellular systems. We presents a novel 0-1 integer programming model for designing optical access network topologies comprised of multi-rings with common-edge in order to guarantee always-on services. The results show that the proposed model yields access network topologies with the optimal reliablity and satisfies both network cost limitations and traffic demand requirements.

Keywords: Network Reliability, Topological Network Design, 3G Cellular Networks.

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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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Authors: C. Lodato, S. Lopes

Abstract:

This paper describes a segmentation algorithm based on the cooperation of an optical flow estimation method with edge detection and region growing procedures. The proposed method has been developed as a pre-processing stage to be used in methodologies and tools for video/image indexing and retrieval by content. The addressed problem consists in extracting whole objects from background for producing images of single complete objects from videos or photos. The extracted images are used for calculating the object visual features necessary for both indexing and retrieval processes. The first task of the algorithm exploits the cues from motion analysis for moving area detection. Objects and background are then refined using respectively edge detection and region growing procedures. These tasks are iteratively performed until objects and background are completely resolved. The developed method has been applied to a variety of indoor and outdoor scenes where objects of different type and shape are represented on variously textured background.

Keywords: Motion Detection, Object Extraction, Optical Flow, Segmentation.

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Authors: Delfim Soares Jr., Webe J. Mansur

Abstract:

The Time-Domain Boundary Element Method (TDBEM) is a well known numerical technique that handles quite properly dynamic analyses considering infinite dimension media. However, when these analyses are also related to nonlinear behavior, very complex numerical procedures arise considering the TD-BEM, which may turn its application prohibitive. In order to avoid this drawback and model nonlinear infinite media, the present work couples two BEM formulations, aiming to achieve the best of two worlds. In this context, the regions expected to behave nonlinearly are discretized by the Domain Boundary Element Method (D-BEM), which has a simpler mathematical formulation but is unable to deal with infinite domain analyses; the TD-BEM is employed as in the sense of an effective non-reflexive boundary. An iterative procedure is considered for the coupling of the TD-BEM and D-BEM, which is based on a relaxed renew of the variables at the common interfaces. Elastoplastic models are focused and different time-steps are allowed to be considered by each BEM formulation in the coupled analysis.

Keywords: Boundary Element Method, Dynamic Elastoplastic Analysis, Iterative Coupling, Multiple Time-Steps.

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Authors: A. Rahdar, V. Arbabi, H. Ghanbari

Abstract:

ZnS nanoparticles of different size have been synthesized using a colloidal particles method. Zns nanoparticles prepared with capping agent (mercaptoethanol) then were characterized using X-ray diffraction (XRD) and UV-Vis spectroscopy. The particle size of the nanoparticles calculated from the XRD patterns has been found in the range 1.85-2.44nm. Absorption spectra have been obtained using UV-Vis spectrophotometer to find the optical band gap and the obtained values have been founded to being range 3.83-4.59eV. It was also found that energy band gap increase with the increase in molar capping agent solution.

Keywords: ZnS, Nanoparticle, X-ray.

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Authors: M. G. M. Khan, V. D. Prasad, D. K. Rao

Abstract:

In this manuscript, we discuss the problem of determining the optimum stratification of a study (or main) variable based on the auxiliary variable that follows a uniform distribution. If the stratification of survey variable is made using the auxiliary variable it may lead to substantial gains in precision of the estimates. This problem is formulated as a Nonlinear Programming Problem (NLPP), which turn out to multistage decision problem and is solved using dynamic programming technique.

Keywords: Auxiliary variable, Dynamic programming technique, Nonlinear programming problem, Optimum stratification, Uniform distribution.

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Authors: D.Elleuch, T.Damak

Abstract:

In this paper, the performance of two adaptive observers applied to interconnected systems is studied. The nonlinearity of systems can be written in a fractional form. The first adaptive observer is an adaptive sliding mode observer for a Lipchitz nonlinear system and the second one is an adaptive sliding mode observer having a filtered error as a sliding surface. After comparing their performances throughout the inverted pendulum mounted on a car system, it was shown that the second one is more robust to estimate the state.

Keywords: Adaptive observer, Lipchitz system, Interconnected fractional nonlinear system, sliding mode.

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Authors: Samrat Vikramaditya Tiwari, Atul Sewaiwar, Yeon-Ho Chung

Abstract:

Device-to-device (D2D) communication is considered a promising technique to provide wireless peer-to-peer communication services. Due to increasing demand on mobile services, available spectrum for radio frequency (RF) based communications becomes scarce. Recently, visible light communications (VLC) has evolved as a high speed wireless data transmission technology for indoor environments with abundant available bandwidth. In this paper, a novel VLC based D2D communication that provides wireless peer-to-peer communication is proposed. Potential low operating power devices for an efficient D2D communication over increasing distance of separation between devices is analyzed. Optical repeaters (OR) are also proposed to enhance the performance in an environment where direct D2D communications yield degraded performance. Simulation results show that VLC plays an important role in providing efficient D2D communication up to a distance of 1 m between devices. It is also found that the OR significantly improves the coverage distance up to 3.5 m.

Keywords: Visible light communication, light emitting diode, device-to-device, optical repeater.

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Authors: Yanling Zhu

Abstract:

In this paper, a higher order nonlinear neutral functional differential equation with distributed delay is studied by using the continuation theorem of coincidence degree theory. Some new results on the existence of periodic solutions are obtained.

Keywords: Neutral functional differential equation, higher order, periodic solution, coincidence degree theory.

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Authors: Roozbeh Keshmiri, Alireza Mohamad Shahri

Abstract:

Fuzzy controllers are potential candidates for the control of nonlinear, time variant and also complicated systems. Anti lock brake system (ABS) which is a nonlinear system, may not be easily controlled by classical control methods. An intelligent Fuzzy control method is very useful for this kind of nonlinear system. A typical antilock brake system (ABS) by sensing the wheel lockup, releases the brakes for a short period of time, and then reapplies again the brakes when the wheel spins up. In this paper, an intelligent fuzzy ABS controller is designed to adjust slipping performance for variety of roads. There are tow major sections in the proposing control system. First section consists of tow Fuzzy-Logic Controllers (FLC) providing optimal brake torque for both front and rear wheels. Second section which is also a FLC provides required amount of slip and torque references properties for different kind of roads. Simulation results of our proposed intelligent ABS for three different kinds of road show more reliable and better performance in compare with two other break systems.

Keywords: Fuzzy Logic Control, ABS, Anti lock BrakingSystem.

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Authors: B. S. Raghavendra, D. Narayana Dutt

Abstract:

Many recent electrophysiological studies have revealed the importance of investigating meditation state in order to achieve an increased understanding of autonomous control of cardiovascular functions. In this paper, we characterize heart rate variability (HRV) time series acquired during meditation using nonlinear dynamical parameters. We have computed minimum embedding dimension (MED), correlation dimension (CD), largest Lyapunov exponent (LLE), and nonlinearity scores (NLS) from HRV time series of eight Chi and four Kundalini meditation practitioners. The pre-meditation state has been used as a baseline (control) state to compare the estimated parameters. The chaotic nature of HRV during both pre-meditation and meditation is confirmed by MED. The meditation state showed a significant decrease in the value of CD and increase in the value of LLE of HRV, in comparison with premeditation state, indicating a less complex and less predictable nature of HRV. In addition, it was shown that the HRV of meditation state is having highest NLS than pre-meditation state. The study indicated highly nonlinear dynamic nature of cardiac states as revealed by HRV during meditation state, rather considering it as a quiescent state.

Keywords: Correlation dimension, Embedding dimension, Heartrate variability, Largest Lyapunov exponent, Meditation, Nonlinearity score.

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Authors: Karuppsamy K., Eswara Prasad C. R.

Abstract:

In this paper analysis of an infinite beam resting on tensionless extensible geosynthetic reinforced granular bed overlying soft soil strata under moving load with constant velocity is presented. The beam is subjected to a concentrated load moving with constant velocity. The upper reinforced granular bed is modeled by a rough elastic membrane embedded in Pasternak shear layer overlying a series of compressible nonlinear Winkler springs representing the under-lied very poor soil. The tensionless extensible geosynthetic layer has been assumed to deform such that at interface the geosynthetic and the soil have some deformation. Nonlinear behavior of granular fill and the very poor soil has been considered in the analysis by means of hyperbolic constitutive relationships. Detailed parametric study has been conducted to study the influence of various parameters on the response of soil foundation system under consideration by means of deflection and bending moment in the beam and tension mobilized in the geosynthetic layer. This study clearly observed that the comparisons of tension and tensionless foundation and magnitude of applied load, relative compressibility of granular fill and ultimate resistance of poor soil has significant influence on the response of soil foundation system.

Keywords: Infinite Beams, Tensionless Extensible Geosynthetic, Granular layer, Moving Load and Nonlinear behavior of poor soil

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Authors: Vishwesh Kulkarni, Nikhil Bellarykar

Abstract:

Cellular complexity stems from the interactions among thousands of different molecular species. Thanks to the emerging fields of systems and synthetic biology, scientists are beginning to unravel these regulatory, signaling, and metabolic interactions and to understand their coordinated action. Reverse engineering of biological networks has has several benefits but a poor quality of data combined with the difficulty in reproducing it limits the applicability of these methods. A few years back, many of the commonly used predictive algorithms were tested on a network constructed in the yeast Saccharomyces cerevisiae (S. cerevisiae) to resolve this issue. The network was a synthetic network of five genes regulating each other for the so-called in vivo reverse-engineering and modeling assessment (IRMA). The network was constructed in S. cereviase since it is a simple and well characterized organism. The synthetic network included a variety of regulatory interactions, thus capturing the behaviour of larger eukaryotic gene networks on a smaller scale. We derive a new set of algorithms by solving a nonlinear optimization problem and show how these algorithms outperform other algorithms on these datasets.

Keywords: Synthetic gene network, network identification, nonlinear modeling, optimization.

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