Sharif Digital Repository

Background: Current development of sequencing technologies is towards generating longer and noisier reads. Evidently, accurate alignment of these reads play an important role in any downstream analysis. Similarly, reducing the overall cost of sequencing is related to the time consumption of the aligner. The tradeoff between accuracy and speed is the main challenge in designing long read aligners. Results: We propose Meta-aligner which aligns long and very long reads to the reference genome very efficiently and accurately. Meta-aligner incorporates available short/long aligners as subcomponents and uses statistics from the reference genome to increase the performance. Meta-aligner estimates... 

A new method for position determination of stationary targets from radio bearings, using triangulation, and based on the partial derivative analysis of bearing error has been proposed. Mathematical derivations have been carried out and a simulation illustrating the effectiveness of the method has been run. It turns out that, the method works best when the noise is excessively high and the traversed path is asymmetric. In such conditions, the method illustrates an error reduction of up to 5% with respect to the Least Square algorithm  

Large signal behavior of the Laser Diode is analyzed with the aim of finding a qualitative relationship between modulation amplitude and the change in the shape of its transfer function. It is found that, at quasi-static conditions, increasing the amplitude of the modulating signal smoothes out the original piecewise-linear transfer function of the diode. It further shifts the now smoothed knee point to lower DC currents. As the frequency increases, however, these effects become less and less pronounced. In addition, the transfer function becomes rather wavy due to the failure of current density to reach the saturation level necessary for adequate stimulated emission. At even higher... 

In this paper the root cause failure of a super-heater boiler tube is discovered. The tube has been worked in caustic media (pH = 8.9∼9.6) for virtually 40 months. The working temperature and pressure were recorded in the range of 204-315°C and 43 bar, respectively According to the chemical analysis, it was revealed that the tube is in accordance with ASTM A213 Gr T22. The corrosion products of the tube were characterized by EDS, XRF and XRD techniques. Visual inspection indicated that the macro-cavity was promoted on the inner surface of the tube. Also, a drastic wall thinning with gouging marks were observed. As a result of steam blanketing phenomenon, the sodium ions are locally... 

In this paper the root cause failure of a super-heater boiler tube is discovered. The tube has been worked in caustic media (pH = 8.9∼9.6) for virtually 40 months. The working temperature and pressure were recorded in the range of 204-315°C and 43 bar, respectively According to the chemical analysis, it was revealed that the tube is in accordance with ASTM A213 Gr T22. The corrosion products of the tube were characterized by EDS, XRF and XRD techniques. Visual inspection indicated that the macro-cavity was promoted on the inner surface of the tube. Also, a drastic wall thinning with gouging marks were observed. As a result of steam blanketing phenomenon, the sodium ions are locally... 

Optical tweezers provide an accurate measurement technique for evaluating mechanical properties of the living cells and many experimental studies have been done to understand the behavior of cells due to external forces. Numerical studies such as finite element methods have been used in order to simulate mechanical behavior of the Red Blood Cells (RBCs). Recent studies have shown that the particle methods are useful tools to simulate the mechanical behavior of living cells. Since in microscopic scales, using discrete models are preferred than continuum methods, a particle-based method is used to simulate the deformation of RBC which is stretched by optical tweezers. The cytoplasm of RBC is... 

The effect of temper rolling and subsequent annealing on texture development and magnetic properties of semi-processed non grain oriented electrical steel has been investigated. The result shows that 5 % temper rolling and final annealing at 850 8C resulted in strong a-fiber component. The etch-pit technique shows that strain induced boundary migration is responsible for new texture component augmentation. Vibrating sample magnetometery reveals that maximum and minimum magnetic permeability are related to rolling and transverse directions, respectively. Average magnetic permeability is improved to some extent as a result of temper rolling and subsequent annealing. © Carl Hanser Verlag GmbH &... 

The objective of this work is to create an analytical framework to study the problem of squeezed film damping in micromirrors considering the bending of the supporting torsion microbeams. Using mathematical and physical justifications, nonlinear Reynolds equation governing the behavior of the squeezed gas underneath the mirror is linearized. The resulting linearized equation is then nondimensionalized and analytically solved for two cases of the infinitesimal and finite tilting angle of the mirror. The obtained pressure distribution from the solution of the Reynolds equation is then utilized for finding the squeezed film damping force and torque applied to the mirror. The results show that... 

The purpose of this paper is to design and analyze a 3-link micro-device proposed as a micro-manipulator. This micro-manipulator includes 3 micro-beams as links connected to one another with no conventional or flexural joints. While the structure of the micro-manipulator is monolithic, end-effector workspace is achieved through deflection of links which is actuated by piezoelectric layers. By combining static analysis of the links through a multilayer piezoelectric beam model and kinematic analysis of the micro-manipulator, inverse kinematic has been solved utilizing the Taylor series expansion technique and the perturbation method. The obtained results through the present model reveal that... 

Valveless micropumps are widely used due to simple structure, durability and low maintenance. Understanding the fluid-membrane interaction and performance criteria is still a challenging problem for the scientists. In this work, a new model for side mounted valve micropumps is developed to obtain dynamic response of micropump with respect to piezoelectric actuation. The parameters of this model are obtained in terms of actuation frequency and geometrical dimensions of the micropump. Balancing elastic, inertial and damping forces result in the governing equation of the micropump system model. Analytical studies for the bottom mounted valve micropump indicate pump flux is independent of the... 

A problem associated with modeling and control of the power factor correction rectifiers is that the ac variations in duty cycle, as well as in the ac input voltage and current are not small, and hence the traditional small signal analysis is not justified. Nonetheless, the low-frequency components of the converter can be modeled via the circuit averaging technique, but the resulting equivalent circuits are, in general, time varying and highly nonlinear. Nonlinear stability analysis methods are not appropriate for analysis and control design of such complicated circuits. In this paper a piecewise affine approximation is introduced for modeling of switching circuits. This approach makes the... 

Design and application of superelements in efficient prediction of the structural behavior in a short time has been one of the research interests in the last decade. Superelements are those elements which are capable of producing the same accurate result instead of several combined simple elements. In this paper a new 16-node cylindrical superelement is presented. Static and modal analyses of laminated hollow cylinders subjected to various kinds of loadings and boundary conditions are performed using this element. Some numerical examples are given to illustrate and validate the developed method. The accuracy of the results is evident from comparison of the findings with exact solution method... 

Valveless piezoelectric micropumps are in wide practical use due to their ability to conduct particles with absence of interior moving mechanical parts. In this paper, an extended numerical study on fluid flow through micropump chamber and diffuser valves is conducted to find out the optimum working conditions of micropump. In order to obtain maximum generality of the reported results, an analytical study along with a dimensional analysis is presented primarily, to investigate the main dimensionless groups of parameters affecting the micropump net flux. Consequently, the parameters appeared in the main dimensionless groups have been changed in order to understand how the pump rectification... 

In this paper, free vibration analysis of laminated composite plates is carried out using first shear deformation theory and finite element method. Effect of axial tension and compression forces on the natural frequencies of the structure is investigated. Applying elastic foundation under the laminated composite plates has enabled us to achieve desired frequencies. The displacements are based C0 - nine plate bending element and each node has three degree of freedom. The equations of motion are derived using Hamilton's principle. Results indicate the tension forces will increase the natural frequency while the compression force reduces the natural frequency. The buckling force of plate is...