Sharif Digital Repository

Motif discovery is a challenging problem in molecular biology and has been attracting researcher's attention for years. Different kind of data and computational methods have been used to unravel this problem, but there is still room for improvement. In this study, our goal was to develop a method with the ability to identify all the TFBS signals, including known and unknown, inside the input set of sequences. We developed a clustering method specialized as part of our algorithm which outperforms other existing clustering methods such as DNACLUST and CD-HIT-EST in clustering short sequences. A scoring system was needed to determine how much a cluster is close to being a real motif. Multiple... 

Energy methods such as Energy Flow and Statistical Energy Analyses have been popularly used to predict the medium to high frequency vibro-acoustic response of several structures. In these energy methods, usually the common simple structural theories are used for simplicity. Since, the effects of shear deformation and rotary inertia at high frequency regions are unavoidable, it is necessary to determine the validity of these theories in each frequency domain. This paper aims to propose a method for defining a criteria to select a proper structural theory based on the order of shear deformation and rotary inertia to be used in vibration analyses. Several common as well as higher-order beam... 

In this paper we present a general formalism for the establishment and mean-square performance analysis of the family of selective partial update affine projection (SPU-AP), selective regressor affine projection (SR-AP), and selective partial update subband adaptive filter (SPU-SAF) algorithms. This analysis is based on energy conservation arguments and does not need to assume a Gaussian or white distribution for the regressors. We demonstrate through simulations that the results are useful in predicting the performance of these adaptive filter algorithms  

This Letter aims at the investigation of free-vibration properties of nanocones based on a nonlocal continuum shell model. A novel approach is used for derivation of the governing equations of motion and the Galerkin technique is used to obtain the natural frequencies of vibrations. The effects of small-scale and geometrical parameters of the nanocone on the natural frequencies are studied and some conclusions are drawn  

A nonlocal continuum shell model is developed to study the stability of nanocones under combined loading: external pressure and compression force. The nonlinear governing equations of motion of nanocone are obtained using Hamiltons principle and the external loads are considered as prestress. Based on Eringens nonlocal elasticity theory the small-scale effect is accounted in the governing equations of motion. To obtain the critical loads, the equations are solved using Galerkin technique and the effect of small-scale parameter and geometry on the stability of nanocone is studied  

In the present study, the effect of using magnetorheological elastomer materials and a magnetic field on the dynamic stability of a sandwich beam under a follower force has been investigated for various boundary conditions. The considered sandwich beam consists of a magnetorheological elastomer core constrained by elastic layers. The structural governing equations are derived using Hamilton’s principle and solved by the finite element method. The validity of the result is examined by comparison with those in the literature. The effects of variation in the parameters such as magnetic field intensity and the thickness of the layers on the stability of the sandwich beam are studied. Finally,... 

The affiliations in the original article contain errors. The correct affiliations are given below. © 2016, Islamic Azad University (IAU)  

This paper aims at developing a modal approach for the non-linear analysis of sloshing in an arbitrary-shape tank under both horizontal and vertical excitations. For this purpose, the perturbation technique is employed and the potential flow is adopted as the liquid sloshing model. The first- and second-order kinematic and dynamic boundary conditions of the liquid-free surface are used along with a boundary element model which is formulated in terms of the velocity potential of the liquid-free surface. The boundary element model is used to determine the natural mode shapes of sloshing and their corresponding frequencies. Using the modal analysis technique, a non-linear model is presented for... 

In this contribution, we have investigated the effects of magnetoelastic loads on free vibration characteristics of the magnetorheological-based sandwich beam. The considered sandwich beam consists of a magnetorheological core with elastic top and base layers. For these means, the structural governing equations are derived using the Hamilton principle and solved by the finite element method. The results are validated in comparison with the existing results in the literature. The effects of variation in the parameters such as magnetic field intensity and the thickness of the core and top layers on the deviation of the first natural frequency and the corresponding loss factor are studied as... 

This paper presents a matrix form model for determination of sloshing frequencies and modes in 3D liquid tanks. The governing equations of the incompressible inviscid potential flow are used to derive the governing boundary integral equation and then the boundary element method along with the collocation method is applied to obtain a matrix form standard eigenvalue problem. The sloshing mass and stiffness matrices are computed using analytical formulas which are given for quadratic boundary elements. Two typical examples are used to validate the introduced model and very good results are achieved in comparison with the exact results in the literature  

This study considers the aeroelastic instability of a partially treated magneto-rheological fluid sandwich panel in supersonic airflow. The linear first-order piston theory is used for modeling the aerodynamic pressure. Using classical Hamilton’s principle along with the finite element method, the equations of motion are derived. The critical value of the non-dimensional aerodynamic pressure is obtained by traditional p-method scheme. The validity of the finite element formulation is examined through comparison with those obtained from the assumed mode formulation and the available results in the literature. Various parametric studies including the effects of applied magnetic field, core and... 

This study considers the aeroelastic instability of a partially treated magneto-rheological fluid sandwich panel in supersonic airflow. The linear first-order piston theory is used for modeling the aerodynamic pressure. Using classical Hamilton’s principle along with the finite element method, the equations of motion are derived. The critical value of the non-dimensional aerodynamic pressure is obtained by traditional p-method scheme. The validity of the finite element formulation is examined through comparison with those obtained from the assumed mode formulation and the available results in the literature. Various parametric studies including the effects of applied magnetic field, core and... 

In this study, modification of polyvinyl chloride (PVC) ultrafiltration membranes with zinc oxide (ZnO) nanoparticle addition was taken into consideration. The ZnO at five different weights was added to the polymeric solution, and the membranes were fabricated by the phase inversion method using water as a nonsolvent and PEG 6 kDa as a pore former additive. The results showed that the pure water flux of the modified membranes increased up to 3 wt% ZnO addition, which was the optimized amount of the nanoparticle addition in this study. Also, at 3 wt% ZnO addition, flux recovery ratio reached from 69% to above 90%, indicated that the nanocomposite membranes were less susceptible to be fouled.... 

In this paper the classical molecular structural mechanics model of graphene is modified to improve its accuracy for the analysis of transverse deformations. To this aim, a sample graphene sheet under a uniform pressure is modeled by both molecular dynamics and molecular structural mechanics methods. The sectional properties of the beam element, by which the covalent bonds are modeled, are modified such that the difference between the results of the molecular mechanics model and molecular dynamics simulation is minimized. Using this modified model, the buckling behavior of graphene under a uniform edge pressure is investigated subjected to different boundary conditions for both zigzag and... 

The small-scale effect on the natural frequencies and buckling of pressurized nanotubes is investigated in this study. Based on the firstorder shear deformable shell theory, the nonlocal theory of elasticity is used to account for the small-scale effect and the governing equations of motion are obtained. Applying modal analysis technique and based on Galerkin's method a procedure is proposed to obtain natural frequencies of vibrations. For the case of nanotubes with simply supported boundary conditions, explicit expressions are obtained which establish the dependency of the natural frequencies and buckling loads of the nanotube on the small-scale parameter and natural frequencies obtained by... 

Investigation of non-covalent interaction of hydrophobic surfaces with the protein G (PrG) is necessary due to their frequent utilization in immunosensors and ELISA. It has been confirmed that surfaces, including carbonous-nanostructures (CNS) could orient proteins for a better activation. Herein, PrG interaction with single-walled carbon nanotube (SWCNT) and graphene (Gra) nanostructures was studied by employing experimental and MD simulation techniques. It is confirmed that the PrG could adequately interact with both SWCNT and Gra and therefore fine dispersion for them was achieved in the media. Results indicated that even though SWCNT was loaded with more content of PrG in comparison with... 

Background: Study of nanostructure-protein interaction for development of various types of nano-devices is very essential. Among carbon nanostructures, carbon nanotube (CNT) provides a suitable platform for functionalization by proteins. Previous studies have confirmed that the CNT induces changes in the protein structure. Methods: Molecular dynamics (MD) simulation study was employed to illustrate the changes occurring in the protein G (PGB) in the presence of a CNT. In order to predict the PGB surface patches for the CNT, Autodock tools were utilized. Results: Docking results indicate the presence of two different surface patches with diverse amino acids: the dominant polar residues in the... 

The present work aims at developing a boundary element method to determine the natural frequencies and mode shapes of liquid sloshing in 3D baffled tanks with arbitrary geometries. Green's theorem is used with the governing equation of potential flow and the walls and free surface boundary conditions are applied. A zoning method is introduced to model arbitrary arrangements of baffles. By discretizing the flow boundaries to quadrilateral elements, the boundary integral equation is formulated into a general matrix eigenvalue problem. The governing equations are then reduced to a more efficient form that is merely represented in terms of the potential values of the free surface nodes, which... 

In order to study the interaction of sloshing and structural vibrations of baffled tanks, a reduced order model based on modal analysis of structure model and boundary element method for fluids motion is developed. For this purpose, the governing equations of elastic structure and incompressible flow are used to derive simple models to simulate both fields. Using the modal analysis technique, the structural motions are applied to the fluid model and on the other hand by using boundary element method, the fluid loads are applied to the structural model. Based on this formulation, a code is developed which is applicable to an arbitrary elastic tank with arbitrary arrangement of baffles. The...