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Total 133 records

    Protein Function Prediction Using Protein Structure and Computational Methods

    , M.Sc. Thesis Sharif University of Technology Abbasi Dezfouli, Mohammad Ebrahim (Author) ; Fatemizadeh, Emad (Supervisor) ; Arab, Shahriar ($item.subfieldsMap.e)
    Abstract
    Predicting the Amino Acids that have a catalytic effect in the enzymes, is a big step in appointing the activity of the enzymes and classifying them. This is a very challenging job, because an Amino Acid can appear in a variety of active sites.The biological activity of a protein usually depends on the existence of a small number of Amino Acids. Detecting these Amino Acids from the sequence of Amino Acids has many applications. Usually, the Amino Acids that are preserved are known as the Amino Acids that build up the active site, but the algorithms for finding the preserved Amino Acids are much more complex. There are a lot of algorithms for predicting the active sites of Amino Acids, but... 

    A Model for Analysis of Computational Learning

    , M.Sc. Thesis Sharif University of Technology Sattari Javid, Ali (Author) ; Daneshgar, Amir (Supervisor)
    Abstract
    The subject of this thesis is about a certain set of algorithms that try to indirectly solve problems. Instead of a programmer crafting an algorithm to solve a problem, these algorithms learn a solution themselves. These methods are usually studied in the Probably Accurately Correct (PAC) learning model. Although, PAC Learning is a generally accepted model, it falls short to describe certain aspects of learning algorithms. Many learning methods rely on convergence to minimize error, or maximize their fitness, yet the PAC model doesn’t explicitly provide any means to measure these behaviours. In this thesis, we first go through different models related to computational requirements of... 

    Modeling of Visual Attention Mechanism by Brain Signals

    , M.Sc. Thesis Sharif University of Technology Pahlevan Aghababa, Fatemeh (Author) ; Beigy, Hamid (Supervisor)
    Abstract
    Attention is a cognitive process in which the mind reacts to certain stimuli or stimuli of the environment while other environmental stimuli are ignored. Attention might be an overt or covert process. Overt attention is a process in which based on the purpose, we selectively choose an object or place among other objects and places to focus on and we are aware of it. However, the covert attention originates from hidden source, and we are not aware of it. In fact, the covert attention causes a clear and rapid movement of the eye toward the stimulus or space to be taken into consideration and the time when the movement of the eye it means overt attention has occurred. Visual attention is given... 

    Investigation of Thermodynamic Relations in Microscopic Systems by Quantum Information Theory

    , M.Sc. Thesis Sharif University of Technology Badiei, Alireza (Author) ; Shafiee, Afshin (Supervisor) ; Shamkhali, Amir Naser (Supervisor)
    Abstract
    Entropy is one of the important quantities in thermodynamics. In this project has tried to make this quantity as a bridge between quantum and thermodynamics. Entropy has many definitions that the Shannon entropy is chosen in this work. By this definition of entropy, we are able to define the entropy for a electronic system in molecules. By this definition, we are seeking an answer for this question,”whether entropy has a similar application in quantum like thermodynamics or not?”. To elucidate this hypothesis, simple diatomic molecules are computed. In fact, displacement of the Shannon entropy has investigated in bond making process. The question is that whether we can use this quantity to... 

    Experimental Study on Extracting Clean Energy from Vortex Induced Vibration

    , M.Sc. Thesis Sharif University of Technology Mohtat, Pouya (Author) ; Abbaspour, Majid (Supervisor)
    Abstract
    Two experimental models were designed and tested to extract energy from vortex induced vibrations of a elastically mounted one degree of freedom rigid cylinder in the Reynolds range of 120000 < Re <220000. In the first model the amplitude and frequency of the movement was measured then a second model was designed to be tested in the Emam Hossein marine laboratory. The model was designed in a way that many of its properties like mass ratio, spring constant and damping coefficient were able to be altered. In this study the vortex induced vibration of an elastically mounted cylinder was scrutinized in high Reynolds and very low mass ratios for the first time and an amplitude ratio of 2.49 were... 

    Investigating the Effect of the Proposed CSF-1R Protein Inhibitor,with a Structure Containing Natural Biomolecules and based on the Approved Drug Vimseltinib

    , M.Sc. Thesis Sharif University of Technology Ebtehaj, Pouria (Author) ; Fattahi, Alireza (Supervisor)
    Abstract
    Vimseltinib, a small molecule inhibitor, represents a promising avenue for combating cancers linked to macrophage-associated processes through its targeted action on the CSF1R tyrosine kinase receptor. CSF1R, a pivotal member of the tyrosine kinase receptor family, plays a crucial role in macrophage differentiation and function. This protein's significance is underscored in conditions such as tenosynovial giant cell tumors (TGCTs) and the presence of tumor-associated macrophages, wherein overproduction of CSF1 by neoplastic cells recruits CSF1R-dependent immune cells, fostering tumor expansion. The intricate interplay extends to tumor-associated macrophages, particularly the M2 subtype,... 

    , Ph.D. Dissertation Sharif University of Technology Koushki, Behzad (Author) ; Matloubi Moghaddam, Firouz (Supervisor)
    Abstract
    We have reported a new and efficient synthesis of a broad spectrum of heterotetracyclic benzoxazocines via unique tandem 1,3-dinucleophilic addition of different bifunctional nucleophiles to quinolinium and isoquinolinium salts. The reaction generally involves the initial addition of nucleophiles to quinolinium salts to form enamine intermediate which can be trapped by intramolecular O/S-alkylation of nucleophiles. In the third part, as continues, we have reported another method which consists of Anthocyanidins and Thioindoles by using water and acetic acid as the solvent. This protocol is a very mild and simple method for construction of eight-membered ring in fused heterocycles in a... 

    Unsupervised, fast and efficient colour-image copy protection

    , Article IEE Proceedings: Communications ; Volume 152, Issue 5 , 2005 , Pages 605-616 ; 13502425 (ISSN) Abadpour, A ; Kasaei, S ; Sharif University of Technology
    2005
    Abstract
    The ubiquity of broadband digital communications and mass storage in modern society has stimulated the widespread acceptance of digital media. However, easy access to royalty-free digital media has also resulted in a reduced perception in society of the intellectual value of digital media and has promoted unauthorised duplication practices. To detect and discourage the unauthorised duplication of media, researchers have investigated watermarking methods to embed ownership data into media. However, some authorities have expressed doubt over the efficacy of watermarking methods to protect digital media. The paper introduces a novel method to discourage unauthorised duplication of digital... 

    Trajectory tracking of a mobile robot using fuzzy logic tuned by genetic algorithm

    , Article International Journal of Engineering, Transactions A: Basics ; Volume 19, Issue 1 , 2006 , Pages 95-104 ; 17281431 (ISSN) Pishkenari, H. N ; Mahboobi, S. H ; Alasty, A ; Sharif University of Technology
    Materials and Energy Research Center  2006
    Abstract
    In recent years, soft computing methods, like fuzzy logic and neural networks have been presented and developed for the purpose of mobile robot trajectory tracking. In this paper we will present a fuzzy approach to the problem of mobile robot path tracking for the CEDRA rescue robot with a complicated kinematical model. After designing the fuzzy tracking controller, the membership functions and rule weights will be optimized by genetic algorithm in order to obtain more acceptable results. Simulation results have demonstrated significant improvements in controller efficacy  

    Towards a bounded-rationality model of multi-agent social learning in games

    , Article 2010 10th International Conference on Intelligent Systems Design and Applications, ISDA'10, Cairo, 29 November 2010 through 1 December 2010 ; 2010 , Pages 142-148 ; 9781424481354 (ISBN) Hemmati, M ; Sadati, N ; Nili, M ; Sharif University of Technology
    2010
    Abstract
    This paper deals with the problem of multi-agent learning of a population of players, engaged in a repeated normal-form game. Assuming boundedly-rational agents, we propose a model of social learning based on trial and error, called "social reinforcement learning". This extension of well-known Q-learning algorithm, allows players within a population to communicate and share their experiences with each other. To illustrate the effectiveness of the proposed learning algorithm, a number of simulations on the benchmark game of "Battle of Sexes" has been carried out. Results show that supplementing communication to the classical form of Q-learning, significantly improves convergence speed towards... 

    Time and space extended-particle in cell model for electromagnetic particle algorithms

    , Article Physics of Plasmas ; Volume 19, Issue 3 , 2012 ; 1070664X (ISSN) Yazdanpanah, J ; Anvari, A ; Sharif University of Technology
    Abstract
    A general method for deriving electromagnetic particle in cell (EMPIC) algorithms has been given by Eastwood [Comput. Phys. Commun. 64, 252 (1991)]. This method devises variation of the action-integral to find discrete governing equations. The most important advantage of this method is automatic inclusion of the time coordinate via the action integral into the computational domain. This inclusion is inevitable because electromagnetic algorithms are based on time evolution of the system from its initial state. The drawback of this method is that it is rather abstract. This causes obscurity of particle-mesh interactions and makes it hard to analyze physical treatments of the computational... 

    Thermal transport in combined pressure - Electroosmotically driven flow in microchannels

    , Article 10th Intersociety Conference on Thermal and Thermomechanical Phenomena and Emerging Technologies in Electronic Systems, ITherm 2006, San Diego, CA, 30 May 2006 through 2 June 2006 ; Volume 2006 , 2006 , Pages 63-70 ; 0780395247 (ISBN); 9780780395244 (ISBN) Qazizade, A ; Taghizadeh Manzari, M ; Kazemzadeh Hannani, S ; Sharif University of Technology
    2006
    Abstract
    An analytical solution is presented to study the heat transfer characteristics of the combined pressure - electroosmotically driven flow in planar microchannels. The physical model includes the Joule heating effect to predict the convective heat transfer coefficient in two dimensional microchannels. The velocity field, which is a function of external electrical field, electroosmotic mobility, fluid viscosity and the pressure gradient, is obtained by solving the hydrodynamically fully-developed laminar Navier-Stokes equations considering the electrokinetic body force for low wall zeta potentials. Then, assuming a thermally fully-developed flow, the temperature distribution and the Nusselt... 

    The moment method for fiber raman amplifier gain ripple minimization

    , Article Optics Communications ; Volume 281, Issue 14 , 2008 , Pages 3673-3680 ; 00304018 (ISSN) Bahrampour, A. R ; Farman, F ; Ghasempour, A ; Sharif University of Technology
    2008
    Abstract
    We aim to propose a novel fiber Raman amplifier modeling based on the moment method, which is previously introduced for modeling the inhomogeneous Erbium doped fiber amplifiers and recently employed to analyze the fiber Raman amplifier with continuous pump spectrum. In this model, the number of governing equations is independent of the number of signals and according to the degree of accuracy it is proportional to the number of pumps. This method is employed to analyze the Raman fiber amplifiers with an arbitrary input signal line shape and to minimize the gain ripple of the fiber Raman amplifier with respect to the pump powers and pump frequencies. © 2008 Elsevier B.V. All rights reserved  

    The effects of hydrodynamics characteristics on mass transfer during droplet formation using computational approach

    , Article 2006 ASME International Mechanical Engineering Congress and Exposition, IMECE2006, Chicago, IL, 5 November 2006 through 10 November 2006 ; 2006 ; 08888116 (ISSN); 0791837904 (ISBN); 9780791837900 (ISBN) Javadi, A ; Taeibi Rahni, M ; Bastani, D ; Javadi, K ; Sharif University of Technology
    American Society of Mechanical Engineers (ASME)  2006
    Abstract
    For the reason that flow expansion model (developed in our previous work) for evaluating mass transfer during droplet formation involves with manifest hydrodynamic aspects, in this research computational simulation of this phenomenon was done for characterization of hydrodynamics effects on the mass transfer during droplet formation. For this purpose, an Eulerian volume tracking computational code based on volume of fluid (VOF) method was developed to solve the transient Navier-Stokes equations for the axisymmetric free-boundary problem of a Newtonian liquid that is dripping vertically and breaking as drops into another immiscible Newtonian fluid. The effects of hydrodynamics effects on the... 

    Tensor-based face representation and recognition using multi-linear subspace analysis

    , Article 2009 14th International CSI Computer Conference, CSICC 2009, 20 October 2009 through 21 October 2009, Tehran ; 2009 , Pages 658-663 ; 9781424442621 (ISBN) Mohseni, H ; Kasaei, S ; Sharif University of Technology
    Abstract
    Discriminative subspace analysis is a popular approach for a variety of applications. There is a growing interest in subspace learning techniques for face recognition. Principal component analysis (PCA) and eigenfaces are two important subspace analysis methods have been widely applied in a variety of areas. However, the excessive dimension of data space often causes the curse of dimensionality dilemma, expensive computational cost, and sometimes the singularity problem. In this paper, a new supervised discriminative subspace analysis is presented by encoding face image as a high order general tensor. As face space can be considered as a nonlinear submanifold embedded in the tensor space, a... 

    SUT-DAM: An integrated software environment for multi-disciplinary geotechnical engineering

    , Article Advances in Engineering Software ; Volume 37, Issue 11 , 2006 , Pages 728-753 ; 09659978 (ISSN) Khoei, A. R ; Gharehbaghi, S. A ; Azami, A. R ; Tabarraie, A. R ; Sharif University of Technology
    Elsevier Ltd  2006
    Abstract
    As computer simulation increasingly supports engineering design, the requirement for a computer software environment providing an integration platform for computational engineering software increases. A key component of an integrated environment is the use of computational engineering to assist and support solutions for complex design. In the present paper, an integrated software environment is demonstrated for multi-disciplinary computational modeling of structural and geotechnical problems. The SUT-DAM is designed in both popularity and functionality with the development of user-friendly pre- and post-processing software. Pre-processing software is used to create the model, generate an... 

    Spoken CAPTCHA: a CAPTCHA system for blind users

    , Article 2009 Second ISECS International Colloquium on Computing, Communication, Control, and Management, CCCM 2009, Sanya, 8 August 2009 through 9 August 2009 ; Volume 1 , 2009 , Pages 221-224 ; 9781424442461 (ISBN) Shirali Shahreza, S ; Abolhassani, H ; Sameti, H ; Shirali Shahreza, M. H ; Yangzhou University; Guangdong University of Business Studies; Wuhan Institute of Technology; IEEE SMC TC on Education Technology and Training; IEEE Technology Management Council ; Sharif University of Technology
    2009
    Abstract
    Today, the Internet is used to offer different services to users. Most of these services are designed for human users, but unfortunately some computer programs are designed which abuse these services. CAPTCHA (Completely Automated Public Turing test to tell Computers and Human Apart) systems are designed to automatically distinguish between human users and computer programs and block such computer programs. Most of current CAPTCHA methods are using visual patterns and hence blind users cannot use them. In this paper, we propose a new CAPTCHA method which is designed for blind people. In this method, a small sound clip is played for the user and he/she is asked to say a word. Then the user... 

    Some computable results on the existence of periodic solutions for singular non-autonomous third order systems

    , Article Applied Mathematics and Computation ; Volume 163, Issue 1 , 2005 , Pages 51-60 ; 00963003 (ISSN) Mehri, B ; Niksirat, M. A ; Sharif University of Technology
    2005
    Abstract
    Here we are concerned with the existence of periodic solution for nonlinear non-autonomous third order system of ordinary differential equations with singular terms. Our method here is based on the topological method in the sense that we conclude some computable results for the focal system from a homotopic nonsingular system. The aim is to obtain sufficient conditions for which the system has periodic solution whenever the value of deformation with respect to the first variation of the nonsingular subsystem is sufficiently small. The method presented here is constructive in the sense that the existence of periodic orbits can be verified numerically as well as computed if any. For this, we... 

    Solving the resource availability cost problem in project scheduling by path relinking and genetic algorithm

    , Article Applied Mathematics and Computation ; Volume 196, Issue 2 , 2008 , Pages 879-888 ; 00963003 (ISSN) Ranjbar, M ; Kianfar, F ; Shadrokh, S ; Sharif University of Technology
    2008
    Abstract
    This paper considers a project scheduling problem with the objective of minimizing resource availability costs required to execute the activities in a project by a given project deadline. The project contains activities interrelated by finish-start-type precedence relations with a time lag of zero, which require a set of renewable resources. Two metaheuristics, path relinking and genetic algorithm, are developed to tackle this problem in which a schedule is created with a precedence feasible priority list given to the schedule generation scheme. In these procedures, each new generation of solutions are created using the combination of current solutions. Comparative computational results... 

    Solving haplotype reconstruction problem in MEC model with hybrid information fusion

    , Article EMS 2008, European Modelling Symposium, 2nd UKSim European Symposium on Computer Modelling and Simulation, Liverpool, 8 September 2008 through 10 September 2008 ; 2008 , Pages 214-218 ; 9780769533254 (ISBN) Asgarian, E ; Moeinzadeh, M. H ; Habibi, J ; Sharifian-R, S ; Rasooli-V, A ; Najafi-A, A ; Sharif University of Technology
    2008
    Abstract
    Single Nucleotide Polymorphisms (SNPs), a single DNA base varying from one individual to another, are believed to be the most frequent form responsible for genetic differences. Genotype is the conflated information of a pair of haplotypes on homologous chromosomes. Although haplotypes have more information for disease associating than individual SNPs and genotype, it is substantially more difficult to determine haplotypes through experiments. Hence, computational methods which can reduce the cost of determining haplotypes become attractive alternatives. MEC, as a standard model for haplotype reconstruction, is fed by fragments as input to infer the best pair of haplotypes with minimum error...