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    Protein Function Prediction using Protein Interaction Networks

    , M.Sc. Thesis Sharif University of Technology Babapour Khosravi, Niloufar (Author) ; Fatemizadeh, Emadoddin (Supervisor)
    Abstract
    Predicting protein function accurately is an important issue in the post genomic era. To achieve this goal, several approaches have been proposed deduce the function of unclassified proteins through sequence similarity, co expression profiles, and other information. Among these methods, the Global Optimization Method is an interesting and powerful tool that assigns functions to unclassified proteins based on their positions in a physical interaction network. To boost both the accuracy and speed of global optimization method, a new prediction method, Accurate Global Optimization Method (AGOM), is presented in this thesis, which employs optimal repetition method enhanced with frequency of... 

    Extending application of Dehaghani Association Equation of State for Modeling Phase Behavior of Water-Alcohol Systems

    , Article Fluid Phase Equilibria ; Volume 482 , 2019 , Pages 126-133 ; 03783812 (ISSN) Saeedi Dehaghani, A. H ; Badizad, M. H ; Sharif University of Technology
    Elsevier B.V  2019
    Abstract
    This paper concerns extending applicability of Dehaghani association equation of state (in short DA-EOS) to model non-ideality in phase behavior caused by hydrogen bonding. Advantageously, this equation only needs two and one parameters to treat self- and cross association, respectively, which were determined for methanol/water and ethanol/water mixture in this study. In this respect, DA was coupled with PR and SRK EOS to account for physical interaction between molecules. Notably, DA-PR persistently provides more accurate prediction than DA-SRK for both aqueous methanol and ethanol solutions  

    Planar molecular dynamics simulation of metallic nanoparticles manipulation

    , Article 2008 8th IEEE Conference on Nanotechnology, IEEE-NANO, Arlington, TX, 18 August 2008 through 21 August 2008 ; 2008 , Pages 163-164 ; 9781424421046 (ISBN) Mahboobi, S. H ; Meghdari, A ; Jalili, N ; Amiri, F ; Sharif University of Technology
    2008
    Abstract
    The aim of this research is to conduct atomistic investigations of physical interaction analysis of nanoscale objects manipulation. The system consists of tip, particle and substrate. The manipulation tool moves with a constant speed while pushing the particle in a desired direction. The focus of the research is on ultra-fine metallic nanoparticles. To perform this research, Nose-Hoover dynamics and Sutton-Chen interatomic potential will be used to investigate the behavior of the aforementioned system which is made from different transition metals. The effects of size, material type and temperature on the success of the process have been investigated by planar molecular dynamics. © 2008 IEEE... 

    Adaptive impedance control of UAVs interacting with environment using a robot manipulator

    , Article 2014 2nd RSI/ISM International Conference on Robotics and Mechatronics, ICRoM 2014 ; Oct , 2014 , p. 636-641 Sayyaadi, H ; Sharifi, M ; Sharif University of Technology
    Abstract
    In this paper, a nonlinear adaptive impedance controller is proposed for UAVs equipped with a robot manipulator that interacts with environment. In this adaptive controller, by considering the nonlinear dynamics model of the UAV plus the robot manipulator in Cartesian coordinates, all of model parameters are considered to be completely uncertain and their estimation is updated using an adaptation law. The objective of the proposed adaptive controller is the control of manipulator's end-effector impedance in Cartesian coordinates to have a stable physical interaction. The adjustable Cartesian impedance is a desired dynamical relationship between the end-effector motion in Cartesian... 

    Multifunctional 3D hierarchical bioactive green carbon-based nanocomposites

    , Article ACS Sustainable Chemistry and Engineering ; Volume 9, Issue 26 , 2021 , Pages 8706-8720 ; 21680485 (ISSN) Rabiee, N ; Bagherzadeh, M ; Ghadiri, A. M ; Kiani, M ; Fatahi, Y ; Tavakolizadeh, M ; Pourjavadi, A ; Jouyandeh, M ; Saeb, M. R ; Mozafari, M ; Shokouhimehr, M ; Varma, R. S ; Sharif University of Technology
    American Chemical Society  2021
    Abstract
    Carbon-based nanocarriers such as multiwall carbon nanotubes (MWCNTs) and reduced graphene oxide (rGO) have shown promising delivery capabilities due to their low immunogenicity, superior internalization, and suitable cell penetration efficiency. Herein, a molecular engineering strategy is advanced for the one-pot synthesized rGO/MWCNT/Fe3O4/ZnO to enhance the stability of the nanocarrier in the biological matrix; green synthesized ZnO was responsible for water uptake and reduced cytotoxicity, while Fe3O4controlled the cellular internalization for gene delivery. Surface morphology of the ensuing nanocomposite was correlated with photocatalytic and gene delivery (CRISPR/Cas9) features. For... 

    Crystalline polysaccharides: A review

    , Article Carbohydrate Polymers ; Volume 275 , 2022 ; 01448617 (ISSN) Seidi, F ; Yazdi, M. K ; Jouyandeh, M ; Habibzadeh, S ; Munir, M. T ; Vahabi, H ; Bagheri, B ; Rabiee, N ; Zarrintaj, P ; Saeb, M. R ; Sharif University of Technology
    Elsevier Ltd  2022
    Abstract
    The biodegradability and mechanical properties of polysaccharides are dependent on their architecture (linear or branched) as well as their crystallinity (size of crystals and crystallinity percent). The amount of crystalline zones in the polysaccharide significantly governs their ultimate properties and applications (from packaging to biomedicine). Although synthesis, characterization, and properties of polysaccharides have been the subject of several review papers, the effects of crystallization kinetics and crystalline domains on the properties and application have not been comprehensively addressed. This review places focus on different aspects of crystallization of polysaccharides as... 

    The effective mechanical properties and the interfacial characterization of CNT reinforced nanocomposites

    , Article Proceedings of SPIE - The International Society for Optical Engineering, 9 March 2009 through 11 March 2009, San Diego, CA ; Volume 7294 , 2009 ; 0277786X (ISSN); 9780819475541 (ISBN) Sadeghia, H ; Naghdabadi, R ; The International Society for Optical Engineering (SPIE) ; Sharif University of Technology
    2009
    Abstract
    A small volume fraction of Carbon Nanotubes (CNTs) added in a polymeric matrix increases significantly the mechanical properties of the polymers. It is experimentally determined from the TEM images of CNT-based nanocomposites that nanotubes don't stand straight in their embedded matrix and they have some curvature in their shape. The load transfer mechanism between CNT and polymer matrix is also one of the most important issues which is not understood explicitly, yet. In this paper a wavy Single Walled Carbon Nanotube (SWCNT) is modeled as inclusion in a polymer matrix and its effective mechanical properties is studied. This model is based on using 3-D Representive Volume Element (RVE) with...