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    ”A Study on the Process of Passive Uptake of Nanoparticles by Coarse-Grained MD Simulation”

    , M.Sc. Thesis Sharif University of Technology Shirzad, Hoda (Author) ; Ejtehadi, Mohammad Reza (Supervisor)
    The aim of this thesis is to investigate the passive wrapping of nanoparticles by a lipid membrane in the uptake process using molecular dynamics computer simulations. The simulations are carried out by the Virtual Cell Model (VCM) software package, a computational framework that creates a large scale coarse-grained multi-component cell model developed by Prof Mohammad Reza Ejtehadi’s Soft Matter Group at Sharif University of Technology. VCM can model the dynamics of different parts of the cell and investigate their mechanical properties.A chapter of this thesis contributes to further development of the membrane model used in the VCM to simulate nanoparticles interactions with a membrane.... 

    Analysis and Simulation of Cell Migration with VCM Software

    , M.Sc. Thesis Sharif University of Technology Sadeghizadeh, Sajjad (Author) ; Ejtehadi, Mohammad Reza (Supervisor)
    Cells in their surrounding environment subjected to biochemical and biomechanical stimuli and respond to this signals. The mechanism by which cells transduce external mechanical signals into responses is called Mechanotransduction and cell use this mechanism to sense and respond to extracellular signals. Cells control processes like migration and division by mechanosensing. Cell migration is one of the most important responses to Cell-ECM interaction. This migration underlies many biological processes including embryogenesis, wound healing, tumorogenesis, morphogenesis and immune defense, so the study of cell migration is of particular importance. If there are external signals in cells...