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    Molecular Dynamics Simulation of Actin: An Investigation into the Mechanical Properties

    , M.Sc. Thesis Sharif University of Technology Mehrafrooz, Behzad (Author) ; Shamloo, Amir (Supervisor) ; Firoozbakhsh, Keikhosrow (Supervisor)
    Abstract
    Actin is the most abundant protein in most eukaryotic cells. It is highly conserved and participates in more protein-protein interactions than any known protein. Actin plays a crucial role in cell motility, adhesion, morphology and intracellular transport. Its biologically active form is the filament (F-actin), which is assembled from monomeric G-actin. In this thesis, the mechanical properties and characteristics of both G- and F-actin are studied using molecular dynamics simulations. In general, this thesis can be categorized into two individual parts: First, steered molecular dynamics simulation was performed to assess tension of monomeric G-actin molecule, and stress-strain curves were... 

    Mechanical Properties of Actin Assemblies

    , M.Sc. Thesis Sharif University of Technology Ghodsi, Hossein (Author) ; Kazemi, Mohammad Taghi (Supervisor)
    Abstract
    Actin filaments are the most abundant component of the cellular cytoskeleton and provide shape for the most eukaryotic cells. Actin constitutes 1-10% of the total protein in most cells and is present at even higher concentrations in muscle cells. The functions of actin are directly connected to its mechanical properties, therefore both experimental and computational understanding of the mechanical properties of actin filaments are essential to elucidate their functions in cells and muscles. Actin exists in two forms, actin monomers (G-actin) and actin filaments (F-actin), which have continuous polymerization and depolymerization processes. In the polymerization process, different... 

    Simulation of Dynamic Behavior of Endothelial Cell During Compression Test

    , M.Sc. Thesis Sharif University of Technology Ghaffari, Hamed (Author) ; Saidi, Mohammad Said (Supervisor) ; Firoozabadi, Bahar (Supervisor)
    Abstract
    Investigation of the behavior of living cells in different biological conditions could play a key role in exploring the main reasons of humans' disorders and diseases. In this regard, many researchers are studying different subjects related to the living cells. Although most of these research activities are based on experimental methods, numerical approach could be utilized to investigate some topics which cannot be studied by experimental methods.In this study a three dimensional model of endothelial cell is proposed for the investigation of cell performance during compression test. The model consists of cell membrane, nucleus and main components of cytoskeleton, namely actin filaments,... 

    Tissue growth into three-dimensional composite scaffolds with controlled micro-features and nanotopographical surfaces

    , Article Journal of Biomedical Materials Research - Part A ; Volume 101, Issue 10 , 2013 , Pages 2796-2807 ; 15493296 (ISSN) Tamjid, E ; Simchi, A ; Dunlop, J. W. C ; Fratzl, P ; Bagheri, R ; Vossoughi, M ; Sharif University of Technology
    2013
    Abstract
    Controlling topographic features at all length scales is of great importance for the interaction of cells with tissue regenerative materials. We utilized an indirect three-dimensional printing method to fabricate polymeric scaffolds with pre-defined and controlled external and internal architecture that had an interconnected structure with macro- (400-500 μm) and micro- (∼25 μm) porosity. Polycaprolactone (PCL) was used as model system to study the kinetics of tissue growth within porous scaffolds. The surface of the scaffolds was decorated with TiO2 and bioactive glass (BG) nanoparticles to the better match to nanoarchitecture of extracellular matrix (ECM). Micrometric BG particles were... 

    Nanomechanics of actin filament: a molecular dynamics simulation

    , Article Cytoskeleton ; Volume 75, Issue 3 , March , 2018 , Pages 118-130 ; 19493584 (ISSN) Shamloo, A ; Mehrafrooz, B ; Sharif University of Technology
    John Wiley and Sons Inc  2018
    Abstract
    Actin is known as the most abundant essentially protein in eukaryotic cells. Actin plays a crucial role in many cellular processes involving mechanical forces such as cell motility, adhesion, muscle contraction, and intracellular transport. However, little is known about the mechanical properties of this protein when subjected to mechanical forces in cellular processes. In this article, a series of large-scale molecular dynamics simulations are carried out to elucidate nanomechanical behavior such as elastic and viscoelastic properties of a single actin filament. Here, we used two individual methods namely, all-atoms and coarse-grained molecular dynamics, to evaluate elastic properties of a... 

    Mechanical differences between ATP and ADP actin states: A molecular dynamics study

    , Article Journal of Theoretical Biology ; Volume 448 , 2018 , Pages 94-103 ; 00225193 (ISSN) Mehrafrooz, B ; Shamloo, A ; Sharif University of Technology
    Academic Press  2018
    Abstract
    This paper aims to give a comprehensive atomistic modeling of the nanomechanical behavior of actin monomer. Actin is a ubiquitous and essential component of cytoskeleton which forms many different cellular structures. Despite for several years great effort has been devoted to the investigation of mechanical properties of the actin filament, studies on the nanomechanical behavior of actin monomer are still lacking. These scales are, however, important for a complete understanding of the role of actin as an important component in the cytoskeleton structure. Based on the accuracy of atomistic modeling methods such as molecular dynamics simulations, steered molecular dynamics method is performed... 

    Theoretical modeling of actin-retrograde-flow passing clusters of confined T cell receptors

    , Article Mathematical Biosciences ; Volume 283 , 2017 , Pages 1-6 ; 00255564 (ISSN) Ghasemi V., A ; Firoozabadi, B ; Saidi, M. S ; Sharif University of Technology
    Elsevier Inc  2017
    Abstract
    Through the activation process of T cells, actin filaments move from the cell periphery toward the cell center. The moving filaments engage with T cell receptors and thus contribute to transportation of the signaling molecules. To study the connection between the moving actin filaments and T cell receptors, an experiment available in the literature has measured filaments flow velocity passing over a region of confined clusters of receptors. It shows that flow velocity decreases in the proximity of the receptors, and then regains its normal value after traversing the region, suggesting a dissipative friction-like connection. In this work, we develop a minimal theoretical model to re-examine... 

    Biomechanical analysis of actin cytoskeleton function based on a spring network cell model

    , Article Proceedings of the Institution of Mechanical Engineers, Part C: Journal of Mechanical Engineering Science ; Volume 231, Issue 7 , 2017 , Pages 1308-1323 ; 09544062 (ISSN) Ghaffari, H ; Saidi, M. S ; Firoozabadi, B ; Sharif University of Technology
    SAGE Publications Ltd  2017
    Abstract
    In this study, a new method for the simulation of the time-dependent behavior of actin cytoskeleton during cell shape change is proposed. For this purpose, a three-dimensional model of endothelial cell consisting of cell membrane, nucleus membrane, and main components of cytoskeleton, namely actin filaments, microtubules, and intermediate filaments is utilized. Actin binding proteins, which play a key role in regulating actin cytoskeleton behavior, are also simulated by using a novel technique. The actin cytoskeleton in this model is more dynamic and adoptable during cell deformation in comparison to previous models. The proposed model is subjected to compressive force between parallel micro...