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    Definition of the persistence length in the coarse-grained models of DNA elasticity

    , Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 86, Issue 5 , November , 2012 ; 15393755 (ISSN) Fathizadeh, A ; Eslami Mossallam, B ; Ejtehadi, M. R ; Sharif University of Technology
    2012
    Abstract
    By considering the detailed structure of DNA in the base pair level, two possible definitions of the persistence length are compared. One definition is related to the orientation of the terminal base pairs, and the other is based on the vectors which connect two adjacent base pairs at each end of the molecule. It is shown that although these definitions approach each other for long DNA molecules, they are dramatically different on short length scales. We show analytically that the difference mostly comes from the shear flexibility of the molecule and can be used to measure the shear modulus of DNA  

    Bending Rigidity of Helical Microtubule structures

    , M.Sc. Thesis Sharif University of Technology Mortazavi, Hamed (Author) ; Ejtehadi, Mohammad Reza (Supervisor)
    Abstract
    Microtubules are hollow cylindrical structures of 25 nanometer diameter inside cell membrane. Microtubule (MT) serves as a cell structure component and vesicular transport inside cell. It has been shown in recent researches that the persistence length in MTs is length dependent and increases about several times of counter length. Also helical structures of MTs have been found recently. In this research using Molecular Dynamic simulation of coarse-grained microtubular structures we compare persistence length of wild and helical microtubular structures. We show that the persistence length in helical structures is independent to the length.
     

    Structure of DNA Confined in Nano-Environment

    , M.Sc. Thesis Sharif University of Technology Khatami, Maryam (Author) ; Ejtehadi, Mohammad Reza (Supervisor)
    Abstract
    Ejtehadi, M. R. (Mohammad Reza)All cells store their hereditary information in the same linear chemical code, DNA molecule. These information organize all activities of the cell. Therefore, studying various properties of DNA is a big step toward understanding life. Physicists are interested in elastic properties of DNA molecule. DNA is somehow a chain of successive atoms that have been arranged in a helical ladder shape. DNA is a stiff polymer so one has to use a large amount of energy to bend it. Interestingly, in most of the natural cases, DNA is highly packed into spaces that are much smaller that its total length. Cell’s nucleus and viral capsids are some examples. Virus maybe the... 

    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... 

    Coarse Grained Molecular Dynamics Simulation of DNA Nanomechanics

    , Ph.D. Dissertation Sharif University of Technology Fathizadeh, Arman (Author) ; Ejtehadi, Mohammad Reza (Supervisor) ; Khoei, Amir Reza (Co-Advisor)
    Abstract
    DNA is the most important biological molecule which contains all the genetic information of living organisms. The mechanical behavior of this molecule has a significant role on its functions. In this study, we introduce a model to for DNA nanomechanics. This model is called rigid base-pair chain in which every base pair is considered as a rigid object. The base-pairs only interact with their nearest neighbors via a harmonic potential. We have used this model to study the nanomechanical behavior of the DNA such as its bending, twisting, and stretching elasticity. Also the model was successful to predict the structure of DNA minicircles with extra amount of twist. After that we used the model... 

    Fluorescent quantification of size and lamellarity of membrane nanotubes

    , Article European Biophysics Journal ; Vol. 43, Issue. 12 , 2014 , pp. 595-602 ; ISSN: 1432-1017 Baroji,Y. F ; Oddershede, L. B ; Reihani, S. N. S ; Bendix, P. M ; Sharif University of Technology
    Abstract
    Membrane nanotubes, ubiquitous in cellular systems, adopt a spectrum of curvatures and shapes that are dictated by their intrinsic physical characteristics as well as their interactions with the local cellular environment. A high bending flexibility is needed in the crowded cytoplasm where tubes often need to bend significantly in the axial direction at sub-micron length scales. We find the stiffness of spontaneously formed membrane nanotubes by measuring the persistence length of reconstituted membrane nanotubes freely suspended in solution and imaged by fluorescence microscopy. By quantifying the tube diameter we demonstrate for the first time that the persistence length scales linearly... 

    Application of perturbation theory to elastic models of DNA

    , Article Proceedings of the 13th Regional Conference on Mathematical Physics, Antalya, Turkey ; October , 2013 , Pages 241-253 ; 9789814417525 (ISBN) Eslami-Mossallam, B ; Ejtehadi, M. R ; Sharif University of Technology
    2013
    Abstract
    In this paper, we demonstrate the applicability of the perturbation methods to different elastic models of DNA molecule. Two different kinds of perturbation methods are presented to find a first approximation for the force-extension characteristic of DNA in the anisotropic wormlike chain model, and the persistence length of DNA in the asymmetric elastic rod model. In both cases we show that it is meaningful to use the perturbation theory, and a first-order calculation is enough to find the result with an acceptable accuracy  

    Elastic properties of actin assemblies in different states of nucleotide binding

    , Article Cellular and Molecular Bioengineering ; Volume 5, Issue 1 , 2012 , Pages 1-13 ; 18655025 (ISSN) Ghodsi, H ; Kazemi, M. T ; Sharif University of Technology
    Abstract
    In this paper, the elastic properties of monomeric actin (G-actin) and the trimer nucleus (G-actin trimer) in different states of nucleotide binding are estimated using steered molecular dynamic (SMD) simulations. Three nucleotide binding states are considered: ADP- and ATP-bound actin and nucleotide-free actin assemblies. Our results show that nucleotide binding and the corresponding changes in structure have significant effects on the mechanical behaviors of actin assemblies. Simulations reveal that the deformation behavior of G-actin monomers is generally elastic up to engineering strains of 16 and 40% in the tension and shear tests, respectively. In addition, the G-actin trimers react... 

    Contribution of nonlocal interactions to DNA elasticity

    , Article Journal of Chemical Physics ; Volume 134, Issue 12 , 2011 ; 00219606 (ISSN) Eslami Mossallam, B ; Ejtehadi, M. R ; Sharif University of Technology
    2011
    Abstract
    A nonlocal harmonic elastic rod model is proposed to describe the elastic behavior of short DNA molecules. We show that the nonlocal interactions contribute to effective bending energy of the molecule and affect its apparent persistence length. It is also shown that the anomalous behavior which has been observed in all-atom molecular dynamic simulations [A. K. Mazur, Biophys. J. 134, 4507 (2006)] can be a consequence of both nonlocal interactions between DNA base pairs and the intrinsic curvature of DNA  

    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...