Search for: steered-molecular-dynamics-simulation
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    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
    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... 

    Steered molecular dynamic simulation approaches for computing the blood brain barrier (BBB) diffusion coefficient

    , Article IFMBE Proceedings ; Volume 51 , 2015 , Pages 1699-1703 ; 16800737 (ISSN) ; 9783319193878 (ISBN) Pedram, M. Z ; Shamloo, A ; Alasti, A ; Zadeh, E. G ; Jaffray D. A ; Sharif University of Technology
    Springer Verlag  2015
    In the recent years a great attention of research deals with different physical and biological aspects of the BBB structure, a robust shield that separates the blood and brain, a recent research held by the authors of this paper has focused on figuring out computing the diffusion coefficient of endothelial cell membrane. In this study, the major efforts have been concentrated on calculating a standardized measure for the amount of permeability and diffusion of this barrier. As a result, this work is dedicated to molecular dynamics (MD) simulation of calculating the interaction force between nano-particle and BBB membrane. data is recorded by using steered molecular dynamics simulation and... 

    Optimal magnetic field for crossing super-para-magnetic nanoparticles through the Brain Blood Barrier: A computational approach

    , Article Biosensors ; Volume 6, Issue 2 , 2016 ; 20796374 (ISSN) Pedram, M. Z ; Shamloo, A ; Alasty, A ; Ghafar Zadeh, E ; Sharif University of Technology
    MDPI AG  2016
    This paper scrutinizes the magnetic field effect to deliver the superparamagnetic nanoparticles (SPMNs) through the Blood Brain Barrier (BBB). Herein we study the interaction between the nanoparticle (NP) and BBB membrane using Molecular Dynamic (MD) techniques. The MD model is used to enhance our understanding of the dynamic behavior of SPMNs crossing the endothelial cells in the presence of a gradient magnetic field. Actuation of NPs under weak magnetic field offers the great advantage of a non-invasive drug delivery without the risk of causing injury to the brain. Furthermore, a weak magnetic portable stimulator can be developed using low complexity prototyping techniques. Based on MD...