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steered-molecular-dynamics
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Molecular dynamics simulation of the dissociation mechanism of P-selectin from PSGL-1
, Article Journal of Theoretical and Computational Chemistry ; Volume 16, Issue 4 , 2017 ; 02196336 (ISSN) ; Niroomand Oscuii, H ; Nikbin, E ; Shamloo, A ; Sharif University of Technology
World Scientific Publishing Co. Pte Ltd
2017
Abstract
Interactions between P-selectin, expressed on activated endothelium, and its counterpart P-selectin glycoprotein ligand-1 (PSGL-1), expressed on leukocytes, play a pivotal role in adhesive events that recruit circulating leukocytes toward inflamed or injured tissues. Atomistic understanding of the association and dissociation of these bonds under blood flow is necessary to define the underlying mechanism. In this study, steered molecular dynamics (SMD) simulations were applied to investigate the conformational changes of P-LE/SGP-3 construct (an effective binding unit of the P-selectin/PSGL-1 complex) under stretching with constant velocity. In the present simulations, a self-built force...
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) ; Shamloo, A ; Alasti, A ; Zadeh, E. G ; Jaffray D. A ; Sharif University of Technology
Springer Verlag
2015
Abstract
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...
Mechanical Properties of Actin Assemblies
, M.Sc. Thesis Sharif University of Technology ; 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 Grain Molecular Dynamics Simulation of Drug Carrier Translocation into Cell Membrane
, M.Sc. Thesis Sharif University of Technology ; Saidi, Mohammad Said (Supervisor) ; Firoozabadi, Bahar (Supervisor)
Abstract
With the increasing development of the pharmaceutical industry and producing drugs with specific performance, its transfer into cells is also very important. Cell membranes are effectively impermeable to hydrophilic compounds unless the permeation is facilitated by dedicated transport systems. This means that many hydrophilic compounds, including many promising drug candidates, fail to reach their intracellular target because they cannot spontaneously cross lipid membranes. As a consequence, there is much interest in finding ways to facilitate the transport of molecules across cell membranes. Cell-penetrating peptides (CPPs) in particular have shown much promise as potential delivery agents...
Manipulation of biomolecules: A molecular dynamics study
, Article Current Applied Physics ; Volume 14, Issue 9 , September , 2014 , Pages 1216-1227 ; ISSN: 15671739 ; Nejat Pishkenari, H ; Mahboobi, S. H ; Meghdari, A ; Sharif University of Technology
Abstract
With the rapid progression of bionanorobotics, manipulation of nano-scale biosamples is becoming increasingly attractive for different biological purposes. Nevertheless, the interaction between a robotic probe and a biological sample is poorly understood and the conditions for appropriate handling is not well-known. Here, we use the molecular dynamics (MD) simulation method to investigate the manipulation process when a nanoprobe tries to move a biosample on a substrate. For this purpose, we have used Ubiquitin (UBQ) as the biomolecule, a single-walled carbon nanotube (SWCNT) as the manipulation probe, and a double-layered graphene sheets as the substrate. A series of simulations were...
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) ; 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...
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) ; Shamloo, A ; Alasty, A ; Ghafar Zadeh, E ; Sharif University of Technology
MDPI AG
2016
Abstract
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...