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Dynamics of Protein-Embedded Vesicles in Simple Shear Flow

Hoore, Masoud | 2014

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  1. Type of Document: M.Sc. Thesis
  2. Language: Farsi
  3. Document No: 45935 (08)
  4. University: Sharif University of Technology
  5. Department: Mechanical Engineering
  6. Advisor(s): Jalali, Mir Abbas; Khoshnood, Atefeh
  7. Abstract:
  8. Studying the dynamics of vesicles in simple shear flow is the first step to decipher the dynamics of cells in flows or the motion of vesicle-based nanoparticles in vessels for drug delivery. The deformation of vesicle in shear flow changes the permeability of its membrane and may lead to its rupture, both of which correlate with the transportation of vesicle cargos to their environment, especially important in drug delivery. The deformation of vesicles in shear flow not only depends on the physical properties of the whole system, such as temperature, but also on the mechanical properties of three media: vesicle membrane plus vesicle’s inner and outer fluid. The effect of the mechanical properties of the inner and outer fluids on vesicles’ behavior and deformation in shear flow has been studied so far, however, the membrane itself has not been considered as a controlling factor in vesicles’ dynamics yet. In practice, we may not be able to control the properties of inner and outer fluids. In this regard, the only controlling factor is the membrane itself. Adding rigid elements to the liquid membrane of vesicles gives us the opportunity to control vesicles’ deformation in shear flow by changing the mechanical properties of vesicles’ membranes.
    In this work, we study the dynamics of protein-embedded vesicles in simple shear flow using coarse-grained molecular dynamics (CGMD). Actually, proteins are stiff structures compared to the liquid lipids of biomembranes. According to this fact, proteins are added to the liquid membranes of our simulation to study their effect on the deformation of vesicles. To this end, we consider uni-particle solvent molecules, liquid chain lipid molecules and stiff protein molecules in our coarse-grained simulation. With reference to our simulation results, at low protein densities in vesicles’ membranes, proteins increase the solidity of liquid bilayers and decrease the deformation of vesicles in shear flow. However, by increasing the density of proteins they tend to make rigid clusters. The formation of protein clusters reduces their interaction periphery with lipids so that their effect on the membrane’s solidity decreases. Our results indicate that protein-embedded vesicles demonstrate two phases of deformation; first, increasing the number of proteins increases the resistance of vesicles against deformation in shear flow. However, by adding more proteins to vesicles, their rigidity reduces abruptly by the formation of protein clusters as if the number of proteins decreases. It is to be noted that vesicle clusters alter the local curvature of vesicle’s membrane so that it becomes difficult to measure vesicle’s deformation accurately by assuming a symmetrical shape for vesicle’s surface. Moreover, the existence of any attached membrane to the inner layer of vesicles’ bilayers gives vesicles the opportunity to expand their surface area and deform further. The so-called theoretical analyses of the problem were based on the assumption that vesicle’s surface area remains constant during deformation. Thus, vesicles with excess bilayers in themselves do not behave respectfully to the equations of motion derived from such analyses. Simulating one sample with extra membrane in itself shows that the number of proteins has nothing to do with vesicle’s deformation if vesicle contains an extra membrane in itself. As a result, regardless of the number of embedded proteins in vesicles’ membranes, vesicles having extra membranes in themselves deform quite larger than their counterparts lacking it do. The results of our simulations indicate that the addition of rigid proteins to the liquid lipid bilayers of vesicles could be considered as a controlling factor to vesicles’ deformation in shear flow. No matter what cargo the vesicles contain and no matter of what their membrane material is made, one could regulate their deformation in a determined shear flow by adding stiff elements to their membrane
  9. Keywords:
  10. Vesicle Shape Transformation ; Coarse Grain Molecular Dynamic ; Lipid Bilayer Membrane ; Membrane Protein Aggregation ; Simple Shear Flow

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