Sharif Digital Repository

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... 

Aggregation of membrane proteins plays a determinative role in many biological processes، such as signal transduction, cell division and endocytosis. In the present study, we have investigated the interaction between proteins in vesicles by means of coarse-grained molecular dynamics simulations. In the first step, a number of periodic lipid bilayers were simulated and their physical properties were calculated. Then, bilayers were immersed in water and converted into spherical vesicles via a selforganizing process . Finally two proteins were embedded into the vesicle and the potential of mean force (PMF) respect to the angle between them was obtained using umbrella sampling. This process was...