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khoshnood--atefeh
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Effects of Graphene Nanopores and Temperature on DNA Sequencing Using Molecular Dynamics
, M.Sc. Thesis Sharif University of Technology ; Meghdari, Ali (Supervisor) ; Khoshnood, Atefeh (Co-Advisor)
Abstract
Distinguishing the structure of DNA is of outmost importance in the medicine and agriculture industry nowadays. Various methods have been suggested so far; however, high costs, incorrect results, and time-taking process are among main defects of them. Scientists try to find new ways for recognizing DNA structure and system in order to overcome such problems. One of these new methods is absorbing and passing DNA through Nano-pores in an electrolyte solution under the influence of an electrical field. The basis of this method is the ionized currents which occur due to the passing of DNA through Nano-pores. Because each DNA base pairs can form a barrier corresponding to a unique measured value,...
The Effect of Hydrophobic Mismatch and Rigidity of Protein on the Cluster Formation of Transmembrane Proteins in Biomembranes
, M.Sc. Thesis Sharif University of Technology ; Ahmadiyan, Mohammad Taghi (Supervisor) ; Jalali, Mir Abbas (Co-Advisor) ; Khoshnood, Atefeh (Co-Advisor)
Abstract
Membrane proteins aggregation is a very important biological phenomenon in a variety of cell functions. It has been suggested that aggregation behavior of membrane proteins is influenced by the shape of the hydrophobic domain of the proteins, proteins hydrophobic mismatch and bilayer curvature. However, in this study by means of coarse grained membrane simulations it has been found that in thermal equilibrium, protein-protein interactions also depend on protein rigidity and structural strength. Based on simulation results, we have observed stable large clusters even in the absence of hydrophobic mismatch between lipids and proteins. Interestingly, our results also indicate that proteins with...
Dynamics of Protein-Embedded Vesicles in Simple Shear Flow
, M.Sc. Thesis Sharif University of Technology ; Jalali, Mir Abbas (Supervisor) ; Khoshnood, Atefeh (Co-Advisor)
Abstract
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...