Sharif Digital Repository

HIV virus in its life cycle in order to leave the host cell uses Gag polyprotein assembling on the inner leaflet of the membrane. Gag polyprotein could interact with the cellular membrane via Myr-MA protein inserted in its amino terminal. Based on the exprimental data, HIV matrix proteins (MA) assemble as hexamers of trimers on the membrane to form a hexagonal lattice. In this study, membrane anchoring of MA proteins and the effect of a hexamer of MA trimers on the local curvature of membrane have been simulated using a coarse-grained model. The results suggest that MA binding to the membrane is mainly due to electrostatically interactions between the HBR motif of MA with PIP2 lipids. In... 

The ever-increasing growth of Nanotechnology has elevated the necessity for the development of new numerical and computational methods that are better capable of evaluating systems at this scale. The existing techniques, such as Molecular Dynamics Methods, in spite of being fully capable of evaluating nanostructures, lack the ability to simulate large systems of practical size and time scales. Therefore, in order to be able to provide a realistic simulation of a large model, simulation of which is limited by the computational cost of the current molecular dynamics methods at hand, Coarse-Graining technique has recently become a very effective and beneficial method which refers to the... 

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... 

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... 

F-BAR protein is one of the Bin/Amphiphysin/Rvs (BAR) superfamily proteins which contributes in curvature generation and stabilization of lipid membranes. These proteins usualy form lattices on the membrane and can sculpt the membrane. In this project the interaction of F-BAR protein with a lipid membrane is modeled using coarse grained molecular dynamics approach. In order to describe the curvature generation and stabilization we would need an appropriate coarse grained model for the lipid membrane. In this project the proposed model for the membrane describes a membrane in liquid phase with a lateral diffusion in the lipid bilayer. Depth and width of the lipids potential is determined in... 

Actin is the most abundant protein in most eukaryotic cells. It is highly conserved and participates in more protein-protein interactions than any known protein. Actin plays a crucial role in cell motility, adhesion, morphology and intracellular transport. Its biologically active form is the filament (F-actin), which is assembled from monomeric G-actin. In this thesis, the mechanical properties and characteristics of both G- and F-actin are studied using molecular dynamics simulations. In general, this thesis can be categorized into two individual parts: First, steered molecular dynamics simulation was performed to assess tension of monomeric G-actin molecule, and stress-strain curves were... 

In this thesis, a method has been exploited to couple the atomistic domain with the coarse-grained domain. Since molecular dynamics has a high computational cost when a large number of atoms exist, coarse-grained molecular dynamics was used in which a number of atoms are assumed as a bigger bid and interatomic potential is modified for bids so that the material’s mechanical properties remain constant. This method not only reduces the computational cost of calculating forces in molecular dynamics simulation but also, the time step used in Coarse-Grained Methods can be more than atomistic simulations as the frequency of occurring phenomena in CG scale is less than atomistic scale.The advantage... 

In the area of material studies, the atom structure models are the basis of all simulations and methods. With improvements in computers power, these models have become more consistent with experimental results. New theoretical methods combined with supercomputers assist to an understanding with detail and accuracy of material behavior at the atomic scale that leads to develop of the Computational Materials Science. Recently, developments in fields such as quantum mechanics, statistical physics, solid-state physics, quantum chemistry, computer science and graphics, allowed for faster computing which leads a powerful tool for material calculations and designs. New computer applications allow...