Sharif Digital Repository

Lipid membranes are fundamental constituents of cell membranes and are now used in lap-on-a-chip technology. Membranes in living cells contain a significant fraction of proteins, which undergo lateral random movements due to thermal fluctuations and shear forces imposed by the solvent fluid. Prominent natural and biotechnological systems where membranes are highly sheared include the plasma membrane of endothelial cells, and membranes used in biosensors for high throughput screening of drug candidates, and in water purification devices. In these systems membrane is in direct contact with the mainstream suspension flow, which is driven by pressure gradients. The efficiency and function of... 

In this project the main aim is to model the interaction between the cytoskeleton and cell membrane. In order to model the membrane and cytoskeleton it is used a discrete model, which contains several beads. For modeling the interaction between the beads it is used different kinds of energies. It is used four potentials in a 2D model for modeling the interaction between the membrane beads and it is used SSLJ potential in order to model the interaction between the cytoskeleton and cell membrane. Furthermore, this potential is used to model the interaction between the cytoskeleton filaments. Due to this potential, the cytoskeleton filaments can cross each other in the 2D model. For modeling... 

owning to the side effects and disadvantages of conventional methods of cancers treatments such as chemotherapy, currently, scientists are attempting to find new methods to replace them. Furthermore, many human diseases like SCID and Hemophilia are due to genetic disorders and scientists are also seeking to find permanent treatments instead of available temporary ones for them. in recent years, regarding the obtained achievement, Gene Therapy is being considered as a promising method for both cancers and genetic disorders treatment. But due to low efficiency of this method at this stage, there is an endevour among researchers for a more profound comprehension of the basics of gene therapy to... 

In recent years, application of nanotechnology in medicine is growing rapidly, specially, in the area of drug delivery. One of most import applications of nanotechnology is the using of nanoparticles as a carrier in targeted drug delivery systems. Simulation of drug delivery and prediction of drug release are developing in experimental and industrial areas. Mathematical modeling is used in drug delivery systems because they are time and cost saving and also can be used to predict drug behavior. The aim of this research, is to provide a framework for designing nano drug carriers. To this end, uptake of nanoparticles into different types of cells with different characteristics, in different... 

Due to the limitations on experiments in the field of cell mechanics, computational modeling of biological cells have attracted attention within two recent decades. In general, some models have been developed in two different scales, known as microstructure and continuum, both of which have their own pros and cons. Nevertheless, viscoelastic behavior of cell membrane has attracted less attention of scientists up to now. Therefore, multi-scale simulation of the viscoelastic behavior of the cell membrane has been chosen as the main goal of this thesis. Toward this goal, at first the energy of the simulation box, consisting of 128 Dipalmitoylphosphatidylcholine and 3655 water molecules, was... 

In this research, we aim to study and simulate how nanoparticels translocate through cell membrane. For this purpose, at first a gold nanoparticle is selected as the drug carrier. The partial charges of the ligands are calculated using quantum mechanics based on HF technique with 6-31Gd basis set. To have a realistic shape for nano drug, number and arrangement of ligands are determined based on optimization. After all atom simulations and comparison of results such as diffusion coefficient with experiments, a coarse-grained model of these drugs is created and put inside solvent beside a membrane. The cytoplasmic membrane includes more than 60 types of phospholipids like animal membranes.... 

Endothelium is the interior layer of an artery made up of tremendous number of endothelial cells which are located side by side. Finding the effective parameters that cause the cells to obtain mechanical strength in different morphologies is a major effort in cell engineering studies. In this work a numerical model for endothelial cells is developed. This model has included cell's plasma membrane (the outer membrane of the cell), nucleus and cytoskeleton main components including intermediate and actin filaments as well as microtubules. The model has been validated by simulating the adhesion of the cells to a flat substrate and also atomic force microscopy (AFM) experiments. The two most... 

In the present thesis, intracellular fluid flows have investigated for study cell motions. It is due to firmly relation between the cell motion and these flows. Generally, the cell firstly adheres to a surface, then, moves forward with the effects of the internal fluid flows. In this study, the cell structure is invided to two general parts; the front part of the cell and the cell body. The front part of the cell plays a essential roles in the cell motion, however, the cell body is considered as a extra cargo that is carried by the front of the cell. Therefor, in the present modellings, the front part is only considered. Here, using four different models for the front part of the cell, many... 

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...