Sharif Digital Repository

With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, a revolutionary sequencing method is needed for the cost-effective and rapid interrogation of individual genomes. Generally there are key factors in the definition and evalution of sequencing methods: 1-read length, 2-throughput, 3-read accuracy, 4-read depth, and 5-cost per base. The purpose of developing new sequencing methods is making better at least one of these factors. In order to reach the goal of rapid and low-cost sequencing method, one cannot rely only on current techniques. Improvements of current... 

Understanding the flow of liquids and particularly water in nanochannels is important for scientific and technological applications, such as for filtration and drug delivery. In this study, we perform molecular dynamics simulations to investigate the transfer of single-file water molecules across straight or nonstraight single-walled carbon nanotubes (SWCNTs). In contrast with the macroscopic scenario, the nonstraight nanostructure can increase the water permeation. Remarkably, compared with the straight SWCNT, the nonstraight SWCNT with the minimal bending angle of 30° in the simulations can enhance the water transport up to 3.9 times. Also increasing length and diameter of carbon nanotubes... 

We investigate heat transfer between parallel plates separated by liquid argon using three-dimensional molecular dynamics (MD) simulations incorporating with 6-12 Lennard-Jones potential between molecule pairs. We use thermal walls constructed from the oscillating molecules, which are connected to their original positions using linear spring forces. Channel walls are maintained at specific temperatures using a recently developed interactive thermal wall model. This approach is much more effective than the one which uses a fixed lattice wall modeling to simulate the heat transfer between wall and fluid. Heat flux and temperature distribution in nanochannels are calculated for channel height... 

Mechanosensitive (MS) channels are ubiquitous molecular force sensors that respond to a number of different mechanical stimuli including tensile, compressive and shear stress. One of the main mechanisms to functionally study these channels is the patch clamp technique. Here we use continuum mechanics to probe the question of how curvature, in a standard patch clamp experiment, at different length scales (global and local) affects a model MS channel. Firstly, to increase the accuracy of the Laplace’s equation in tension estimation in a patch membrane and to be able to more precisely describe the transient phenomena happening during patch clamping, we propose a modified Laplace’s equation. In... 

By studying change of ion concentrations in animal cells, researchers have reach to important information about cell cycles such as cell growth, muscle cell contraction and cell migration. Manner and amount of passage of ions through cell membrane are basic information that for studying the cell cycle is required. In this thesis, by using two methods, Forward-Reverse constant velocity Steered Molecular Dynamics (FR-cv-SMD) and classical Equilibrium Molecular Dynamics (EMD), diffusion coefficient and Potential of Mean Force (PMF) of sodium and potassium permeation through their protein channels are obtained. For verification the molecular dynamics (MD) methods, diffusion coefficient of K+... 

The nuclear pore complex mediates all transport between the cell cytoplasm and the nucleus. Being inspired by this biological system, in this project we intended to design an artificial gate by using polyelectrolyte brushes in a cylindrical nanochannel, which will be opened by applying a tangent electrical field and will close by eliminating the field. Grafted polyelecrolyte brushes have the potential to be useful for the design of advanced gating systems for many applications like functional and conrolleble MEMS devices. In order to design the desired gating system we have employed the ESPResSo software to conduct a coarse-grained molecular dynamics simulation in NVT ensemble to simulate...