Sharif Digital Repository

Nanobiotechnology is the application of nanotechnology in nanomedicine. Recently, the use of antimicrobial peptides as a substitute for antibiotics and anticancer drugs has attracted increasing attention. Therefore, the study of the structural behavior of these peptides such as Melittin and their interactions with biocompatible and biodegradable polymers is important. This study was performed to evaluate the critical interactions in the formation of the Melittin-polymers complexes. The aim of the current study was to investigate molecular mechanisms of Melittin encapsulation in biopolymers by molecular dynamics (MD) simulation. The results indicated that the basic residues of Melittin could... 

In the context of nanodiamond/chitosan (ND/CS) nanocomposites and utilizing atomistic molecular dynamics, the interaction mechanism of adsorbed CS layer around a model ND has been investigated at three level of hydration: in bulk of water, water as a droplet, and completely dry condition. The effect of amination and carboxylation of ND has been studied. To ensure that the comparison of these model systems is meaningful (energetically and geometrically), the CS interphases around NDs were characterized through holistic concentration profiles and density distribution maps. Our results revealed that in a completely dry condition or hydrated by a molecularly small droplet, both of the... 

An important issue in the study of the nanostructures behaviors is the surface effects, which increases with the increase of the surface-to-volume ratio. Continuum theories are capable of modeling structures at micro and larger scales with enough precision and low computational costs. However, these theories are unable to predict the mechanical properties of nanostructures accurately. On the other hand, due to their high precision, atomistic modeling techniques are extensively employed for the study of systems at nanoscale; however, computational costs of these techniques are relatively high. In this research, we aim to study the vibrational behavior of nanobeams made of three FCC metals;... 

In the present study, a model was proposed to determine the elastic properties of the family of fullerenes at different temperatures (between 300 and 2000 K) using a combination of molecular dynamics simulation and continuum shell theory. The fullerenes molecules examined here are eight spherical fullerenes, including C60, C80, C180, C240, C260, C320, C500, and C720. First, the breathing mode frequency and the radius of gyration of the molecules were obtained at different temperatures by molecular dynamics simulations using AIREBO potential. Then, these data were used in a continuum model to obtain the elastic coefficients of these closed clusters of carbon in terms of temperature changes.... 

The aim of this research is to conduct atomistic investigations of physical interaction analysis of nanoscale objects manipulation. The system consists of tip, particle and substrate. The manipulation tool moves with a constant speed while pushing the particle in a desired direction. The focus of the research is on ultra-fine metallic nanoparticles. To perform this research, Nose-Hoover dynamics and Sutton-Chen interatomic potential will be used to investigate the behavior of the aforementioned system which is made from different transition metals. The effects of size, material type and temperature on the success of the process have been investigated by planar molecular dynamics. © 2008 IEEE... 

The classical methods utilized for modeling nano-scale systems are not practical because of the enlarged surface e ects that appear at small dimensions. Contrarily, implementing more accurate methods is followed by prolonged computations as these methods are highly dependent on quantum and atomistic models, and they can be employed for very small sizes in brief time periods. In order to speed up the Molecular Dynamics (MD) simulations of the silicon structures, Coarse-Graining (CG) models are put forward in this research. The procedure involves establishing a map between the main structure's atoms and the beads comprising the CG model and modifying the parameters of the system so that the... 

Coiled carbon nanotubes (CCNTs) have increasingly become a vital factor in the new generation of nanodevices and energy-absorbing materials due to their outstanding properties. Here, the multiobjective optimization of CCNTs is applied to assess their mechanical properties. The best trade-off between conflicting mechanical properties (e.g., yield stress and yield strain) is demonstrated and the optimization of the geometry enables us to find the astonishing CCNTs with a stretchability of 400%. These structures have been recognized for the first time in the field. We derived several highly accurate analytical equations for the yield stress and yield strain by the implementation of... 

We investigate the effect of wall roughness on water electrolyte transport characteristics at different temperatures through carbon nanotubes by using nonequilibrium molecular dynamics simulations. Our results reveal that shearing stress and the nominal viscosity increase with ion concentration in corrugated carbon nanotubes (CNTs), in contrast to cases in smooth CNTs. Also, the temperature increase leads to the reduction of shearing stress and the nominal viscosity at moderate degrees of wall roughness. At high degrees of wall roughness, the temperature increase will enhance radial movements and increases resistance against fluid motion. As the fluid velocity increases, the particles do not... 

We investigate the effect of wall roughness on water electrolyte transport characteristics at different temperatures through carbon nanotubes by using nonequilibrium molecular dynamics simulations. Our results reveal that shearing stress and the nominal viscosity increase with ion concentration in corrugated carbon nanotubes (CNTs), in contrast to cases in smooth CNTs. Also, the temperature increase leads to the reduction of shearing stress and the nominal viscosity at moderate degrees of wall roughness. At high degrees of wall roughness, the temperature increase will enhance radial movements and increases resistance against fluid motion. As the fluid velocity increases, the particles do not... 

We use coarse grained molecular dynamics simulations to investigate diffusion properties of sheared lipid membranes with embedded transmembrane proteins. In membranes without proteins, we find normal in-plane diffusion of lipids in all flow conditions. Protein embedded membranes behave quite differently: by imposing a simple shear flow and sliding the monolayers of the membrane over each other, the motion of protein clusters becomes strongly superdiffusive in the shear direction. In such a circumstance, the subdiffusion regime is predominant perpendicular to the flow. We show that superdiffusion is a result of accelerated chaotic motions of protein-lipid complexes within the membrane voids,... 

We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is performed by gradually decreasing the diameter of a spherical shell which envelopes a confined chain. The latter procedure is carried out by injecting the chain inside a spherical shell through a hole on the shell surface. The chain is modeled with a rigid body molecular dynamics simulation and its parameters are adjusted to DNA base-pair elasticity. Directional order parameter is employed to analyze and compare the confined chain and the conformations of the... 

The structure and autoionization of water at the water-phospholipid interface are investigated by ab initio molecular dynamics and ab initio Monte Carlo simulations using local density approximation (LDA) and generalized gradient approximation (GGA) for the exchange-correlation energy functional. Depending on the lipid headgroup, strongly enhanced ionization is observed, leading to the dissociation of several water molecules into H+ and OH- per lipid. The results can shed light on the phenomena of the high proton conductivity along membranes that has been reported experimentally  

Lipoproteins are biochemical compounds containing both proteins and lipids. These particles carry chemicals like cholesterol and triglycerides that are not soluble in aqueous solutions. This paper presents modeling of lipoprotein system using coarse grain molecular dynamics technique and stability analysis of this system in a water solution like blood. A high density lipoprotein (HDL) that consists of two annular monomers is modeled. Also there are lipid bilayers located in center of the rings, so the whole HDL and lipid bilayers are called lipoprotein system. First, all atom model is provided and then coarse-grain model is obtained using MARTINI technique. Modeling of the system in all atom... 

A very important part of the living cells of biological systems is the lipid membrane. The mechanical properties of this membrane play an important role in biophysical studies. Investigation as to how the insertion of additional phospholipids in one leaflet of a bilayer affects the physical properties of the obtained asymmetric lipid membrane is of recent practical interest. In this work a coarse-grained molecular dynamics simulation was carried out in order to compute the pressure tensor, the lateral pressure, the surface tension and the first moment of lateral pressure in each leaflet of such a bilayer. Our simulations indicate that adding more phospholipids into one monolayer results in... 

A lubrication model is used to study the dynamics of nanoscale droplets on wettability gradient surfaces. The effects of the gradient size, size of the nanodroplets and the slip on the dynamics have been studied. Our results indicate that the position of the center of mass of the droplets can be well described in terms of a third-order polynomial function of the time of the motion for all the cases considered. By increasing the size of the droplets the dynamics increases. It is also shown that the slip can considerably enhance the dynamics. The results have been compared with the results obtained using theoretical models and molecular dynamics simulations  

Molecular dynamics simulations are carried out to investigate the manipulation of metallic clusters on double-layer surfaces. The system parts are made of transition metals. The conditions which are subjected to change in the tests are material combinations for cluster, main substrate and lubricant layer (adlayer). In addition to qualitative observations, two criteria which represent the particle deformation and substrate abrasion are utilized as evaluation tools and are computed for each case. Obtaining this sort of knowledge is highly beneficial for further experiments in order to be able to plan the conditions and routines, which guarantee better success in the manipulation process  

In recent years, nanocars with p-carborane wheels have been a subject of interest as an artificial molecular machine. Researchers aim to discover compositions that are easier to fabricate, efficient and are more stable on the surface. The p-carborane molecule has all these key elements, making it a viable choice as a nanocar wheel, and the mobility of a nanocar is heavily influenced by the motion of its wheels. In this research, we use classical Molecular Dynamics (MD) in isothermal conditions to specify the regime of motion of p-carborane at different temperatures. We find that by raising the temperature, three different regimes of motion may be observed: jumps to adjacent cells, long...