Sharif Digital Repository

Formation of nanoparticles by the gas phase condensation process is one of the most promising methods for the nanoparticles synthesis. Finding the correlations between adjustable parameters of the process and nanoparticles properties depends on how parameters affect the mechanism of nucleation and growth. The use of classical nucleation theory at nanoscale leads to unacceptable results; hence, approaches such as molecular dynamic simulation (MD) have been proposed to investigate the mechanism of nucleation and growth at atomic scale. In the present work, the formation of iron clusters from a supersaturated gas phase was investigated via molecular dynamics simulation. For thermalization of... 

Hydrogen fuel cell is one important choice to supply energy for vehicles in near future. The lack of a safe but inexpensive technology to store hydrogen in a vehicle tank is a serious challenge to commercialize the application of fuel cells. Past experiments have shown that carbon nanostructures, especially single walled carbon nanotubes, have considerable capacity to boost up hydrogen storage. Therefore, many studies have been performed to investigate the possibility of higher hydrogen storage capability using nanostructures for the past decade. Molecular dynamics method which is considered as one of the most important tools in studying nanostructures has shown vast applications in these... 

Actin filaments are the most abundant component of the cellular cytoskeleton and provide shape for the most eukaryotic cells. Actin constitutes 1-10% of the total protein in most cells and is present at even higher concentrations in muscle cells. The functions of actin are directly connected to its mechanical properties, therefore both experimental and computational understanding of the mechanical properties of actin filaments are essential to elucidate their functions in cells and muscles. Actin exists in two forms, actin monomers (G-actin) and actin filaments (F-actin), which have continuous polymerization and depolymerization processes. In the polymerization process, different... 

Nanotechnology is the knowledge of future. Some people Compare the initialization of nanotechnology to the beginning of the industrial revolution. Experimental modeling of nano-materials can be so expensive, but, with the aid of computational nanomechanics, we can perform less experiments and more numerical simulation. In the past decades, applications of nanotubes in medicine, electrical engineering, mechanical engineering, building nano sensors, nano engines and etc caused a pervasive study on the mechanics of carbon nanotubes. In this Thesis, the writer has implemented the Tersoff interatomic potential to perform molecular dynamics simulations of carbon nanotubes. In this work, tensile... 

Computational chemistry is used to study solvent and substituent effects on kinetics and mechanism of some organic reactions. It also is used to study enzyme reactions and enzyme structures. Organic reactions were studied by ab initio quantum mechanics and Monte Carlo simulations. The enzyme studies were done by QM/MM and MD methods in Lund University. The studied organic reactions are 1) Reactions of hydroxylamine and aminoxide anion with methyl iodide. 2) Rearrangement of allyl p-tolyl ether. 3) Reactions of 1,4-Benzoquinone with Cyclopentadiene and Cyclohexadiene derivatives and reaction of cyclopentadiene and vinyl acetate. In the enzyme studies the catalytic reaction of Glyoxalase... 

In this project, two multiscale modeling procedures have been implemented to study the mechanical behavior of SWCNT/polymer composites. First, a new three-phase molecular structural mechanics/ finite element (MSM/FE) multiscale model has been introduced which consists of three components, i.e. a carbon nanotube, an interphase layer and outer polymer matrix. The nanotube is modeled at the atomistic scale using MSM, whereas the interphase layer and polymer matrix are analyzed by the FE method. Using this model, we have investigated the macroscopic material properties of nanocomposite with and without considering the interphase and compared the results with molecular dynamics (MD) simulations.... 

Phospholipid membranes and vesicles play important roles in the cellular functioning, otein signaling and material transport inside cells. Protein-embedded vesiclesare also used for targeted drug delivery. In this thesis, we use molecular dynamicsmethods and study (i) the formation of vesicles from flat lipid bilayers (ii) the mechanicalproperties of vesicles under compressive forces (iii) the shape variations ofvesicles with and without transmembrane proteins (iv) protein clustering.We grow our vesicles from lipid bilayers, which may contain proteins with differentconcentrations. We start with a random initial distribution of proteins that allowsus to monitor the clustering and... 

In continuum mechanics, the constitutive models are usually based on the Cauchy-Born (CB) hypothesis which seeks the intrinsic characteristics of the material via the atomistic information and it is valid in small deformation. The main purpose of this thesis is to investigate the temperature effect on the stability and size dependency of Cauchy-Born hypothesis and a novel temperature-dependent multi-scale method is developed to investigate the role of temperature on surface effects in the analysis of nano-scale materials. Three-dimensional temperature-related Cauchy-Born formulation are developed for crystalline structure and the stability and size dependency of temperature-related... 

Formation of Cyclobutane Pyrimidine Dimer (CPD), one of the most abundant types of damages in DNA double helices, is caused by UV radiation and plays a major role in causing skin cancer. DNA photolyase is an efficient enzyme that repairs this UV-induced damaged DNA-base. Previous studies have shown that the enzyme flips the dimer out of the DNA double helix into its binding pocket.
In this project, several nanoseconds of molecular dynamics simulations was performed to investigate the process of base flipping energetically. These simulations are consist of equilibration of repaired and damaged double strands for 3 and 8 nanoseconds respectively. All these simulations ran over NVT... 

This thesis is devoted to the simulation of biomolecules manipulation using Molecular dynamics (MD). In order to investigate the manipulation behavior, we have used the Ubiquitin as biomolecule, a single-walled carbon nanotube (SWCNT) as manipulation probe, a graphene sample as substrate. Along this line, a lot of simulations are conducted to study the effects of different conditions on the success of manipulation process. These conditions include tip diameter, vertical gap between tip and substrate, initial orientation of protein, and the simulation environment (dry or wet). The results demonstrate that tips with bigger diameters and smaller distances with respect to the substrate increase... 

The physical characteristics of Pt nanoclusters with different sizes (256-8788 atoms) have been investigated via molecular dynamics simulations. The Pt-Pt radial distribution function, internal energy, heat capacity, enthalpy, entropy of the nanoclusters are calculated at some temperatures. The melting point predicted by the various properties is consistent with each other and shows that the melting temperature increases with the particle size. We have calculated the Gibbs free energy for the Pt bulk and also for its nanoparticle. We have used the thermodynamic integration method to obtain the Gibbs free energy. The total Gibbs free energy is taken as the sum of its central bulk and its... 

In this thesis a mutliScale model based on the Cauchy-Born hypothesis and via usage of XFEM is proposed for crack modeling. By solving an example, the important of surface effects in the surface stresses region is shown. Considering not being able to model the surface effects with the Cauchy-Born method, the boundary Cauchy-Born method for modeling crack effects is used. Moreover, three Molecular Dynamics method for modeling crack will be proposed. According to the obtained results from these methods, it was deduced that for calculating the correct surface stresses in Molecular Dynamics the mutual interaction of upper and lower atoms of crack should be omitted. Finally, the validation of... 

Mindboggling advances in nanotechnology have urged researchers to develop state-of-the-art numerical methods to enable them to simulate and to interpret phenomena at this scale. Unfortunately, Classical models have numerous shortcomings which hinder their applications in new contexts. For instance, classical Continuum Mechanics fails to appropriately depict material behavior at small scales, and, on the other hand, Molecular Dynamics simulations are computationally prohibitive. As a consequence, researchers have devised multi-scale methods during the past decade to overcome these obstacles. In fact, in multi-scale methods information is passed from one mathematical description to the other.... 

In this thesis, proteinnanoparticle interactions have been studied using Molecular Dynamics simulation. sT fN, is the studied protein in this work. It is one of the most important proteins in the blood fluid. In this work, nanoparticle has been modeled as a surface; because the radius of gyration of sT fN is less than 3nm, so when it is near an enough big nanoparticle (100200 nm), nanoparticle seems as a surface from the view of protein. The surface of nanoparticle consists of sodium ions. Surface of nanoparticle, has been modeled using two types of surface:flat surface and nonflat surface. Protein interaction with surface, has been studied in two different initial orientations with respect... 

Unique and interesting properties of Graphene with two dimentional and CarbonNanotubes rod-like and their increasing applications such as application in electronic industry, sensors, displays, supercapasitors, pharmacy, etc, they hase become an important field of condensed matter and nanotechnology. Crystalization process and the distribution of light atoms and molecules on graphene surface hase become one of the reaserche arease of interest and hase attracted much attention. These studies play an important role in design of nanosensors graphene based. Most of the experimental observatins of surface diffusion in the chemical and physics systems have been classically described and... 

In addition to chemical stability and biocompatibility, because of the characteristics of quantum dimensions, gold nanoparticles are used in detecting cancers, imaging and therapeutics .Atomic interactions between gold particles and bioparticles are influenced by the dimensions of gold particles .Therefore, in this project, after introduction of various water models and used potentials for modeling by the method of TIP3P, we studied gold clusters in different dimensions and densities, by using EAM potential in the aquatic environment .Then we can pave the way for studying proteins besides gold nanoparticles, in the future studies. Besides, gold particles were studied as colloid, so as to... 

The transport behavior of water molecules inside a model carbon nanotube is investigated by using nonequilibrium molecular dynamics simulations. The shearing stress between the nanotube wall and the water molecules is identified as a key factor in determining the nanofluidic properties. Due to the effect of nanoscale confinement, the effective shearing stress is not only size sensitive but also strongly dependent on the fluid flow rate. Consequently, the nominal viscosity of the confined water decreases rapidly as the tube radius is reduced or when a faster flow rate is maintained. The effect of ion concentration and temperature rise on fluid flow and shearing stress is also investigated.... 

Ion channels are present in all cell membranes which are the important part of the performances in regulating the flow across the membrane as well as the signaling. We have investigated the water permeation through carbon nanotube (CNT) membranes as a model for the synthetic ion channels, i.e. peptide nanotube channels (PNCs). The effect of different charge configured CNTs which tailored based on these ion channels on the water permeation has been studied. In addition, the temperature dependence of the permeation using statistical models such as continuous time random walk model (CTRW) via molecular dynamics simulation has been investigated. We have found that there is a jump in 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... 

In present research forming process of nanopowders, which is a part of powder metallurgy was investigated by molecular dynamics method. Powder metallurgy is a relatively new method for production of industrial parts by pouring powder into die and compaction to desired density. One can reach parts with higher quality and strength by decreasing size of powder’s particles and entering the nano scale. Particle with smaller size have higher specific surface and due more intensity to react. Classic methods for investigation of this process don’t cover the atomic scale effects, so using newer procedures such as molecular dynamics is highly recommended. In present research, at first compaction of...