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 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... 

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... 

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... 

A Coiled Carbon Nanotube (CCNT) can be geometrically viewed as a graphene sheet whose rolled and twisted to form a helically coiled nanotube. It is the strongest material ever measured with strengthexceeding more than hundred times of steel.The strength of a CCNT iscritically influenced by temperature, tube diameter, strain rate and pitch angle. In this study,a Molecular Dynamics (MD) simulationis performed to understand the effect of temperature, strain rate, tube diameter and pitch angle on the mechanical properties of CCNTs. Results indicate thatexisting the stone-wales defects is necessaryfor thermodynamic stability of CCNTs.According to the stress-strain curves it was observed thatyield... 

Thermal barrier coatings (TBCs) are used for increasing the efficiency and reducing pollutants of internal combustion engines (ICEs). In this paper, an optimization framework is developed in order to obtain the optimal dimensions for conventional coat, and the optimal dimensions and material property for functionally graded (FG) coat of a partially coated piston. A thermo mechanical analysis is investigated for Nano coat by finite element method. The conventional and Nano coats are made of MgZrO_3 as the insulating ceramic overlay and NiCrAl as the metallic bond-coat. The properties of the FG coat is assumed to vary according to power law through the thickness. For all tree conventional, FG... 

Alzheimer’s disease (AD) is the most common type of dementia in the elderly. The neuropathology and treatment of AD is not precisely determined yet, but according to the pathological studies, AD is associated with presence of toxic soluble oligomers and insoluble senile plaques formed by amyloidosis of Amyloid Beta (Aβ) in neocortical region of brain. An attractive therapeutic approach to treat AD is to identify small ligands that are capable of binding to critical residues in order to inhibit or reverse Aβ amyloidosis process as source of neurotoxicity. In this area, therapeutic efforts designed various organic agents and most of them focused on the N-terminal sequence of Aβ. The aim of...