Sharif Digital Repository

Nowadays, water desalination is a widely-used method for producing clean and fresh water. Recent researches in this area have mostly focused on Reverse Osmosis technology which is one of the most efficient technologies in water desalination. A new idea to increase the efficiency of a recently-designed reverse osmosis membrane called “Honeycomb Carbon Nanotube Membrane” is presented through molecular dynamics simulation. Although in this study only the inlet area of the honeycomb structure which is a Y-shaped entrance, is modeled and studied, but obviously, any improvement in the membrane inlet, equals better results at outlet which means a more efficient desalination process. Present thesis... 

In recent years carbon nanotubes and other carbon nanostructures such as graphene sheets have attracted a lot of attention due to their unique mechanical, thermal and electrical properties. These structures can be used in desalination of sea water, removal of hazardous substances from water tanks, gases separation, and so on. The nano porous single layer graphene membranes are very efficient for desalinating water due to their very low thickness. In this study, the mechanism of passing water and salt ions through nano porous single-layer graphene membrane are simulated using classical molecular dynamics. In the simulation, in order to separate salt ions from the water, the effects of applied... 

The broad range of applicability of nano devices particularly in electronics, optoelectronics, and micro/ nano-electro- mechanical systems has drawn the attentions of the industrial and scientific communities of various disciplines. This work is devoted to study the effect of surface and interface elasticity in the analysis of the mechanical behavior of ultra-thin objects in the presence of some statical or dynamical loadings. Based on the fact that the surface-volume ratio increases in nano-scale, description of the behavior of such a small structure via usual classical theories, which generally neglect the surface/interface effect, ceases to hold. In the present study, first, a... 

Low salinity water flooding (LSWF) is a relatively new EOR method in which low salinity or modified ionic composition water is injected into the reservoir to alter its wettability toward a more water-wettable state to accelerate oil recovery. Ease of field deployment and relatively low cost, as well as laboratory results confirming the positive effect of this method in improving the oil recovery factor, have made this technique attractive in the oil industry.Despite the many advantages of this method, overcoming the mixing between low and high salinity water which occurs due to a high mobility ratio between these two fluids is essential because it negatively affects the efficiency of LSWF.... 

In this research, the behavior of surfactin at the presence of water, decane, and asphaltene is investigated. Decane is chosen instead of crude oil to simplify the model. In the first chapter, basic molecular structures are introduced. Furthermore, in the second chapter molecular dynamics simulation, as the main tool in these simulations, is introduced. In the third chapter, one of the most important quantities in chemical engineering, diffusion coefficient, is chosen to investigate the efficiency and accuracy of molecular dynamics simulation method to calculate such a quantity and results show that molecular dynamics simulation can present accurate quantities, more accurate than common... 

The ever-increasing growth of Nanotechnology has elevated the necessity for the development of new numerical and computational methods that are better capable of evaluating systems at this scale. The existing techniques, such as Molecular Dynamics Methods, in spite of being fully capable of evaluating nanostructures, lack the ability to simulate large systems of practical size and time scales. Therefore, in order to be able to provide a realistic simulation of a large model, simulation of which is limited by the computational cost of the current molecular dynamics methods at hand, Coarse-Graining technique has recently become a very effective and beneficial method which refers to the... 

Polymer/clay nanocomposites (PCNs) are multifunctional materials that have superior mechanical and thermal properties than polymer-based materials. These materials are obtained by adding small amounts of nanoclays to a polymer matrix. In this work, a molecular dynamics simulation was carried out to investigate the thermomechanical properties of thermosetting clay nanocomposites. The polymer matrix was composed of phenolic molecules with the crosslink density of 0.74, and different structures of PCNS were considered by varying the amount of polymer molecules. Molecular dynamics simulations of different nanocomposite structures were used to provide the atomistic insights, the molecular... 

In recent decades, metal nanoparticles have been used in medicine for example in cancer treatment. There have always been debates on the nanoparticles specifications such as particle size, amount of surface charge and the particle material. Meanwhile, the study on selecting appropriate properties of nanoparticles for this purpose is very essential and expensive in medical science. In order to access the best efficiency and the least mortality of the patients in treatments, simulation studies can support the medical scientists. In this thesis, the goal is to study transferring nanoparticles as a drug or included drugs through created hypothetical micro-channels in cancerous cells membrane.... 

Inorganic scale deposition has been found to affect many industrial processes,including water injection into the oil reservoirs. Major formation damage because of incompatibility of high sulfate ion content of seawater with formation water containing calcium ion results in formation damage and production decline.In this study, several simultaneous techniques are utilized for qualitative and quantitative analysis of calcium sulfate scale to get more insight into the damage of formation during smart water flooding at micro and Nano scales. In the experimental section, calcium sulfate deposition due to the mixing of the formation water and seawater samples was investigated using the dynamic... 

In the field of high-pressure material science, diverse carbon systems under pressure have been intensively studied with interest in synthesizing new phases. A variety of these synthetic phases which have met various applications in today technology are called the amorphous diamond. The pressure-induced structural transition of carbonaceous material to amorphous diamond is realized by shock compression and rapid quenching. The shock compression and rapid quenching generate the high pressure (several GPa) and the temperature (several hundred K) in a fraction of a microsecond.Since the mechanical and electrical properties of the synthetic diamond are severely sensitive to the atomic structure,... 

Water plays an essential role in the daily lives of humans, plants, and animals. Due to the lack of safe water on the planet, in recent years there have been many challenges in the field of water treatment, which has made water desalination technology always one of the most advanced technologies. The most advanced technology in this field is the use of nanotechnology in water and wastewater treatment, especially the use of Membrane processes such as reverse osmosis. Unlike conventional reverse osmosis membranes, nanoporous membranes can ensure rapid water transfer during the displacement process. The purpose of this thesis is to introduce new monolayers that have an incredible performance in... 

Actin is the most abundant protein in most eukaryotic cells. It is highly conserved and participates in more protein-protein interactions than any known protein. Actin plays a crucial role in cell motility, adhesion, morphology and intracellular transport. Its biologically active form is the filament (F-actin), which is assembled from monomeric G-actin. In this thesis, the mechanical properties and characteristics of both G- and F-actin are studied using molecular dynamics simulations. In general, this thesis can be categorized into two individual parts: First, steered molecular dynamics simulation was performed to assess tension of monomeric G-actin molecule, and stress-strain curves were... 

Shape memory alloys (SMA) exhibit a number of features which are not easily explained by equilibrium thermodynamics, including hysteresis in the phase transformation and ‘‘reverse’’ shape memory in the high symmetry phase. Processing can change these features: repeated cycling can ‘‘train’’ the reverse shape memory effect, while changing the amount of hysteresis and other functional properties. These effects are likely to be due to formations of localised defects and these can be studied by atomistic methods. Here we present a molecular dynamics simulation study of such behaviour employing a two-dimensional, binary Lennard–Jones model. Our atomistic model exhibits a symmetry breaking,... 

Membrane filtration systems are one of the most widely used and effective methods for desalination of saline water in the seas and oceans and treatment of industrial and domestic effluents in order to provide the fresh water resources needed for human survival on the earth and also meet the needs of various industries. The low efficacy of the traditional technologies necessitates the introduction of novel desalination methods. For this purpose, carbon-based membranes have been proposed as high-performance membranes because of their high mechanical strength, ultrafast permeation, and controllable pore size. In this study, by conducting molecular dynamics simulations, the effects of electric... 

Microtubules are hollow cylindrical structures of 25 nanometer diameter inside cell membrane. Microtubule (MT) serves as a cell structure component and vesicular transport inside cell. It has been shown in recent researches that the persistence length in MTs is length dependent and increases about several times of counter length. Also helical structures of MTs have been found recently. In this research using Molecular Dynamic simulation of coarse-grained microtubular structures we compare persistence length of wild and helical microtubular structures. We show that the persistence length in helical structures is independent to the length.
 

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... 

Distinguishing the structure of DNA is of outmost importance in the medicine and agriculture industry nowadays. Various methods have been suggested so far; however, high costs, incorrect results, and time-taking process are among main defects of them. Scientists try to find new ways for recognizing DNA structure and system in order to overcome such problems. One of these new methods is absorbing and passing DNA through Nano-pores in an electrolyte solution under the influence of an electrical field. The basis of this method is the ionized currents which occur due to the passing of DNA through Nano-pores. Because each DNA base pairs can form a barrier corresponding to a unique measured value,... 

Silicon dioxide or silica with the chemical formula SiO2 is the basic component of many minerals. SiO2 films and sheets are widely used in mechanics, optics and electronics due to their outstanding mechanical and electronic performance. The main reason for research in the field of materials with negative Poisson's ratio is their unusual properties, which arise due to the inherent property of negative Poisson's ratio. In this research, the mechanical properties of four two-dimensional silica structures at a temperature of one Kelvin were investigated with the help of molecular dynamics simulation. Also, the sensitivity of the results to the system size and strain rate was studied, and the... 

SHP2 has been reported as a critical non-receptor phosphatase enzyme that plays crucial roles in numerous disorders like cancer. The previous studies on this enzyme showed that inhibiting the action of the enzyme comes as a way of controlling enzyme activity. SHP099 was discovered as an Allosteric inhibitor of the enzyme with the most inhibitory effect among all of the studied compounds. In this study we aimed to design novel dipeptide-and sugar-based inhibitors for the allosteric binding site of this enzyme with in-silico studies including docking, molecular dynamic simulation, and free binding energy analysis. Our novel designed drugs possess enough binding properties, low toxicity, and... 

In this work, structures of Cu-Zr bulk metallic glasses at atomic scale were studied by molecular dynamics simulation. Bulk metallic glasses have high glass form ability, which makes it possible to more effectively examine the relationship between structure and properties in glassy materials. Due to this reason, this family of materials has been selected in this research. Voronoi tessellation method, coordination number analysis, short-range order examination, glass transition temperature and pair distribution function have been selected to investigate the structure in atomic scale. Results show that full icosahedron (with the highest five-fold symmetry) and some distorted icosahedra have...