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 this study, the nano-scale deformation mechanism of cementite was investigated with aid of Molecular dynamics (MD) simulation using MEAM potential. For this purpose, flow localization was evaluated in various structures such as single crystal cementite, nanocrystalline (NC) cementite, and lamellar cementite at various temperatures and different stress conditions. In order to understand the deformation mechanism in the cementite single crystal, two cylindrical samples with 15 nm length and 5 nm diameter oriented along [001] and [011] were constructed. The result of tensile test simulation at 100 K, 300 K, 700 K and 1100 K revealed that the deformation mechanism in single crystal cementite... 

Low salinity/smart waterflooding is simple to apply and a promising enhanced oil recovery method in which ion-tuned saltwater is injected into subsurface oil reservoirs. Many aspects of this operation, in particular those pertaining to nano-scale, are not yet fully understood. The present dissertation is an attempt to shed light on the microscopic properties and behavior of rock/brine/oil interfaces throughout low salinity/smart waterflooding. Several simulations were carried out for oil/brine and calcite/brine categories each containing various ions and hydrocarbons compounds. The surface contribution of non-functional oil compounds (aromatics and aliphatics) near brine medium was... 

Various studies have confirmed that water salinity and its composition significantly affect the efficiency of the waterflooding process. Field-scale operation of low-salinity water injection has been proven to be a cost-effective enhanced oil recovery (EOR) method which is also compatible with the environmental regulations. Although this method has satisfactory results, it faces some challenges, such as in-situ mixing of the injection low-salinity water with the saline water in the host reservoir. The salinity of the injected water increases, as it contacts the high-salinity reservoir brine in the pores. This phenomenon significantly impairs the efficiency of this technique, and increases... 

IL-1 family of cytokines plays a critical role in the regulation of immune response.These cytokines transfer the signals to the target cells through binding to the IL-1 receptors.Interleukin 1 Receptor Type II (IL-1RII) is the decoy receptor of the IL-1 cytokines. IL-1RII is homologous to the signaling Interleukin 1 Receptor Type I (IL1RI) in its extracellular region and can bind to the same cytokines with higher affinity and the same accessory protein. It down-regulates the signaling and suppresses the downstream pathways due to the lack of the intracellular Toll-Interleukin Receptor (TIR) domain. IL-1RII is decorated by carbohydrate units in-vivo. Dynamics and ligand binding of receptors... 

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... 

Many experimental and theoretical studies have suggested that zinc binding to Aβ could promote amyloid-β aggregation and reactive oxygen species (ROS) production induced by AD disease. Therefore, the introduction of multifunctional drugs capable of chelating zinc metal ion and inhibiting Aβ aggregation is a promising strategy in the development of AD treatment. In present study molecular docking and molecular dynamics (MD) simulations were used to evaluate the efficacy of two new bifunctional peptide drug, composed of two different domains: C-terminal hydrophobic region of Aβ and Zn2+ chelator region. To evaluate the multifunctionality of the ligands, a comprehensive set of MD simulations up... 

Phase change processes have been used in heat transfer industries for decades. However, the heat transfer rate enhancement of the surfaces is still a challenging issue for the researchers. In this path, emerging nanostructured surfaces have shown great potentials. We demonstrate that using nanostructured surfaces in the condensation processes enhances the heat transfer behaviour of the fluid through interfacial contact area increase. In the present study molecular dynamics simulation have been employed to monitor the atomic behaviour of the system components at nanoscale. The argon liquid is considered as the working fluid and the copper surfaces as the phase change site. The effect of... 

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.... 

Carbon nanotubes have special thermodynamic properties which makes suitable as a thermo-acoustic sound source. Recently it is shown that by using these nanotubes it is possible to generate strog sound waves in air or water. Experimental analysis of phenomenon can be complicated and expensive. Hence this fact, in this study using molecular dynamic simulation, numerical analysis of sound generation with CNTs in air and water is discussed. For this purpose, the required structue of the system is generated and it has reaced equilibrium. This process has been done for 6 different CNT and for each CNT there are 5 different distances between them. Althogether, 30 different cases has is used for... 

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.... 

The formation of gas hydrates in oil and gas industries has been the subject of long-standing problems. For example, the hydrate formation may occur and block gas pipelines which can lead to safety hazards. All of these will result in catastrophic economic losses and ecological risks. Therefore, various methods were developed to mitigate the formation of gas hydrate. In many cases, the hydrate inhibition by adding kinetic and thermodynamic inhibitors to the system is the only viable option. But recently using ionic liquids as novel hydrate inhibitors and the discovery of dual function thermo-kinetic inhibitors have been studied. In this project the performance of six imidazolium-based ionic... 

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 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... 

In this study, a novel multiscale analysis is proposed to utilize atomistic properties of crystalline nano-materials as an input to continuum problems in the range of large deformation. The main purpose of presented work is investigating the capability of different hyperelasticity models based on molecular statics (MS) and molecular dynamics methods to attain proper hyperelastic strain energy density function to illustrate atomistic information under various types of deformation loadings. Also, the proficiency of hyperelastic model is investigated for nano-structure including different percentages of voids. The material parameters of hyperelastic strain energy density can be obtained from... 

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... 

Achievements in the synthesis of polycatenanes promise new opportunities for having and designing new smart materials. However, the out-of-equilibrium dynamic of polycate-nane is largely unstudied. This research studies the interplay of poly[2]catenane topology and hydrodynamic interactions in pure shear flow using the MPCD method. To question the effect of topological interaction, we simulated systems with bonded rings alongside systems with poly[2]catenane. In order to investigate the effect of hydrodynamic interaction, each system was examined using the random solvent method as well. Our study shows the poly[2]catenane structure can control the shear and stress by twist and rotation... 

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... 

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... 

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...