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 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 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... 

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... 

Ionic polymer metal nanocomposites (IPMNCs) are among the advance materials which have been widely used recently as smart materials. These nanocomposites, which are made of polymeric layers (Nafion) plated by metallic or non-metallic conductive electrodes, show large deformations under low applied voltages. The advance materials like these nanocomposites have resolved the problems of the conventional actuators and helped in producing accurate systems.
Several methods have been used to predict the behavior of IPMNCs which any of them consider some simplifying assumptions. In these materials physical phenomena happen at the molecular scale and deformations observed at the large scale.... 

DNA is the most important biological molecule which contains all the genetic information of living organisms. The mechanical behavior of this molecule has a significant role on its functions. In this study, we introduce a model to for DNA nanomechanics. This model is called rigid base-pair chain in which every base pair is considered as a rigid object. The base-pairs only interact with their nearest neighbors via a harmonic potential. We have used this model to study the nanomechanical behavior of the DNA such as its bending, twisting, and stretching elasticity. Also the model was successful to predict the structure of DNA minicircles with extra amount of twist. After that we used the model... 

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... 

Iodine isotopes are among the most significant medical radioisotopes with a wide range of applications in therapy and diagnosis. The I-131 isotope is usually synthesized by irradiation of natural tellurium in atomic reactors. But there is an alternative route in which this isotopes is produced along with two other significant medical radioisotopes (i.e. Mo-99, Xe-131) by neutronic irradiation of uranium in the reactors. To separate iodine isotopes especially in the extraction process of fission fragments, it is necessary to be selective adsorption of iodine on a selective adsorbent. One of the most selective adsorbent for this application is copper. The aim of this study is to compare 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 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 use of superhydrophobic surfaces is one the most promising methods for reducing the friction and increasing the flow rate in fluid transfer systems. Since in such systems the surface structure plays a key role, in the first part of this study, the performance of the hierarchical nanostructures is explored. These nanostructures are inspired by the superhydrophobic surface of the lotus leaf. The flow is considered between two walls with hierarchical nanostructures and simulate the system via the molecular dynamics (MD) method. The size of the nanostructures and the distance between them have been studied to find whether a design with maximum flow rate exists. The nanostructures have two... 

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... 

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... 

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... 

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,... 

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,... 

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... 

Mechanical properties such as Young's and bulk modulus and strength of material is improved by adding Nano fillers to polymer substrates. Hence by adding Nano fillers such as graphene and carbon nanotubes to polymer substrates it is possible to achieve better properties in resultant nano composites. The aim of this study is to investigate the improvement in polymer-based composites properties by adding graphene Nano fillers for shock absorption. In this study, molecular dynamics method is used to model the molecular behavior of the material. First, a sample cell that have the properties of the whole material, is modeled, then by applying impact loading in modeling software, the response of...