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.... 

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... 

In the area of material studies, the atom structure models are the basis of all simulations and methods. With improvements in computers power, these models have become more consistent with experimental results. New theoretical methods combined with supercomputers assist to an understanding with detail and accuracy of material behavior at the atomic scale that leads to develop of the Computational Materials Science. Recently, developments in fields such as quantum mechanics, statistical physics, solid-state physics, quantum chemistry, computer science and graphics, allowed for faster computing which leads a powerful tool for material calculations and designs. New computer applications allow... 

In this thesis ،molecular dynamics simulation of structural and mechanical properties of pure aluminium and copper crystals as well as of the alloyed crystals including 10%,30%,50%,70% and 90% aluminium alloyed have been investigated using two various all-atom and coarse-grained models. Molecular dynamics simulations calculate the realistic behavior of the system and then use them in order to calculate the time average properties of the system. Embedded atom method (eam) and the numerical iterative Boltzmann Inversion method are employed to describe the interaction between atoms. The results are then compared with coarse-grained model. The demonstrated peaks in the radial distribution... 

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 pioneer multiscale hierarchical molecular dynamics (MD) – finite element (FE) coupling method is proposed to illustrate the influence of large deformation on mechanical properties of heterogeneous nano-crystalline structures. The embedded-atom method (EAM) of many-body interatomic potential is applied to evaluate pairwise interactions between atoms in the metallic alloys with face-centered-cubic (FCC) lattice structure at room temperature. In addition, the Nose-Hoover thermostat is used to control the instability of temperature. A weight average between the lattice parameters of atomic structures is utilized in order to calculate the equivalent lattice parameter. The... 

In this work, we investigate the application of coarse graining (CG) methods to molecular dynamics (MD) simulations. These methods provide access to length and time scales previously inaccessible to traditional materials, simulation techniques. However, care must be taken when applying any coarse graining strategy to ensure that we preserve the material properties of the system we are interested in. The most prominent of these techniques is the so called multi scale coarse graining (MS-CG) method. In this study we will focus on the modeling of crystalline Nano structures using coarse graining as one of the approaches in multi scale analysis the force matching method is mainly followed to... 

The molecular dynamic (MD) method was first reported by Alder and Wainwright in the late 1950s to study the interaction of hard spheres. Molecular dynamic (MD) simulation is a technique for computing equilibrium and forwarding properties for classical many-body systems. This is a reasonable and often excellent approximation for a wide range of systems and properties. Although molecular dynamics method provide the kind of detail necessary to resolve molecular structure and localized interaction, this fidelity comes with a price. Namely, both the size and time scales of the model are limited by numerical and computational boundaries.The multi scale approach taken by the computational materials... 

In this study, a novel and unprecedented multi-scale hierarchical molecular dynamics (MD) – finite element (FE) coupling method is proposed to demonstrate the influence of temperature on mechanical properties of heterogeneous Nano-crystalline structures. The embedded-atom method (EAM) many-body interatomic potential is implemented to consider pairwise interactions between atoms in the metallic alloys with face-centered-cubic (FCC) lattice structure at different temperatures. In addition, the Nose-Hoover thermostat is employed to adjust the fluctuation of temperature. In order to calculate the equivalent lattice parameter, a weight average between the lattice parameters of atomic structures... 

In this study, a novel multi-scale hierarchical method has been employed to explore the role of edge dislocation on Nano-plates with hexagonal atomic structure in large deformation. multiscale hierarchical atomistic/molecular dynamics (MD) finite element (FE) coupling methods are proposed to demonstrate the impact of dislocation on mechanical properties of Magnesium in large deformation. The atomic nonlinear elastic parameters are attained via computing first-order derivation of stress with respect to strain of Representative Volume Element (RVE). To associate between atomistic and continuum level, the mechanical characteristics are captured in the atomistic scale and transferred to the... 

In this study, two multiscale hierarchical atomisyic/molecular dynamics (MD)–finite element (FE) coupling methods are proposed to illustrate the influence of temperature on mechanical properties of SLGS in large deformation. The Tersoff interatomic potential is implemented, in addition, the Nose-Hoover thermostat and local harmonic approximation are employed to adjust the fluctuation of temperature in CB and MD, respectively. The atomic nonlinear elastic parameters are obtained via computing second-order derivative of Representative atom’s energy and RVE’s strain energy density with respect to deformation criterions (deformation gradient and Green strain tensor). To bridge between atomistic... 

In this study, a new multi-scale hierarchical technique has been employed to investigate the role of edge dislocation on nano-plates with hex atomic structure in large deformation. Two multiscale hierarchical atomistic/molecular dynamics (MD)–finite element (FE) coupling methods are proposed to illustrate the influence of temperature on mechanical properties of Magnesium in large deformation. The atomic nonlinear elastic parameters are obtained via computing second-order derivative of Representative atom’s energy and RVE’s strain energy density with respect to deformation criterions (deformation gradient and Green strain tensor) to bridge between atomistic and continuum level, the... 

Carbon nanotubes are cylinders in Nano scale formed of carbon atoms with covalent bonds that contain a significant electrical and mechanical features. Carbon nanotubes are divided into two main types: multi-walled carbon nanotubes (MWCNTs) and single walled carbon nanotubes (SWCNTs). A SWCNT is a rolled graphene sheet (graphene is in fact a single sheet of graphite). SWCNTs has lately been considered as one of most interesting research cases. The reason why researchers have been fond of investigating about graphene has been its unconventional quantum hall effects, high room-temperature electrical conductivity and its mechanical stability despite of being composed of single layer atom... 

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 study, a new multi-scale hierarchical technique has been employed to investigate the role of temperature on nano-plates with hex atomic structure. Different number of primary edge dislocations is considered and the temperature varies from 0 up to 800 K. Primary edge dislocations are created by proper adjustment of atomic positions to resemble discrete dislocations (DD’s) and then the application of equations of motion to the relaxed configuration of this adjustment. The interatomic potential used for atomistic simulation is Finnis-Sinclair Embedded-Atom-Method (FS-EAM) as many-body interatomic potential and the Nose-Hoover thermostat has been implemented to adjust the modulation of... 

In this study, a novel multiscale hierarchical molecular dynamics (MD) – finite element (FE) coupling method is proposed to illustrate the influence of temperature on mechanical properties of heterogeneous nano-crystalline structures. The embedded-atom method (EAM) many-body interatomic potential is implemented to consider pairwise interactions between atoms in the metallic alloys with face-centered-cubic (FCC) lattice structure at different temperatures. In addition, the Nose-Hoover thermostat is employed to adjust the fluctuation of temperature. In order to calculate the equivalent lattice parameter, a weight average between the lattice parameters of atomic structures is utilized. The... 

Due to high cost and ineffectiveness of molecular models a new method for coupling continuum models with molecular models is used. In this method, the continuum and molecular domains are overlapped. Comparing the results obtained from the concurrent simulations and molecular dynamic simulations proves the accuracy of the method used. The method is used for modeling single layered graphene sheets, stress contours are presented for multiscale and both static and dynamic simulations of concurrent. For multiscale simulations two different carbon nano tubes are investigated and strees-bond angle and strees-bond length are also presented  

We carry out computer simulations in the hope of understanding the properties of assemblies of molecules in terms of their structure and the microscopic interactions between them. This serves as a complement to conventional experiments, enabling us to learn something new, something that cannot be found out in other ways. One of the main families of simulation technique are molecular dynamics (MD). Over the last decade , nanoscience and nanotechnology have emerged as two of the pillars of the research that will lead us to the next industrial revolution. The fundamental entities of interest to nanoscience and nanotechnology are the isolated individual nanostructures and their assemblies. Nano... 

In the present thesis, the movement of the clusters of fullerenes and nanocars are separately investigated on graphene surface, using molecular dynamics simulations. Investigating the fullerene clusters with different populations, it is concluded that, as the number of molecules inside the cluster increases, the displacement range of the motion decreases. In fact, some parts of the energy of the fullerene cluster are wasted through the intermolecular interactions, and as a result, the mobility of the cluster diminishes. During the investigation of the three-dimensional structures of fullerene, the wetting property of the clusters is revealed relative to the graphene surface. The decrease of...