Sharif Digital Repository

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... 

One of the most promising strategies for fighting cancer is the drug delivery process using synthetic nanoparticles. Once in biological milieu, the nanoparticle surfaces get covered with a layer of biomolecules called the “Protein Corona”. The protein corona formation changes the nanoparticles interaction with the human body dictating a new fate for them. The protein corona composition is not only dependent on the nanoparticle itself, but also it is affected by the health condition of patients as recently discovered through the experimental studies. Here, the effect of disease on the protein corona formation is discussed through the molecular dynamics simulations. A multiscale simulation... 

Due to the limitations on experiments in the field of cell mechanics, computational modeling of biological cells have attracted attention within two recent decades. In general, some models have been developed in two different scales, known as microstructure and continuum, both of which have their own pros and cons. Nevertheless, viscoelastic behavior of cell membrane has attracted less attention of scientists up to now. Therefore, multi-scale simulation of the viscoelastic behavior of the cell membrane has been chosen as the main goal of this thesis. Toward this goal, at first the energy of the simulation box, consisting of 128 Dipalmitoylphosphatidylcholine and 3655 water molecules, was... 

Advanced reservoir characterization methods can yield geological models at a very fine resolution, containing 1011-1018 cells while the common reservoir simulators can handle much fewer numbers of cells due to computer hardware limitations. The process of coarsening the fine-scale model to simulation models is known as upscaling. There are three fundamental steps in the procedure of upscaling, i.e. defining the coarse grid geometry, calculating the average properties for the generated coarse grid and simulation of the two-phase flow equations on the generated coarse-scale model. In this thesis, the focus will be on investigating the applicability of optimization in the context of coarse grid... 

In this study, a modern multiscale sequential molecular dynamics (MD) – finite element (FE) coupling method is proposed to represent the role of grain boundary (GB) planar defect on mechanical properties of crystalline structures at various temperatures. Different Grain Boundary misorientation angle is considered and the temperature varies from 0 up to 800 K. The embedded-atom method (EAM) many-body interatomic potential is implemented to consider pairwise interactions between atoms in the crystalline structures with face-centered-cubic (FCC) lattice structure at different temperatures. In addition, the Nose-Hoover thermostat is employed to adjust the fluctuation of temperature. The atomic... 

Atherosclerosis in coronary arteries is one of the most important topics due to its high prevalence and the importance of these arteries for supplying blood to the heart. The morphology of endothelial cells (ECs) is an independent index for determining the atheroprone sites. The ECs show a regular elongated and aligned configuration to the blood flow, at the atheroprotected regions; on the other hand, at the atheroprone regions, the cells have a polygonal, randomly oriented morphology. The thesis intended to propose a method for coronary artery simulation, which is able to determine the atheroprone sites regarding the ECs morphology. In addition, the attempts were made to investigate the... 

Integrated modeling of learning makes happen simultaneous investigation and analysis of the interaction among different scales, abstraction levels and contexts within an organization. Enquiry of the organization, organizational unit and individual employee scales at levels of low and high abstraction within temporal, spatial and event-driven contexts may have conspicuous impact on perspicuousness of learning concept, as well as the creation of productive policy making opportunities which improves system performance measurements and their influencing causes. By development in multi-method approach to system modeling, integrated representation of learning has got recently feasible. Thus, a... 

The primary purpose of this study is to perform nonlinear behavior simulations in the compaction and forming of metal powders and their alloys and investigate their behavior in the plastic state. Powder compression is one of the methods of producing metal parts with high precision and improved mechanical properties, which is why it has been considered in addition to its need in the industry.There are various methods for performing these simulations, including multi-scale methods with optimal performance. Given that only the use of high-scale methods or only low-scale methods will have problems and disadvantages in such simulations, multi-scale methods will be a good alternative in which both... 

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... 

The present research focuses on the simulation of the metallic powder compaction process with the Peridynamics theory. Various methods are exploited to simulate this process in literature. Studying the nonlinear behavior of powders includes different phenomena such as dislocation and grain boundary, making it complicated. However, numerous research has been shaped to consider these phenomena on the micro-scale. There is also another batch of nano-scale studies underway. In this class of simulations, considering atoms as rigid particles, interatomic potentials, and molecular dynamics methods are used. Because of atomic-scale precision, this approach has very high accuracy. The massive...