Sharif Digital Repository

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 this project, the equilibrium structure of clamped-free silicon nano-beams is investigated using molecular dynamics (MD) simulations. Four main interatomic potentials for silicon nanostructures, i.e. Tersoff, MEAM, Stillinger-Weber and EDIP, are implemented in the current study. Using aforementioned potentials, the structural stability of Si nano-beams are studied and effects of thickness, width, length, size, lattice direction, facets of cross section, and temperature on the equilibrium structure of nano-beams are investigated. The conducted simulations demonstrate that equilibrium structure of nano-beam is completely dependent on the type of atomic potential used for modeling.... 

In this study, chapter 1 is dedicated to GEO satellites. In chapter 2, slosh dynamics of fluid and its governing dynamical equations are investigated due to the importance of this phenomena in geostationary transfer orbit. In chapter 3, dynamics of satellite orbit and satellite attitude are investigated and governing equations are derived by considering these effects: orbital noise (e.g. shape of earth, gravitation of sun and moon), moment noise (e.g. slosh dynamics of fuel and oxidizer, and liquid apogee motor misalignment). Following the third chapter, some simulations are carried out before the implementation of controllers. In chapter 4, a PID controller and a classical fuzzy controller... 

In this project the main aim is to model the interaction between the cytoskeleton and cell membrane. In order to model the membrane and cytoskeleton it is used a discrete model, which contains several beads. For modeling the interaction between the beads it is used different kinds of energies. It is used four potentials in a 2D model for modeling the interaction between the membrane beads and it is used SSLJ potential in order to model the interaction between the cytoskeleton and cell membrane. Furthermore, this potential is used to model the interaction between the cytoskeleton filaments. Due to this potential, the cytoskeleton filaments can cross each other in the 2D model. For modeling... 

Atomic force microscopy (AFM), as an indispensable tool for nanoscale characterization, has major drawback for operation in a liquid environment arising from the large hydrodynamic drag on the vibrating cantilever. The newly introduced “Trolling Mode” (TR-Mode) AFM resolves this complication utilizing a specialized nanoneedle cantilever that keeps the cantilever outside of the liquid. Herein, a mechanical model with a lumped mass was developed to capture the dynamics of such cantilever with a nanoneedle tip. This new developed model was applied to investigate the effects of the needle – liquid interface on the performance of the AFM, including the imaging capability in liquid. Also... 

Trolling mode atomic force microscope (TR-AFM) significantly reduces the hydrodynamic drag generated during operation in liquid environments. This is achieved by utilizing a long nanoneedle and keeping the cantilever out of liquid. In this research, a continuous mathematical model is developed to study TR-AFM dynamics near a sample submerged in the liquid. Effects of cantilever torsion, nanoneedle flexibility, and liquid-nanoneedle interactions are considered in the model. The finite element model of the TR-AFM resonator considering the effects of fluid and nanoneedle flexibility is presented in this research, for the first time. The model is verified by ABAQUS software. The effect of... 

With the rapid progress of technology, the fabrication of smaller electronic and mechanical systems becomes more necessary. To make a small-scale system with better performance, one way is to create it from molecular components. In recent decade, many attempts have been devoted to the fabrication of molecular machines for manipulation of particles at nanoscales. In this project, the motion of two of most basic nanocars namely the Nanocar and the Nanotruck were simulated on gold and silver substrate at different conditions, both of four wheels and the nanotruck chassis is flexible. In the first chapter of this report, some of the most important natural and artificial machines are mentioned... 

Submerging of the Micro-beam of the AFM is indispensible in case of imaging bio-samples. (Bio-samples are unstable in non-aquos environment.), so hydrodynamical interaction of liquid and beam (viscous and meniscus forces) will result into quality factor decrease. This will cause image resolution decrement as well as damage to the sample because of large tip-sample forces during imaging of the bio-samples. The proposed method “Trolling mode AFM” keeps the micro-beam of the AFM out of the liquid, by adding a nano-needle to the end of the AFM tip. This would lead to resolve the aforementioned problems. Modeling of a part of the operation of this mechanism was done in this thesis, in order to... 

In this research, we aim to study and simulate how nanoparticels translocate through cell membrane. For this purpose, at first a gold nanoparticle is selected as the drug carrier. The partial charges of the ligands are calculated using quantum mechanics based on HF technique with 6-31Gd basis set. To have a realistic shape for nano drug, number and arrangement of ligands are determined based on optimization. After all atom simulations and comparison of results such as diffusion coefficient with experiments, a coarse-grained model of these drugs is created and put inside solvent beside a membrane. The cytoplasmic membrane includes more than 60 types of phospholipids like animal membranes.... 

Nowadays, nano-positioners play an important role in advanced technologies, such as atomic force microscopy, genetic manipulation, nano-metrology, nano-fabrication, semi-conductors and etc.In this paper, a dynamical model has been derived for a nano-positioner. This nanopositioner was designed and fabricated in Sharif university of technology. In this paper the mentioned mechanism has been considered as a planar mechanism. First, a finite element model has been developed in Comsol multi-physics software. This model was used as the reference model in the next steps. Afterward, a 10 degrees of freedom model was proposed to estimate the Comsol model. The mass, stiffness, as well as damping... 

One of the most significant aerial vehicles which has been subject of study of so many engineers and students is quadrotor or quadcopter, which is a cross sectional configuration of motors and propellers. This aerial robot is controlled through slight differences between the angular velocities of the four motors, and robot dynamics is completely nonlinear, thus sophisticated control algorithms are needed. The aim of this project consists of design, fabrication and control of a quadrotor capable of stable hovering. First, some preliminary decisions about general charachteristics of the robot were made. According to these decisions, other mechanical parts were designed and fabricated. Then,... 

Micro-robotics is one of the currently emerging technologies which has attracted attentions for its probable applications in different fields including biotechnology, diagnosis and treatment in medical engineering as well as general studies in micro-scale science and engineering. Magnetic micro-robotics is considered as the most promising group, primarily due to the biocompatibility of magnetic fields and advances in electronic circuits to produce and control such fields. One critical point in utilizing these robots is their high density in comparison with the working fluid and their tendency to sink. In this thesis, a method to fabricate buoyant magnetic robots has been proposed based on... 

Providing energy for small but out-of-access devices has led industries to harvest energy from the environment, especially environmental vibrations. The problem of vibrational energy harvesters with linear behavior, is their small bandwidth and consequently, their high sensitivity to frequency content and excitation spectra. Particularly in random excitations with vibrational energy spreading over a frequency range, linear harvesters do not seem appropriate. Under these conditions, harvesters with nonlinear stiffness are possible substitutes for linear systems. However, prediction and estimation of the behavior of systems with nonlinear stiffness under random excitation has been complicated,... 

With the continued improvement of sequencing technologies, the prospect of genome-based medicine is now at the forefront of scientific research. To realize this potential, however, a revolutionary sequencing method is needed for the cost-effective and rapid interrogation of individual genomes. Generally there are key factors in the definition and evalution of sequencing methods: 1-read length, 2-throughput, 3-read accuracy, 4-read depth, and 5-cost per base. The purpose of developing new sequencing methods is making better at least one of these factors. In order to reach the goal of rapid and low-cost sequencing method, one cannot rely only on current techniques. Improvements of current... 

Imaging using ultrasonic waves is one of the common non-invasive diagnostic methods which have gained a lot of attention in recent years. The imaging resolution depends mainly on the center frequency of the ultrasonic transducer. High frequency ultrasonic imaging is mainly used in intravascular, skin and eye diseases and also in small animal studies. The main Goal of this thesis is to design two high frequency ultrasound imaging probes (between 10 to 50 MHz) which millimetric dimensions which can be used to image skin, eye or intravascular systems. In this thesis after discussing the science of high frequency ultrasound and reviewing the importance papers and books on the subject, two... 

Nanopositioning is technology of positioning & manipulation of Nano-scale object. This technology can be considered as one of the fundamental necessities in Nano & Micro research and fabrication and made lots of unbelievable advancement in researches and technologies. There are lots of mechanical systems designed for large scale positioning with sub millimeter resolution, but when it’s come to Nano scale, the range of access should be limited to some micrometer. Also in Nano-scale motion some difficulties like backlash, stick-slip and friction is phenomenon. For increasing the workspace using coarse and fine positioning systems may be an appropriate method. In this method a fine positioning... 

Endoscopy is a medical operation in which a camera is sent into the patient's body and the physician starts taking pictures at specified times. In the traditional endoscopic procedure, a camera is sent into the body by a guiding wire. This can cause severe pain to the patient. In the newer method, a camera is mounted on a small capsule and the patient swallows the capsule. Then the camera inside the capsule starts taking photos and sends them out. This procedure, in addition to being painless, allows the physician to access the innermost parts of the body or the digestive tract.In capsule endoscopy, unlike the older method, one has to find the position and orientation of the capsule at any... 

Humans can take lots of advantages from influencing on small particles. Since manipulation of micro sizes by humans or macro robots, due to their precession and size, is not possible, a new field of study, called Microrobotics, has been introduced. To better understand the working principles in small dimensions, we first need to know the governing physics laws. This step helps us to identify the dominant forces in the small dimensions, which, in turn, leads to better actuation of miniature robots. Because of the size of the miniature robots, one of the best actuation methods is the interaction of the magnetic field on magnetic dipoles. To use the magnetic field as an actuation force, the... 

In this study, the attitude control of an under-actuated satellite has been investigated. The investigated satellite uses reaction wheels for attitude control. For having full controllability of a satellite attitude, at least three reaction wheels are required. However, due to the high failure rate of reaction wheels, in this study assumed the satellite has two perpendicular reaction wheels, which causes the satellite to be under-actuated. The path planning method is used for controlling the satellite, which is an offline method. In the beginning, tries to define the control input of the satellite in term of limited parameters with different methods. In this regard, the control input is... 

Modeling and Controlling of a satellites fuel slosh is considered a vital problem in the field of satellite attitude control. In this paper modeling and control of the attitude of a satellite carrying a partially filled spherical fuel tank, which uses the diaphragm as a propellant management device (PMD), has been studied. The fuel slosh dynamics is modeled using a spherical pendulum with two degrees of freedom and a rigid arm, which represents the first mode of sloshing. The effects of the diaphragm that surround the fuel surface, are considered as torsional springs and dampers attached to the satellite body. The combined dynamics equations of the satellite rigid motion and the fuel slosh...