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    Simulation of Imaging in Trolling Mode Atomic Force Microscopy by Molecular Dynamics Method

    , M.Sc. Thesis Sharif University of Technology Abdi Nemat Abad, Ahmad (Author) ; Nejat Pishkenari, Hossein (Supervisor)
    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... 

    Dynamic Modeling and Control of Atomic Force Microscope in Trolling Mode

    , Ph.D. Dissertation Sharif University of Technology Sajadi, Mohammad Reza (Author) ; Vosoughi, Gholamreza (Supervisor) ; Nejat Pishkenari, Hossein (Supervisor)
    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... 

    Determination of the Surface Properties and Topography in AFM Using System Dynamics

    , M.Sc. Thesis Sharif University of Technology Seifnejad Haghighi, Milad (Author) ; Nejat, Hossein (Supervisor)
    Nowadays, the atomic force microscopy (AFM) has become a useful laboratory tool with variety of applications. In the traditional imaging technique, usually the amplitude or frequency of AFM tip oscillations is set at a desired value using a feedback control system which is a relatively slow process. In the current research, we propose an estimation approach which uses an adaptive fading extended Kalman filter (augmented with forgetting factor) as a system observer and couples with the system dynamics to determine the sample topography. As a result, in addition to state variables of system dynamic, the sample height as an unknown parameter is estimated with high accuracy in a relatively short... 

    Modeling of Force Interactions between Tip of Atomic Force Microscopy in Trolling Mode and Environment

    , M.Sc. Thesis Sharif University of Technology Falsafi, Ali (Author) ; Nejat Pishkenari, Hossein (Supervisor)
    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... 

    Dynamic and Vibration Analysis of Non-Rotating and Rotating FGM Cantilever Beams Under Moving Mass

    , M.Sc. Thesis Sharif University of Technology Rahaeifard, Masoud (Author) ; Ahmadian, Mohammad Taghi (Supervisor) ; Hoviattalab, Maryam (Supervisor)
    The purpose of this work, is to design a cantilever arm made of functionally graded materials so that the arm has maximum natural frequency and minimum mass. In this work the arm is modeled by Euler-Bernoulli beam theory and properties are assumed to be varying through the thickness. The beam is considered to be made of Aluminum and Alumina as metal and ceramic respectively and Genetic Algorithm method is used for optimization step. Finally using FGMs in atomic force microscopes is proposed as a new application of these materials  

    Nonlinear Distributed-Parameters Vibration Analysis of an AFM Microcantilever Beam in Dynamic Mode

    , Ph.D. Dissertation Sharif University of Technology Delnavaz, Aidin (Author) ; Zohoor, Hassan (Supervisor)
    Dynamic and vibration behavior of AFM microcantilever beam subject to the tip-sample interaction and/or contact is systematically investigated. An Euler-Bernoli microcantilever in 2D plane is considered with longitudinal and bending displacements. Inextensibility assumption and extended Hamilton’s principle is utilized to extract the single-variable integro partial equation of motion under: 1) tip-nanoparticle interactions, 2) tip-surface interactions in non-contact mode and 3) tip-surface interactions and contacts in intermittent-contact mode. Galerkin’s first mode approximation is then used to discretize the derived equations; and multiple time scales method is adopted to analyze the... 

    Investigation of Mechanical Properties of Graphene

    , Ph.D. Dissertation Sharif University of Technology Rasuli, Reza (Author) ; Iraji Zad, Azam (Supervisor) ; Rafii-tabar, Hashem (Supervisor)
    The unique properties of graphene due to the presence of massless Dirac fermions, high surface to volume ratio, high crystal quality in 2D, and high mechanical strength, recommend it as a promising material for technologies such as nanoelectromechanical systems (NEMS) and nanosensors. Use of graphene in nanodevices is accompanied by induced strains and stresses. Therefore it is important to study the mechanical properties of graphene. In present thesis, we synthesized graphene using both mechanical cleavage of graphite and chemical method. In the chemical method graphene oxide is prepared by oxidation and exfoliation of graphite. The graphene oxide sheets were reduced to prepare graphene... 

    An Investigation on the Resonant, Frequency and Nonlinear Behavior of Atomic Force Microscope (AFM) Modeled on the Basis of the Nonlocal Theory

    , M.Sc. Thesis Sharif University of Technology khosravani, Ehsan (Author) ; Ahmadian, Mohammad Taghi (Supervisor) ; Mehdigholi, Hamid (Supervisor)
    Atomic force microscope (AFM) has a significant capability of imaging surface topography on an atomic scale. It is also widely used for Nanolithography in MEMS/NEMS (micro/nanoelectromechanical systems). Although the conventional AFMs have a significant capability of nano-scale surface measurements, their probe tips cannot come in close proximity to the sidewalls, no matter how sharp they are. Therefore, no accurate nano-scale measurements at sidewalls and edges can be achieved by these conventional AFMs. In addition, regarding the increasing applications of micro-structures such as micro nozzles, micro gears, micro holes and micro trenches which all of them have sidewalls and edges,... 

    The Analysis of Cracked Atomic Force Microscope Micro-Cantilever by Strain Gradient Theory

    , M.Sc. Thesis Sharif University of Technology Ganji, Hamid (Author) ; Asghari, Mohsen (Supervisor)
    The present study deals with the analysis of Atomic Microscope with crack by making use of Strain Gradient Elasticity theory. Empirical observations represent that in micro dimensions, materials show behaviors, which the classic continuum mechanics theories are not able to explain. Thus, taking advantage of non-classic theories, which are capable of explaining such phenomena or behaviors in analyzing materials in micro dimensions seems necessary and of much significance. In this direction, by applying an Euler-Bernoulli beam assumption and neglecting the shear effects, governing equations and boundary conditions of the problem were obtained via taking advantage of variations in Hamilton... 

    Simulation of the Biomolecule Imaging and Manipulation Via AFM by Molecular Dynamics Method

    , M.Sc. Thesis Sharif University of Technology Kheiroddin, Mohsen (Author) ; Meghdari, Ali (Supervisor) ; Moosavi, Ali (Supervisor)
    In this thesis we try to find optimized parameters for imaging and manipulation of a biosample with AFM. For this we have prepared a numerous Molecular Dynamics simulation and find some reliable result. So, first we have focused on imaging process in Non contact mode (the less harmful mode). Then we headed into the manipulation process. The main problem about manipulating a biosample is the environment. In imaging section, the process of imaging a biomolecule by AFM is modeled using molecular dynamics simulations. Since the large normal force exerted by the tip on the biosample in contact and tapping modes may damage the sample structure and produce irreversible deformation, the non-contact... 

    Developing a Molecular Dynamics Simulation Software for Modeling of Nano-Contact Processes (CEDRA Molecular Dynamics Software )

    , M.Sc. Thesis Sharif University of Technology Taheri, Alireza (Author) ; Meghdari, Ali (Supervisor) ; Mahboobi, Hanif (Supervisor)
    Molecular Dynamics as a powerful method in the field of Nano-simulation has been widely used in recent years. Different contact processes such as Nano-manipulation, AFM Imaging, and Nano-indentation can be simulated using this method. There have been numerous researches done on calculating techniques of simulation of different phenomena in Nano-technology. Specifically, friction and Nano-indentation which are parts of Nano-contact processes have been simulated by different investigators. However, on some other parts, e.g. Nano-manipulation and AFM Imaging, there are few studies done up to now. Thus, a simulation and computational software seems necessary in this field. The main goal of... 

    Modeling and Simulation of High-Speed Atomic Force Microscope

    , M.Sc. Thesis Sharif University of Technology Bahrami, Mohammadreza (Author) ; Ramezani, Asghar (Supervisor) ; Ghaemi Osgoui, Kambiz (Co-Advisor)
    This thesis is aimed at the modeling and control of atomic force microscope (AFM) in order to improve the scanning speed and achieving video-rate imaging to realize the real-time observation of dynamic phenomena at the nanoscale. The lumped parameter model of the AFM in the non-contact operation mode is studied in this project. The tip-sample interaction is the Van der Waals force, which makes the model nonlinear. Two mathematical models of the AFM cantilever are derived and investigated in order to gain detailed insights into the system dynamics. These models are tip excited and base excited cantilever. The former is solved by the method of multiple scales and the latter is analyzed by the... 

    Characterization of polymeric membranes for membrane distillation using atomic force microscopy

    , Article Desalination and Water Treatment ; Volume 51, Issue 31-33 , 2013 , Pages 6003-6008 ; 19443994 (ISSN) Shirazi, M. M ; Bastani, D ; Kargari, A ; Tabatabaei, M ; Sharif University of Technology
    Taylor and Francis Inc  2013
    As membrane distillation (MD) is an under-developed separation process, specific membranes for MD applications are not yet commercially available. Therefore, microporous polymeric membranes made of hydrophobic materials fabricated for microfiltration purposes are usually used for MD applications. Characterization of such kind of membranes is important in order to achieve a better in-depth understanding of their performance and to fabricate specific membranes for MD process. One of the emerging characterization methods is atomic force microscopy (AFM) analysis. AFM is a newly developed high-resolution method that is useful for studying the surface topography of various types of membranes, and... 

    Dynamic & Vibration Analysis of AFM Probe Affected by the Non Uniform Potential Field

    , M.Sc. Thesis Sharif University of Technology Kahrobaiyan, Mohammad Hossein (Author) ; Ahmadian, Mohammad Taghi (Supervisor)
    Atomic force microscope (AFM) has a significant capability of imaging surface topography on an atomic scale. It is also widely used for Nanolithography in MEMS/NEMS (micro/nanoelectromechanical systems). Conventional AFMs consist of a cantilever with a sharp conical or pyramidal tip located at the free end of the cantilever that plays an important role in AFM measurements. Scanning across a surface, AFM interacts with the sample surface through its tip. Although the dynamic behavior of the AFM cantilever is complicated, the researchers have been interested in studying AFM dynamic behavior because it has a great influence on the surface imaging process. The imaging rate and contrast of... 

    Using Surface Properties of Immiscible Fluids in Capillary Tubes for Identification and Separation of Cancerous Blood Cells

    , M.Sc. Thesis Sharif University of Technology Alinejad, Amin (Author) ; Ayatollahi, Shahabodin (Supervisor) ; Vossoughi, Manochehr (Supervisor)
    Cancer has been known as one of the main reasons for disease-related deaths in the last decades. Early diagnosis could significantly reduce the level of fatality chances. Among the known cancer types, lung cancer is one of the most malignant ones. The common diagnosticmethods are expensive and using high-technology methods; therefore, the introduction of simple and cheap methods is very urgent to detect it. In this project, surface and interfacial tension measurement of cancerous and normal lung cells have been investigated as an easy detection technique. Among the common measurement methods, Pendant Drop and Capillary height techniques have been utilized in this research work. The obtained... 

    Feasibility Study of Deposition by SUT-PF

    , M.Sc. Thesis Sharif University of Technology Safarzadehamiri, Ali (Author) ; Vosoughi, Naser (Supervisor)
    Sharif University of Technology Plasma Focus (SUT-PF) is a Mather Type DPF device which has a 39 μF capacitor bank with 14 KV charging ability at its ultimate limit corresponding to 7 KJ stored energy. In the first step of this experiment, a test has been done at three distances 5, 7, 10 cm from anode tip with the different number of shots 20, 30, and 40 at 0 constant angles.In the following, a test is done at 5 and 10 degrees with 40 shots, and PF chamber has been filled up with nitrogen gas. Various tests have carried out for survey of this experiment, the result of which are as follow:The X-ray diffraction (XRD) analysis are used in order to reveal if the Nickel or Nickel nitride have... 

    Simulation of a Simple Model of Endothelial Cell Using Dissipative Particle Dynamics Method

    , M.Sc. Thesis Sharif University of Technology Kiyoumarsi Oskouei, Amir (Author) ; Saeedi, Mohammad Saeed (Supervisor) ; Firoozabadi, Bahar (Co-Advisor)
    Endothelium is the interior layer of an artery made up of tremendous number of endothelial cells which are located side by side. Finding the effective parameters that cause the cells to obtain mechanical strength in different morphologies is a major effort in cell engineering studies. In this work a numerical model for endothelial cells is developed. This model has included cell's plasma membrane (the outer membrane of the cell), nucleus and cytoskeleton main components including intermediate and actin filaments as well as microtubules. The model has been validated by simulating the adhesion of the cells to a flat substrate and also atomic force microscopy (AFM) experiments. The two most... 

    Design and Fabrication of Tip for a Nanolithography System

    , M.Sc. Thesis Sharif University of Technology Tayefeh Younesi, Ali (Author) ; Rashidian, Bijan (Supervisor)
    Various applications of nanostructures in electronics, optoelectronics, MEMS, photonics and plasmonic make their fabrication an interesting research topic recently. Progress in nanotechnology depends on the capability to fabricate, position and interconnect nanometer-scale structures. The development of fabrication devices with nanoscales is mainly dependent on the existence of a suitable nanolithography approach. Patterning materials with nanoscale features aimed at improving integration and device performance faced several challenges. The limitation of conventional lithography systems including resolution related issues, operational costs and lack of flexibility to pattern organic and... 

    Manipulation of biomolecules: A molecular dynamics study

    , Article Current Applied Physics ; Volume 14, Issue 9 , September , 2014 , Pages 1216-1227 ; ISSN: 15671739 Mahdjour Firouzi, M. A ; Nejat Pishkenari, H ; Mahboobi, S. H ; Meghdari, A ; Sharif University of Technology
    With the rapid progression of bionanorobotics, manipulation of nano-scale biosamples is becoming increasingly attractive for different biological purposes. Nevertheless, the interaction between a robotic probe and a biological sample is poorly understood and the conditions for appropriate handling is not well-known. Here, we use the molecular dynamics (MD) simulation method to investigate the manipulation process when a nanoprobe tries to move a biosample on a substrate. For this purpose, we have used Ubiquitin (UBQ) as the biomolecule, a single-walled carbon nanotube (SWCNT) as the manipulation probe, and a double-layered graphene sheets as the substrate. A series of simulations were... 

    Modeling and Control of Atomic Force Microscope Based Nanoparticle Manipulation

    , M.Sc. Thesis Sharif University of Technology Babahosseini, Hesam (Author) ; Meghdari, Ali (Supervisor)
    In the recent years, there has been great interest in exploring methods for assembly and manipulation at the micro/nanoscale to build miniaturized systems, devices, structures, and machines. This thesis aims at two-dimensional manipulation of nanoparticle using Atomic Force Microscope (AFM) probe. The nanoprobe is used to push the spherical micro/nanoparticle. Continuum based modeling and simulation of the manipulation task is presented. The proposed nanomanipulation model consists of all effective phenomena in nanoscale. Nanoscale interaction forces, elastic deformation in contact areas, and friction forces in tip/nanoparticle/substrate system are considered. The utilized friction models...