Master Degree / Yüksek Lisans Tezleri

Permanent URI for this collectionhttps://hdl.handle.net/11147/3008

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Access type: Open accessSubject: search.filters.subject.Atomic force microscopy

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Now showing 1 - 8 of 8
  • Master Thesis
    Nonlinear Controller Design for High Speed Dynamic Atomic Force Microscope System
    (Izmir Institute of Technology, 2018) Coşar, Alper; Balantekin, Müjdat
    In this study, the performances of conventionally used PI controller and a nonlinear H∞ controller, are compared in the state-of-the-art High-Speed Dynamic Atomic Force Microscope (HS-AFM). The state-of-the-art HS-AFM system is modeled via MATLAB/ SIMULINK for four different cantilevers, i.e., small high-frequency and regular lowfrequency cantilevers used in air and liquid environments. For the modeled system, PI and H∞ controllers are designed and implemented by using both analytical methods and toolboxes available in MATLAB. Simulations are performed in ideal condition, and under exogenous effects such as noise, disturbance and parametric uncertainty. In ideal condition, achieved maximum frame rate, and the percentage of topography acquisition error with two controllers are calculated for each cantilever. Also, performances of controllers in the system are tested under exogenous effects. It is observed that with the H∞ controller, the topography of the selected sample can be obtained with up to 2 times less acquisition error. It is also observed that PI controller is better in disturbance rejection, but H∞ controller is more robust under the effect of noise. For each cantilever, similar results to the ideal condition is obtained in case of uncertainty. Most distinctive results are obtained with high-frequency cantilevers, as H∞ controller enables a 2 times higher frame rate (14.3 fps) compared to the PI controller (7.1 fps) with the same level of acquisition error in the state-of-the-art HS-AFM operated in liquid environment.
  • Master Thesis
    Analysis of Cantilevers for High-Speed Atomic Force Microscopy
    (Izmir Institute of Technology, 2018) Brar, Harpreet Singh; Balantekin, Müjdat
    In life sciences, High-Speed Atomic Force Microscopy (HS-AFM) is now widely accepted as a dynamic event visualizer for numerous biological samples such as live cells, membrane lipids, ATP-proteins, enzymatic reactions, DNA-protein interactions, etc. HSAFM’s unique ability to observe surface topography of the samples with height data and with a resolution of up-to a single atom makes it a prominent tool in Nano measurements. HS-AFM Imaging technique’s speed and response is limited by various factors including cantilever probes, operating environment, scanning techniques etc. Cantilevers are indispensable and integral part of HS-AFM Systems, thereby necessitating their own critical evaluations. Therefore, evaluation of various parameters like resonance frequency, stiffness and Q-factor of cantilevers is an active area of research. The simulated research work mimics the experimental conditions of HS-AFM operation in air and liquid environment. The damping mechanisms such as viscous and acoustic damping of the medium, squeeze film damping, and damping due to viscoelasticity of the material are included in the finite element simulations. High frequency soft cantilevers suitable for HS-AFM with the stiffness of ~1 N/m and with the first flexural eigenmode resonance frequency of ~1.5 MHz (in liquid) and ~5 MHz (in air) are studied. Numerous small rectangular and modified cantilevers of Silicon and Polymer (SU-8) materials with the length of ~5 to 10 μm, width of ~1 to 2.5 μm and thickness of ~0.1 to 0.6 μm are analyzed. Our aim in this research is to identify appropriate cantilever geometries and materials for HS-AFM applications.
  • Master Thesis
    Investigation Od the Surfaces of Dealkalized and Wethered Float Glass
    (Izmir Institute of Technology, 2016) Seziş, Ümmügülsüm; Şentürk, Ufuk; Zareie, Hadi M.
    In this study, the effects of surface dealkalization due to SO2 or SO3 gas treatment of commercial soda lime silica float glass on the weathering behavior was investigated. Only the air side of the glass was studied. The changes in the glass surface were analyzed for their topography and structure. The surface topography was studied using atomic force microscopy (AFM). The findings show the formation of micro-cracks on the surfaces of as-produced glass surfaces when treated with sulfur gas. The weathered surfaces show an increased roughness with increased weathering. The surface structure was investigated using attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy, specular reflectance infrared (SR-IR) spectroscopy, and micro-Raman spectroscopy techniques The results of the studies, ATR-FTIR and SR-IR techniques provided a reasonable insight on the surface structural changes while micro-Raman spectroscopy failed to detects these differences. ATR-FTIR and SR-IR the overall comparison of the effects of peak position with and without sulfur gas treatment suggests a wide scatter within each group. This scatter implies that sulfur gas treatment does not have any statistically significant effects. Also, the change in peak positions are no clear evidence of a decreasing or increasing peak position as the weathering period is increased by weathering effect. Additionally, the calculated penetration depth is found to be ~0,6-1 μm for these techniques. Namely, the penetration depth greater than the surface modification was observed. The results showed was not significantly affected by the surface dealkalization and weathering reactions. The analysis of the surface topography using AFM technique showed the formation of micro-cracks like features on the surfaces of sulfur treated glasses. These features are thought to occur under the sodium sulfate salt residue that is formed during the high temperature dealkalization reactions on the surface. Results sample preparation, i.e. cleaning, was found to have a significant effect on the surface properties. A method has been developed to minimize the effects of sample preparation on the surface of the glass.
  • Master Thesis
    Characterization of Changes Induced by Lineage Commitment and External Mechanical Stimuli on Cellular Ultrastructure of Adult Mesenchymal Stem Cells
    (Izmir Institute of Technology, 2014) Demiray, Levent; Özçivici, Engin
    Mechanical vibrations have great impact on the regulation of bone cells and their precursor’s Mesenchymal stem cells. Anabolic effects of high frequency low magnitude mechanical vibrations on these cells are well identified whereas sensing mechanism of cells and their early response to mechanical stimuli is largely unknown. Here, we hypothesed that daily bouts of low intensity vibrations will affect cellular ultrastructure and the effect will interact with the osteogenic induction. To test this hypothesis mouse bone marrow stem cell line D1 ORL UVA were subjected to mechanical vibrations (0.15g, 90 Hz, 15min/d) for 7 days to both during quiescence and osteogenic commitment. Ultrastructural changes were identified on cellular and molecular levels. To characterize alterations in cell surface, Atomic force microscopy is used. Mechanical vibrations increased cell surface height, cell surface roughness and nucleus height significantly during quiescence and under osteogenic conditions. Moreover, in order to identify the changes in cytoskeleton structure, actin were stained with phalloidin and imaged with inverted microscope. To quantify phalloidin signals pixel frequency analysis were performed, signal intensities and thickness of actin fibers were measured. It was observed that mechanical stimulation and osteogenic induction effects number of actin fibers and their thickness significantly. Molecular level analysis of cytoskeleton elements and osteogenic markers were performed with Real time RT-PCR. Significant increases in osteogenic markers were detected with osteogenic induction. Unlikely, no relation between mechanical stimulation and osteogenic marker expression was observed. These results indicate that mesenchymal stem cells responds to mechanical vibrations by altering their ultrastructure in particular cytoskeleton during both quiescence and osteoblastogenesis.
  • Master Thesis
    Electrical Surface Modification and Characterization of Metallic Thin Films Using Scanning Probe Microscope (spm) Nanolithography Method
    (Izmir Institute of Technology, 2009) Büyükköse, Serkan; Okur, Salih
    This thesis focuses on local oxidation of metallic thin films using atomic force microscopy (AFM). The primary aim of this thesis is to investigate the growth kinetics of oxide forms of these metallic materials and characterize the resulted oxide structures. In this study, tantalum, hafnium and zirconium thin films were used to be oxidized via AFM. During this work, metallic thin films were grown on Si and SiOx substrates with DC magnetron sputtering method. Thin films were characterized via x-ray diffraction, scanning electron microscopy and atomic force microscopy. Oxidation experiments were performed under different environmental conditions to explore the effect of influential parameters; such as bias voltage, oxidation time and relative humidity, and line shape oxide structures were created on metallic films. Dimensional analysis of created oxide structures was carried out measuring height and line-width of oxide lines as a function of applied voltage, oxidation time and relative humidity. In addition to the dimensional analysis, electrical characterization of metal-oxides was performed via AFM electrical characterization methods which are two terminal I-V measurements, electric force microscopy and spreading resistance measurements. At the end of the thesis, the capability of this method to create lateral metal-oxide-metal junction was shown oxidizing a tantalum stripe and performing in-situ resistance measurement. Patterning of tantalum stripes was accomplished by standard photolithography process and lift-off technique.
  • Master Thesis
    Design and Characterization of Shell Structure of Microbubbles Used in Ultrasound Imaging
    (Izmir Institute of Technology, 2012) Bölükçü, Elif Şeniz; Kılıç Özdemir, Sevgi
    The main goal of the study is to redesign the microbubble (MB) shell structure and investigate the interactions between the shell components in the mixed monolayers treated as a model for MBs’ shell in order to improve the stability. To examine effects of emulsifier type (DSPC/PEG40 St, DSPC/DSPE-PEGn) and additional components (DSPC/PEG40 St/DSPG, DSPC/PEG40 St/DSPA, DSPC/PEG40 St/DSPE) on stability, molecular interactions and morphological properties, mixtures having various compositions were investigated by Langmuir Blodgett (LB) method and Atomic Force Microscope (AFM) and Brewster Angle Microscope (BAM). For DSPC/PEG40 St monolayers thermodynamically analysis indicated that the attractive forces between the components in the monolayer of 30% PEG40 St were very strong. It was observed that addition of large amount of peg-grafted phospholipids (lipopolymer) increased the attractive forces between molecules in DSPC/DSPE-PEG1000 and DSPC/DSPE-PEG350 monolayers unlike DSPC/DSPE-PEG2000 monolayers. Additionally, the use of different phospholipid as an additional component such as DSPG, DSPE and DSPA in DSPC/PEG40 St mixture signified that intermolecular forces were influenced by the monolayers’ compositions and polar headgroups differences. It was noticed that among the ternary mixtures consisting 70% DSPC, DSPC/PEG40 St/DSPE monolayers exhibited stronger molecular interaction than DSPC/PEG40 St/DSPG and DSPC/PEG40 St/DSPA monolayers while DSPC/PEG40 St/DSPA mixtures showed stronger interaction for mixtures composed of 50% PEG40 St. However, phase separations detected at some regions for these monolayers by BAM and AFM may affect the stability negatively. Therefore, thermodynamically analysis, BAM and AFM results should be evaluated together to assess potential MBs’ shell structures.
  • Master Thesis
    Determining Charge Distribution of Metal Oxide Surfaces With Afm Using Colloid Probe Technique
    (Izmir Institute of Technology, 2012) Güler, Ayşe; Polat, Mehmet
    Colloidal systems of micron-sized particles dispersed in a solvent are widely encountered in numerous industries. Homogeneity, dispersibility, rheology and forming characteristics of these systems depend solely on particles-particle interactions which in turn are determined by Van der Waals (vdW) and Electrical Double Layer (EDL) forces. The vdW forces are not affected by system chemistry. However, the EDL forces, which arise from the charging of on solid surfaces in a solvent, vary significantly with solution chemistry. So, manipulation of electrical forces is used widely in industrial applications to manipulate colloidal systems. Colloidal particles in solution carry a distribution of positive, negative and neutral charges depending on solution chemistry. Electrophoretic potential mesurements or colloidal titration methods yield only an average charge for the whole population, not the charge distribution on each particle surface. The streaming potential techniques also provide an average charge on the surface. Currently, there is no accepted technique to determine the charge distribution on solid surfaces. This work aims at using Atomic Force Microscopy (AFM) as a charge probe to achieve exactly this. The work improves on a recent study (Yelken, 2010) which used commercial SiN4 cantilevers to determine the charge distribution on quartz and sapphire surfaces by replacing SiN4 cantilevers with custom-made colloid probes of desired material (quartz in this case) to probe the surface. The current work which improves the flexibility and resolution of the method was tested with two quartz and
  • Master Thesis
    Development of Nanopatterns on Self Assembled Monolayer (sam) Organic Films Using Scanning Probe Microscope (spm) Nanolithography Techique
    (Izmir Institute of Technology, 2006) Gül, Semra; Okur, Salih
    Patterning and fabrication of nanostructures on surfaces is a great demand for nanoscale electronic and mechanical devices. Current techniques such as electron beam lithography and photolithography provides limited resolution and they are not capable of reproducible in nanoscale. Among those, Scanning Probe Microscopy (SPM) lithography that uses a nanometer sharpened tip has demonstrated outstanding capabilities for nanometer level patterning on various surfaces. Moreover, SPM techniques offer creating nanopatterns of Self Assembled Monolayers (SAMs) with molecular precision and visualizing surfaces with the highest spatial resolution. In this work, nanoscratches on gold surfaces and oxidation patterns on titanium surface were successfully performed as example of SPM lithography. In the second stage, Octadecylamine-HCl, Octadecanetiol (ODT) and Decylmercaptan (DM) SAM organic films were fabricated on various substrates; i.e., mica, silica, titanium surface deposited on silicon, n and p type silicon, using self assembly film preparation techniques. The film thicknesses were measured with Atomic Force Microscope (AFM). Nanopatterns were fabricated on SAM films using AFM tip by exerting a local high pressure at the contact that causes the displacement of SAM molecules by a high shear force. It was observed that there was no formation of SAMs on n type Si and silica substrates whereas there were organic assemblies on the other substrates. Fabricated nanopatterns were examined and thickness measurement was done. Molecular lengths of the organics were evaluated by using of SPARTAM 02 LINUX-UNIX with the method of PM3 and the measured values were compared with the calculated ones and it was concluded that monolayers were formed on the surfaces.