Browsing by Subject "Atomic force microscopy"
Now showing 1 - 20 of 67
Results Per Page
Sort Options
Item Open Access Analysis of amplitude modulation atomic force microscopy in aqueous salt solutions(Elsevier, 2014-11-01) Karayaylali, P.; Baykara, M. Z.We present a numerical analysis of amplitude modulation atomic force microscopy in aqueous salt solutions, by considering the interaction of the microscope tip with a model sample surface consisting of a hard substrate and soft biological material through Hertz and electrostatic double layer forces. Despite the significant improvements reported in the literature concerning contact-mode atomic force microscopy measurements of biological material due to electrostatic interactions in aqueous solutions, our results reveal that only modest gains of similar to 15% in imaging contrast at high amplitude setpoints are expected under typical experimental conditions for amplitude modulation atomic force microscopy, together with relatively unaffected sample indentation and maximum tip-sample interaction values.Item Open Access Artifacts related to tip asymmetry in high-resolution atomic force microscopy and scanning tunneling microscopy measurements of graphitic surfaces(American Institute of Physics Inc., 2015) Uluutku, B.; Baykara, M. Z.The effect of tip asymmetry on atomic-resolution scanning tunneling microscopy and atomic force microscopy measurements of graphitic surfaces has been investigated via numerical simulations. Employing a three-dimensional, crystalline, metallic tip apex and a two-layer thick graphene sample as a model system, basic calculations of the tip-sample interaction have revealed a significant effect of tip asymmetry on obtained results, including artificial modulation of site-specific chemical interaction forces and spatial distortion of observed features. Related artifacts are shown to be enhanced for tips with low lateral stiffness values. Our results emphasize that potentially erroneous interpretations of atomic-scale surface properties via imaging and spectroscopy measurements can be caused or enhanced by tip asymmetry.Item Open Access Atomic force microscopy for the investigation of molecular and cellular behavior(Elsevier, 2016-10) Ozkan A.D.; Topal, A. E.; Dana, A.; Güler, Mustafa O.; Tekinay, A. B.The present review details the methods used for the measurement of cells and their exudates using atomic force microscopy (AFM) and outlines the general conclusions drawn by the mechanical characterization of biological materials through this method. AFM is a material characterization technique that can be operated in liquid conditions, allowing its use for the investigation of the mechanical properties of biological materials in their native environments. AFM has been used for the mechanical investigation of proteins, nucleic acids, biofilms, secretions, membrane bilayers, tissues and bacterial or eukaryotic cells; however, comparison between studies is difficult due to variances between tip sizes and morphologies, sample fixation and immobilization strategies, conditions of measurement and the mechanical parameters used for the quantification of biomaterial response. Although standard protocols for the AFM investigation of biological materials are limited and minor differences in measurement conditions may create large discrepancies, the method is nonetheless highly effective for comparatively evaluating the mechanical integrity of biomaterials and can be used for the real-time acquisition of elasticity data following the introduction of a chemical or mechanical stimulus. While it is currently of limited diagnostic value, the technique is also useful for basic research in cancer biology and the characterization of disease progression and wound healing processes.Item Open Access Atomic force microscopy: Methods and applications(Elsevier, 2017) Baykara, Mehmet Z.; Schwarz, U. D.; Lindon, J.; Tranter, G. E.; Koppenaal, D.This chapter provides an overview of atomic force microscopy, covering the fundamental aspects of the associated instrumentation and methodology as well as representative results from the literature highlighting a variety of application areas. In particular, atomic-resolution imaging and spectroscopy capabilities are emphasized, in addition to applications in biology, nanotribology and catalysis research. Finally, an outlook on emerging aspects and future prospects of atomic force microscopy is provided.Item Open Access Characterization of AlInN/AlN/GaN heterostructures with different AlN buffer thickness(Springer New York LLC, 2016) Çörekçi, S.; Dugan, S.; Öztürk, M. K.; Çetin, S. Ş.; Çakmak, M.; Özçelik, S.; Özbay, EkmelTwo AlInN/AlN/GaN heterostructures with 280-nm- and 400-nm-thick AlN buffer grown on sapphire substrates by metal-organic chemical vapor deposition (MOCVD) have been investigated by x-ray diffraction (XRD), atomic force microscopy (AFM), photoluminescence (PL) and Hall-effect measurements. The symmetric (0002) plane with respect to the asymmetric (101 ¯ 2) plane in the 280-nm-thick AlN buffer has a higher crystal quality, as opposed to the 400-nm-thick buffer. The thinner buffer improves the crystallinity of both (0002) and (101 ¯ 2) planes in the GaN layers, it also provides a sizeable reduction in dislocation density of GaN. Furthermore, the lower buffer thickness leads to a good quality surface with an rms roughness of 0.30 nm and a dark spot density of 4.0 × 108 cm−2. The optical and transport properties of the AlInN/AlN/GaN structure with the relatively thin buffer are compatible with the enhancement in its structural quality, as verified by XRD and AFM results.Item Open Access Characterization of self-assembly and self-healing of peptide amphiphiles by atomic force microscopy(Bilkent University, 2017-10) Dikeçoğlu, Fatma BegümBiological feedback mechanisms exert precise control over the initiation and termination of molecular self-assembly in response to environmental stimuli, while minimizing the formation and propagation of defects through self-repair processes. Peptide amphiphile (PA) molecules can self-assemble at physiological conditions to form supramolecular nanostructures that structurally and functionally resemble the nanofibrous proteins of the extracellular matrix (ECM), and their ability to reconfigure themselves in response to external stimuli is crucial for the design of intelligent systems. In this thesis, we investigated the real-time self-assembly, deformation, and self-healing of ECM-mimetic PA nanofibers in aqueous solution by using a force-stabilizing double-pass scanning AFM imaging method to disrupt the self-assembled peptide nanofibers in a force-dependent manner. We showed that nanofiber damage occurs at tip forces exceeding 1 nN, and that the damaged fibers subsequently recover under sub-nN tip forces. Fiber ends occasionally failed to reconnect following breakage and continue to grow as two individual nanofibers. Energy minimization calculations of nanofibers with increasing cross-sectional ellipticity (corresponding to varying levels of tip-induced fiber deformation) supported our observations, with high-ellipticity nanofibers exhibiting lower stability compared to their non-deformed counterparts. As a result, tip-mediated mechanical forces can provide an effective means of altering nanofiber integrity and visualizing the self-recovery of PA assemblies.Item Open Access CO2 laser polishing of microfluidic channels fabricated by femtosecond laser assisted carving(Institute of Physics Publishing, 2016-10) Serhatlioglu, M.; Ortaç, B.; Elbuken, C.; Bıyıklı, Necmi; Solmaz, M. E.In this study, we investigate the effects of CO2 laser polishing on microscopic structures fabricated by femtosecond laser assisted carving (FLAC). FLAC is the peripheral laser irradiation of 2.5D structures suitable for low repetition rate lasers and is first used to define the microwell structures in fused silica followed by chemical etching. Subsequently, the bottom surface of patterned microwells is irradiated with a pulsed CO2 laser. The surfaces were characterized using an atomic force microscope (AFM) and scanning electron microscope (SEM) in terms of roughness and high quality optical imaging before and after the CO2 laser treatment. The AFM measurements show that the surface roughness improves more than threefold after CO2 laser polishing, which promises good channel quality for applications that require optical imaging. In order to demonstrate the ability of this method to produce low surface roughness systems, we have fabricated a microfluidic channel. The channel is filled with polystyrene bead-laden fluid and imaged with transmission mode microscopy. The high quality optical images prove CO2 laser processing as a practical method to reduce the surface roughness of microfluidic channels fabricated by femtosecond laser irradiation. We further compared the traditional and laser-based glass micromachining approaches, which includes FLAC followed by the CO2 polishing technique.Item Open Access Comparison of trimethylgallium and triethylgallium as "ga" source materials for the growth of ultrathin GaN films on Si (100) substrates via hollow-cathode plasma-assisted atomic layer deposition(AVS Science and Technology Society, 2016-02) Alevli, M.; Haider A.; Kizir S.; Leghari, S. A.; Bıyıklı, NecmiGaN films grown by hollow cathode plasma-assisted atomic layer deposition using trimethylgallium (TMG) and triethylgallium (TEG) as gallium precursors are compared. Optimized and saturated TMG/TEG pulse widths were used in order to study the effect of group-III precursors. The films were characterized by grazing incidence x-ray diffraction, atomic force microscopy, x-ray photoelectron spectroscopy, and spectroscopic ellipsometry. Refractive index follows the same trend of crystalline quality, mean grain, and crystallite sizes. GaN layers grown using TMG precursor exhibited improved structural and optical properties when compared to GaN films grown with TEG precursor.Item Open Access Diode behavior in ultra-thin low temperature ALD grown zinc-oxide on silicon(AIP Publishing, 2013) El-Atab, N.; Alqatari, S.; Oruc F.B.; Souier, T.; Chiesa, M.; Okyay, Ali Kemal; Nayfeh, A.A thin-film ZnO(n)/Si(p+) heterojunction diode is demonstrated. The thin film ZnO layer is deposited by Atomic Layer Deposition (ALD) at different temperatures on a p-type silicon substrate. Atomic force microscopy (AFM) AC-in-Air method in addition to conductive AFM (CAFM) were used for the characterization of ZnO layer and to measure the current-voltage characteristics. Forward and reverse bias n-p diode behavior with good rectification properties is achieved. The diode with ZnO grown at 80°C exhibited the highest on/off ratio with a turn-on voltage (VON) ∼3.5 V. The measured breakdown voltage (VBR) and electric field (EBR) for this diode are 5.4 V and 3.86 MV/cm, respectively. © 2013 © 2013 Author(s).Item Open Access Direct measurement of interatomic force gradients using an ultra-low-amplitude atomic force microscope(The Royal Society Publishing, 2001) Hoffmann, P. M.; Oral, A.; Grimble, R. A.; Özer, H. Ö.; Jeffery, S.; Pethica, J. B.Interatomic force gradients between a W tip and a 7 × 7 reconstructed Si(111) surface were measured using an off-resonance, ultra-low-amplitude atomic force microscope (AFM) technique. The amplitudes used were less than 1 Å (peak-to-peak), which allowed direct measurement of the interaction force gradients as a function of separation. The force gradient curves are shown to consist of an attractive van der Waals part and short-range attractive and repulsive interactions. The van der Waals background can be subtracted, leaving a short-range interaction with an energy parameter of 1.9-3.4 eV and an interaction length-scale of 0.54-1.26 Å, characteristic of a single atomic bond. This correlates well with our observation of single-atom resolved force gradient images. In general, the interaction is reversible up to the zero intercept of the force gradient (inflection point of the energy). Beyond this point hysteresis tends to be observed and the onset of inelastic deformation can be clearly discerned. An analysis of the atomic scale contact gives reasonable values for the interfacial energy, yield strength, and the energy per atom needed to initiate plastic deformation.Item Open Access Electrostatic effects on nanofiber formation of self-assembling peptide amphiphiles(Elsevier, 2011) Toksoz, S.; Mammadov R.; Tekinay, A. B.; Güler, Mustafa O.Self-assembling peptide amphiphile molecules have been of interest to various tissue engineering studies. These molecules self-assemble into nanofibers which organize into three-dimensional networks to form hydrocolloid systems mimicking the extracellular matrix. The formation of nanofibers is affected by the electrostatic interactions among the peptides. In this work, we studied the effect of charged groups on the peptides on nanofiber formation. The self-assembly process was studied by pH and zeta potential measurements, FT-IR, circular dichroism, rheology, atomic force microscopy, scanning electron microscopy and transmission electron microscopy. The aggregation of the peptides was triggered upon neutralization of the charged residues by pH change or addition of electrolyte or biomacromolecules. Understanding the controlled formation of the hydrocolloid gels composed of peptide amphiphile nanofibers can lead us to develop in situ gel forming bioactive collagen mimetic nanofibers for various tissue engineering studies including bioactive surface coatings. © 2010 Elsevier Inc.Item Open Access Electrostatic force spectroscopy of near surface localized states(Institute of Physics Publishing Ltd., 2005) Dâna, A.; Yamamoto, Y.Electrostatic force microscopy at cryogenic temperatures is used to probe the electrostatic interaction of a conductive atomic force microscopy tip and electronic charges trapped in localized states in an insulating layer on a semiconductor. Measurement of the frequency shift of the cantilever as a function of tip-sample bias voltage shows discrete peaks at certain voltages when the tip is located near trap centres. These discrete changes in frequency are attributed to one by one filling of individual electronic states when the quantized energies traverse the substrate conduction band Fermi energy as the tip-sample voltage is increased. Theoretical analysis of the experiment suggests that such a measurement of the cantilever frequency shift as a function of bias voltage can be interpreted as an AC force measurement, from which spectroscopic information about the location and energy of localized states can be deduced. Experimental results from the study of a sample with InAs quantum dots as trap centres are presented.Item Open Access Energy dissipation in atomic force microscopy and atomic loss processes(American Physical Society, 2001) Hoffmann, P. M.; Jeffery, S.; Pethica, J. B.; Özer, H. Ö.; Oral, A.Atomic scale dissipation is of great interest in nanomechanics and atomic manipulation. We present dissipation measurements with a linearized, ultrasmall amplitude atomic force microscope which is capable of measuring dissipation at chosen, fixed separations. We show that the dynamic dissipation in the noncontact regime is of the order of a few 10–100 meV per cycle. This dissipation is likely due to the motion of a bistable atomic defect in the tip-surface region. In the contact regime we observe dc hysteresis associated with nanoscale plasticity. We find the hysteretic energy loss to be 1 order of magnitude higher for a silicon surface than for copper.Item Open Access Enhancing higher harmonics of a tapping cantilever by excitation at a submultiple of its resonance frequency(American Physical Society, 2005-03) Balantekin, M.; Atalar, AbdullahIn a tapping-mode atomic force microscope, the frequency spectrum of the oscillating cantilever contains higher harmonics at integer multiples of the excitation frequency. When the cantilever oscillates at its fundamental resonance frequency w 1, the high Q-factor damps the amplitudes of the higher harmonics to negligible levels, unless the higher flexural eigenmodes are coincident with those harmonics. One can enhance the nth harmonic by the Q factor when the cantilever is excited at a submultiple of its resonance frequency (w 1/n). Hence, the magnitude of the nth harmonic can be measured easily and it can be utilized to examine the material properties. We show theoretically that the amplitude of enhanced higher harmonic increases monotonically for a range of sample stiffness, if the interaction is dominated by elastic force.Item Open Access Examination of the temperature related structural defects of InGaN/GaN solar cells(Academic Press, 2015) Durukan, İ. K.; Bayal, Ö.; Kurtuluş, G.; Baş, Y.; Gültekin, A.; Öztürk, M. K.; Çörekçi, S.; Tamer, M.; Özçelik, S.; Özbay, EkmelIn this study the effects of the annealing temperature on the InGaN/GaN solar cells with different In-contents grown on sapphire substrate by the Metal Organic Chemical Vapor Deposition (MOCVD) are analyzed by High Resolution X-ray Diffraction (HRXRD) and an Atomic Force Microscope (AFM). The plane angles, mosaic crystal sizes, mixed stress, dislocation intensities of the structure of the GaN and InGaN layers are determined. According to the test results, there are no general characteristic trends observed due to temperature at both structures. There are fluctuating failures determined at both structures as of 350 °C. The defect density increased on the GaN layer starting from 350 °C and reaching above 400 °C. A similar trend is observed on the InGaN layer, too.Item Open Access Femtosecond laser crystallization of amorphous Ge(American Institute of Physics, 2011) Salihoglu, O.; Kürüm, U.; Yaglıoglu, G. H.; Elmali, A.; Aydınlı, AtillaUltrafast crystallization of amorphous germanium (a-Ge) in ambient has been studied. Plasma enhanced chemical vapor deposition grown a-Ge was irradiated with single femtosecond laser pulses of various durations with a range of fluences from below melting to above ablation threshold. Extensive use of Raman scattering has been employed to determine post solidification features aided by scanning electron microscopy and atomic force microscopy measurements. Linewidth of the Ge optic phonon at 300 cm -1 as a function of laser fluence provides a signature for the crystallization of a-Ge. Various crystallization regimes including nanostructures in the form of nanospheres have been identified.Item Open Access Force and time-dependent self-assembly, disruption and recovery of supramolecular peptide amphiphile nanofibers(Institute of Physics Publishing, 2018) Dikecoglu, F. B.; Topal, A. E.; Ozkan A.D.; Tekin, E. D.; Tekinay, A. B.; Güler, Mustafa O.; Dana, A.Biological feedback mechanisms exert precise control over the initiation and termination of molecular self-assembly in response to environmental stimuli, while minimizing the formation and propagation of defects through self-repair processes. Peptide amphiphile (PA) molecules can self-assemble at physiological conditions to form supramolecular nanostructures that structurally and functionally resemble the nanofibrous proteins of the extracellular matrix, and their ability to reconfigure themselves in response to external stimuli is crucial for the design of intelligent biomaterials systems. Here, we investigated real-time self-assembly, deformation, and recovery of PA nanofibers in aqueous solution by using a force-stabilizing double-pass scanning atomic force microscopy imaging method to disrupt the self-assembled peptide nanofibers in a force-dependent manner. We demonstrate that nanofiber damage occurs at tip-sample interaction forces exceeding 1 nN, and the damaged fibers subsequently recover when the tip pressure is reduced. Nanofiber ends occasionally fail to reconnect following breakage and continue to grow as two individual nanofibers. Energy minimization calculations of nanofibers with increasing cross-sectional ellipticity (corresponding to varying levels of tip-induced fiber deformation) support our observations, with high-ellipticity nanofibers exhibiting lower stability compared to their non-deformed counterparts. Consequently, tip-mediated mechanical forces can provide an effective means of altering nanofiber integrity and visualizing the self-recovery of PA assemblies.Item Open Access Genetically-tunable mechanical properties of bacterial functional amyloid nanofibers(American Chemical Society, 2017) Abdelwahab, M. T.; Kalyoncu, E.; Onur, T.; Baykara, M. Z.; Seker U.O.S.Bacterial biofilms are highly ordered, complex, dynamic material systems including cells, carbohydrates, and proteins. They are known to be resistant against chemical, physical, and biological disturbances. These superior properties make them promising candidates for next generation biomaterials. Here we investigated the morphological and mechanical properties (in terms of Young’s modulus) of genetically-engineered bacterial amyloid nanofibers of Escherichia coli (E. coli) by imaging and force spectroscopy conducted via atomic force microscopy (AFM). In particular, we tuned the expression and biochemical properties of the major and minor biofilm proteins of E. coli (CsgA and CsgB, respectively). Using appropriate mutants, amyloid nanofibers constituting biofilm backbones are formed with different combinations of CsgA and CsgB, as well as the optional addition of tagging sequences. AFM imaging and force spectroscopy are used to probe the morphology and measure the Young’s moduli of biofilm protein nanofibers as a function of protein composition. The obtained results reveal that genetically-controlled secretion of biofilm protein components may lead to the rational tuning of Young’s moduli of biofilms as promising candidates at the bionano interface.Item Open Access Growth of high crystalline quality semi-insulating GaN layers for high electron mobility transistor applications(2006) Yu H.; Caliskan, D.; Özbay, EkmelSemi-insulating character (sheet resistivity of 3.26 × 10 11 Ω/sq) of thick GaN layers was developed for AlGaN/GaN high electron mobility transistor (HEMT) applications on an AlN buffer layer. Electrical and structural properties were characterized by a dark current-voltage transmission line model, x-ray diffraction, and atomic force microscope measurements. The experimental results showed that compared to semi-insulating GaN grown on low temperature GaN nucleation, the crystal quality as well as surface morphology were remarkably improved. It was ascribed to the utilization of a high quality insulating AlN buffer layer and the GaN initial coalescence growth mode. Moreover, the significant increase of electron mobility in a HEMT structure suggests that this is a very promising method to obtain high performance AlGaN/GaN HEMT structures on sapphire substrates. © 2006 American Institute of Physics.Item Open Access Growth of ∼3-nm ZnO nano-islands using Atomic layer deposition(IEEE, 2016) El-Atab, N.; Chowdhury, F. I.; Ulusoy, Türkan Gamze; Ghobadi, Amir; Nazirzadeh, Amin; Okyay, Ali Kemal; Nayfeh, A.In this work, the deposition of 3-nm dispersed Zinc-Oxide (ZnO) nanislands by thermal Atomic Layer Deposition (ALD) is demonstrated. The physical and electronic properties of the islands are studied using Atomic Force Microscopy, UV-Vis-NIR spectroscopy, and X-ray Photoelectron Spectroscopy. The results show that there is quantum confinement in 1D in the nanoislands which is manifested by the increase of the bandgap and the reduction of the electron affinity of the ZnO islands. The results are promising for the fabrication of future electronic and optoelectronic devices by single ALD step.