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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Publication Metadata only Silk as a biodegradable resist for field-emission scanning probe lithography(Institute of Physics (IOP) Publishing, 2020) Sadeghi, Sadra; Rangelow, Ivo W.; Department of Mechanical Engineering; Department of Electrical and Electronics Engineering; N/A; N/A; Department of Electrical and Electronics Engineering; Alaca, Burhanettin Erdem; Kumar, Baskaran Ganesh; Melikov, Rustamzhon; Doğru-Yüksel, Itır Bakış; Nizamoğlu, Sedat; Faculty Member; Other; PhD Student; PhD Student; Faculty Member; Department of Mechanical Engineering; Department of Electrical and Electronics Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştirmalari Merkezi (KUYTAM); N/A; N/A; N/A; N/A; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; 115108; N/A; N/A; N/A; 130295The patterning of silk allows for manufacturing various structures with advanced functionalities for optical and tissue engineering and drug delivery applications. Here, we propose a high-resolution nanoscale patterning method based on field-emission scanning probe lithography (FE-SPL) that crosslinks the biomaterial silk on conductive indium tin oxide (ITO) promoting the use of a biodegradable material as resist and water as a developer. During the lithographic process, Fowler-Nordheim electron emission from a sharp tip was used to manipulate the structure of silk fibroin from random coil to beta sheet and the emission formed nanoscale latent patterns with a critical dimension (CD) of similar to 50 nm. To demonstrate the versatility of the method, we patterned standard and complex shapes. This method is particularly attractive due to its ease of operation without relying on a vacuum or a special gaseous environment and without any need for complex electronics or optics. Therefore, this study paves a practical and cost-effective way toward patterning biopolymers at ultra-high level resolution.Publication Metadata only Structural changes in a Schiff base molecular assembly initiated by scanning tunneling microscopy tip(Institute of Physics (IOP) Publishing, 2016) Tomak, A.; Bacaksiz, C.; Mendirek, G.; Sahin, H.; Hur, D.; Gorgun, K.; Senger, R. T.; Peeters, F. M.; Zareie, H. M.; N/A; Birer, Özgür; Researcher; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); N/A; N/AWe report the controlled self-organization and switching of newly designed Schiff base (E)-4-((4-(phenylethynyl) benzylidene) amino) benzenethiol (EPBB) molecules on a Au (111) surface at room temperature. Scanning tunneling microscopy and spectroscopy (STM/STS) were used to image and analyze the conformational changes of the EPBB molecules. The conformational change of the molecules was induced by using the STM tip while increasing the tunneling current. The switching of a domain or island of molecules was shown to be induced by the STM tip during scanning. Unambiguous fingerprints of the switching mechanism were observed via STM/STS measurements. Surface-enhanced Raman scattering was employed, to control and identify quantitatively the switching mechanism of molecules in a monolayer. Density functional theory calculations were also performed in order to understand the microscopic details of the switching mechanism. These calculations revealed that the molecular switching behavior stemmed from the strong interaction of the EPBB molecules with the STM tip. Our approach to controlling intermolecular mechanics provides a path towards the bottom-up assembly of more sophisticated molecular machines.Publication Metadata only Survival probability in a quantum walk on a one-dimensional lattice with partially absorbing traps(American Scientific Publishers, 2013) Gonulol, Meltem; Aydiner, Ekrem; Shikano, Yutaka; Department of Physics; Müstecaplıoğlu, Özgür Esat; Faculty Member; Department of Physics; College of Sciences; 1674Time dependence of the survival probability in a one dimensional lattice with randomly distributed and partial absorbing traps is analyzed as a function of concentration and absorption probability of the traps. The short and long time behaviors of the non-interacting quantum walks are identified with stretched exponentials. Dynamical scaling laws of the short and long time regimes as well as the crossover time between them are characterized. It is found that the short time behavior is more sensitive to the absorption probability and the crossover takes longer time for more transparent traps. Moreover, the stretching exponents increase with the transparency of the traps.Publication Metadata only Ray tracing-based maritime channel analysis for millimeter radiowaves(Springer, 2019) Ozdemir, Mehmet Kemal; N/A; Mehrnia, Niloofar; PhD Student; Graduate School of Sciences and Engineering; N/AIn this work, we present and analyze the simulation results of millimeter-wave propagation channel performed over the sea surface for ship to ship scenario. We present a channel characterization study where channel parameters such as path loss, received power, root mean square delay spread, and power delay profile are inspected by taking the ray tracing advantages of the Wireless InSite software. 35 GHz and 94 GHz are the bands of interest, as they have minimum water and oxygen attenuation and their performances in practice would be the best among the other frequency bands. In our study, we investigate the effect of ray spacing, Earth's curvature, and the sea surface roughness on marine channel characteristics. Our results demonstrate that 2-ray analytical model should be only used for some short ranges over the sea surface propagating at high frequencies. Besides, free-space path loss model cannot predict the behavior of channel over the sea surface in high frequencies even for the short ranges. Therefore, a new path loss model is proposed to compensate the defects of existing path loss models by the means of changing the reflection coefficient and modifying the original 2-ray path loss model. This proposed model is able to better follow the simulated or measured propagation loss with less error, when it is compared with Free Space and 2-ray path loss models. Hence, this new model can be used for the path loss calculations at the mentioned frequencies especially for large distances between transmitter and receiver.Publication Metadata only Monolithic integration of silicon nanowires with a microgripper(Institute of Electrical and Electronics Engineers (IEEE), 2009) Ozsun, Ozgur; Leblebici, Yusuf; Yalcinkaya, Arda D.; Zervas, Michalis; Department of Mechanical Engineering; N/A; N/A; Alaca, Burhanettin Erdem; Yıldız, İzzet; Yılmaz, Mehmet; Faculty Member; Master Student; Master Student; Department of Mechanical Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştirmalari Merkezi (KUYTAM); College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; 115108; N/A; N/ASi nanowire (NW) stacks are fabricated by utilizing the scalloping effect of inductively coupled plasma deep reactive ion etching. When two etch windows are brought close enough, scallops from both sides will ideally meet along the dividing center-line of the windows turning the separating material column into an array of vertically stacked strings. Upon further thinning of these NW precursors by oxidation followed by oxide etching, Si NWs with diameters ranging from 50 nm to above 100 nm are obtained. The pattern of NWs is determined solely by photolithography. Various geometries ranging from T-junctions to circular coils are demonstrated in addition to straight NWs along specific crystallographic orientations. The number of NWs in a stack is determined by the number of etch cycles utilized. Due to the precise lithographic definition of NW location and orientation, the technique provides a convenient batch-compatible tool for the integration of NWs with MEMS. This aspect is demonstrated with a microgripper, where an electrostatic actuation mechanism is simultaneously fabricated with the accompanying NW end-effectors. Mechanical integrity of the NW-MEMS bond and the manipulation capability of the gripper are demonstrated. Overall, the proposed technique exhibits a batch-compatible approach to the issue of micronanointegration.Publication Metadata only Aerogels for optofluidic waveguides(MDPI, 2017) Jonas, Alexandr; N/A; Department of Physics; Department of Chemical and Biological Engineering; Özbakır, Yaprak; Erkey, Can; Kiraz, Alper; PhD Student; Faculty Member; Faculty Member; Department of Physics; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; N/A; 29633; 22542Aerogels-solid materials keeping their internal structure of interconnected submicron-sized pores intact upon exchanging the pore liquid with a gas-were first synthesized in 1932 by Samuel Kistler. Overall, an aerogel is a special form of a highly porous material with a very low solid density and it is composed of individual nano-sized particles or fibers that are connected to form a three-dimensional network. The unique properties of these materials, such as open pores and high surface areas, are attributed to their high porosity and irregular solid structure, which can be tuned through proper selection of the preparation conditions. Moreover, their low refractive index makes them a remarkable solid-cladding material for developing liquid-core optofluidic waveguides based on total internal reflection of light. This paper is a comprehensive review of the literature on the use of aerogels for optofluidic waveguide applications. First, an overview of different types of aerogels and their physicochemical properties is presented. Subsequently, possible techniques to fabricate channels in aerogel monoliths are discussed and methods to make the channel surfaces hydrophobic are described in detail. Studies in the literature on the characterization of light propagation in liquid-filled channels within aerogel monoliths as well as their light-guiding characteristics are discussed. Finally, possible applications of aerogel-based optofluidic waveguides are described.Publication Metadata only Electronic and optical properties of stanane and armchair stanane nanoribbons(Springer Heidelberg, 2020) Dideban, Daryoosh; Gulseren, Oguz; N/A; N/A; N/A; N/AIn this study, we performed a density functional theory based investigation of the structural, electronic, and optical properties of a stanane, fully hydrogenated stanene SnH, and armchair stanane nanoribbons ASnHNRs. Our full geometry optimization calculations show stanane has 0.84 angstrom buckled height and the buckled structure is preserved in ASnHNRs. The optimized lattice parameter of stanane, Sn-Sn, and Sn-H bond length are 4.58 angstrom, 2.75 angstrom, and 1.73 angstrom, respectively. Electronic structure calculations show that stanane is a moderate-band-gap semiconductor with a direct band gap of 1.2 eV and ASnHNRs are wide-band-gap semiconductors. The band gap of ASnHNRs decreases as the ribbons width increases. We investigated the optical properties for two directions of polarization. For perpendicular-polarized light, the imaginary part of dielectric function epsilon 2(omega) of stanane peaks between 5 and 10 eV; while for the parallel-polarized light, the peaks are seen in a wide range of energy. According to the results, stanane is a good absorptive matter, especially for visible regions of the electromagnetic spectrum. The presence of anisotropy with respect to the type of light polarization is observed in ASnHNRs also. In these structures, the main peak of epsilon 2(omega) is located at 3.4 eV for parallel- and in 6-8 eV for perpendicular-polarized light.Publication Metadata only Observation of whispering-gallery modes in a diamond microsphere(IEEE-Inst Electrical Electronics Engineers Inc, 2018) N/A; N/A; Department of Physics; Bayer, Mustafa Mert; Çirkinoğlu, Hüseyin Ozan; Serpengüzel, Ali; Master Student; Master Student; Faculty Member; Department of Physics; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; 27855We demonstrate a Type Ib diamond (nitrogen impurity of >5 ppm) microsphere whispering-gallery mode resonator in the near-infrared wavelengths between 1426.10 nm and 1427.42 nm in the 90 degrees elastic-light-scattering for both transverse magnetic (TM) and transverse electric (TE) polarizations. The highest measured whispering-gallery mode quality-factor is in the order of 10(4), and the mode spacing is 0.332 nm both for TM and TE polarizations. The coupling of the continuous-wave tunable infrared excitation laser to the diamond microsphere is achieved by a single-mode silica optical-fiber half-coupler. Such a diamond resonator can further be used as stable optical-frequency-comb generating or lasing microcavities by exploiting the nitrogen-vacancy centers present within the diamond.Publication Metadata only Automatic CNN-based Arabic numeral spotting and handwritten digit recognition by using deep transfer learning in Ottoman population registers(Mdpi, 2020) N/A; Department of History; Can, Yekta Said; Kabadayı, Mustafa Erdem; Researcher; Faculty Member; Department of History; College of Social Sciences and Humanities; College of Social Sciences and Humanities; N/A; 33267Historical manuscripts and archival documentation are handwritten texts which are the backbone sources for historical inquiry. Recent developments in the digital humanities field and the need for extracting information from the historical documents have fastened the digitization processes. Cutting edge machine learning methods are applied to extract meaning from these documents. Page segmentation (layout analysis), keyword, number and symbol spotting, handwritten text recognition algorithms are tested on historical documents. For most of the languages, these techniques are widely studied and high performance techniques are developed. However, the properties of Arabic scripts (i.e., diacritics, varying script styles, diacritics, and ligatures) create additional problems for these algorithms and, therefore, the number of research is limited. In this research, we first automatically spotted the Arabic numerals from the very first series of population registers of the Ottoman Empire conducted in the mid-nineteenth century and recognized these numbers. They are important because they held information about the number of households, registered individuals and ages of individuals. We applied a red color filter to separate numerals from the document by taking advantage of the structure of the studied registers (numerals are written in red). We first used a CNN-based segmentation method for spotting these numerals. In the second part, we annotated a local Arabic handwritten digit dataset from the spotted numerals by selecting uni-digit ones and tested the Deep Transfer Learning method from large open Arabic handwritten digit datasets for digit recognition. We achieved promising results for recognizing digits in these historical documents.Publication Metadata only Investigation of the spontaneous emission rate of perylene dye molecules encapsulated into three-dimensional nanofibers via FLIM method(Springer, 2014) Acikgoz, Sabriye; Demir, Mustafa M.; Yapasan, Ece; Unal, Ahmet A.; Inci, M. Naci; Department of Physics; Kiraz, Alper; Faculty Member; Department of Physics; College of Sciences; 22542The decay dynamics of perylene dye molecules encapsulated in polymer nanofibers produced by electrospinning of polymethyl methacrylate are investigated using a confocal fluorescence lifetime imaging microscopy technique. Time-resolved experiments show that the fluorescence lifetime of perylene dye molecules is enhanced when the dye molecules are encapsulated in a three-dimensional photonic environment. It is hard to produce a sustainable host with exactly the same dimensions all the time during fabrication to accommodate dye molecules for enhancement of spontaneous emission rate. The electrospinning method allows us to have a control over fiber diameter. It is observed that the wavelength of monomer excitation of perylene dye molecules is too short to cause enhancement within nanofiber photonic environment of 330 nm diameters. However, when these nanofibers are doped with more concentrated perylene, in addition to monomer excitation, an excimer excitation is generated. This causes observation of the Purcell effect in the three-dimensional nanocylindrical photonic fiber geometry.