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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Publication Metadata only Biomedical optical fibers(Royal Soc Chemistry, 2021) Jiang, Nan; Yetişen, Ali K.; N/A; N/A; Department of Mechanical Engineering; Sarabi, Misagh Rezapour; Öztürk, Ece; Taşoğlu, Savaş; PhD Student; Faculty Member; Faculty Member; Department of Mechanical Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); KU Arçelik Research Center for Creative Industries (KUAR) / KU Arçelik Yaratıcı Endüstriler Uygulama ve Araştırma Merkezi (KUAR); Graduate School of Sciences and Engineering; School of Medicine; College of Engineering; N/A; 326940; 291971Optical fibers with the ability to propagate and transfer data via optical signals have been used for decades in medicine. Biomaterials featuring the properties of softness, biocompatibility, and biodegradability enable the introduction of optical fibers' uses in biomedical engineering applications such as medical implants and health monitoring systems. Here, we review the emerging medical and health-field applications of optical fibers, illustrating the new wave for the fabrication of implantable devices, wearable sensors, and photodetection and therapy setups. A glimpse of fabrication methods is also provided, with the introduction of 3D printing as an emerging fabrication technology. The use of artificial intelligence for solving issues such as data analysis and outcome prediction is also discussed, paving the way for the new optical treatments for human health.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 Multiscale coupling based on quasicontinuum method in nanowires at finite temperatures(IEEE, 2015) Sonne, Mads Rostgaard; Hattel, Jesper Henri; N/A; Department of Mechanical Engineering; Esfahani, Mohammad Nasr; Alaca, Burhanettin Erdem; PhD Student; Faculty Member; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 115108Nanoelectromechanical systems have been developed for ultra-high frequency oscillators because of their small size and excellent material properties. Using flexural modes and electrothermal features in nanowires for frequency tuning necessitates a sound modeling approach. The quasicontinuum method was developed to link atomistic models with the continuum finite element method in order to study the material behavior across multiple length scales. These significant efforts to develop a continuum theory based on atomistic models have so far been limited to zero temperature. The purpose of this work is to develop the theoretical framework needed to study the mechanical response in nanoscale components such as nanowires at finite temperatures. This is achieved up to a temperature of 1000 K by integrating Engineering Molecular Mechanics and the Cauchy-Born hypothesis. The proposed method is verified with Molecular Dynamics and Molecular Mechanics simulations reported in literature. Bending properties of nanowires at finite temperatures were studied with the proposed method. Thermomechanical properties were investigated by including surface effects.Publication Metadata only Modeling and characterization of comb-actuated resonant microscanners(Iop Publishing Ltd, 2006) N/A; Department of Electrical and Electronics Engineering; Ataman, Çağlar; Ürey, Hakan; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 8579The dynamics of the out-of-plane comb-drive actuator used in a torsional resonant mode microscanner is discussed. The microscanner is fabricated using the standard SOI technology by Fraunhofer, IPMS and utilized in various display, barcode scanning, spectroscopy and other imaging applications. The device is a parametrically excited system and exhibits hysteretic frequency response, nonlinear transient response, subharmonic oscillations, multiple parametric resonances, and alternating-oscillation-frequency behavior. Analytical and numerical models are developed to predict the parametric system dynamics. The analytical model is based on the solution of the linear Mathieu equation and valid for small angular displacements. The numerical model is valid for both small and large deflection angles. The analytical and numerical models are validated with the experimental results under various ambient pressures and excitation schemes and successfully predict the dynamics of the parametric nature of the microscanner. As many as four parametric resonances are observed at 30 mTorr. The models developed in this paper can be used to optimize the structure and the actuator.Publication Metadata only Resonant PZT MEMS scanners with integrated angle sensors(IEEE Computer Society, 2014) Brown, Dean; Davis, Wyatt; N/A; Department of Electrical and Electronics Engineering; N/A; Department of Electrical and Electronics Engineering; Baran, Utku; Holmstrom, Sven; Çakmak, Onur; Ürey, Hakan; Master Student; Researcher; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; N/A; 8579Several high performing PZT-actuated MEMS laser scanners utilizing mechanical coupling are designed, fabricated, and characterized. Optical angles up to 59.3 deg. and θoptD·fn-products up to 3052 deg.·mm·Hz are demonstrated. These are the highest performing MEMS scanners in the literature. An angle sensor is integrated into one scanner design without any additional processing. The sensor response shows a linear relationship with the mirror rotation. A closed-loop drive was demonstrated using the scanner output.Publication Metadata only Comb-actuated resonant torsional microscanner with mechanical amplification(IEEE-Inst Electrical Electronics Engineers Inc, 2010) Brown, Dean; Davis, Wyatt O.; Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; N/A; Department of Electrical and Electronics Engineering; Arslan, Aslıhan; Holmstrom, Sven; Gökçe, Sertan Kutal; Ürey, Hakan; Researcher; Researcher; Master Student; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; N/A; 8579A comb-actuated torsional microscanner is developed for high-resolution laser-scanning display systems. Typical torsional comb-drive scanners have fingers placed around the perimeter of the scanning mirror. In contrast, the structure in this paper uses cascaded frames, where the comb fingers are placed on an outer drive frame, and the motion is transferred to the inner mirror frame with a mechanical gain. The structure works only in resonant mode without requiring any offset in the comb fingers, keeping the silicon-on-insulator-based process quite simple. The design intent is to improve actuator efficiency by removing the high-drag fingers from the high-velocity scanning mirror. Placing them on the lower velocity drive frame reduces their contribution to the damping torque. Furthermore, placement on the drive frame allows an increase of the number of fingers and their capacity to impart torque. The microscanner exhibits a parametric response, and as such, the maximum deflection is found when actuated at twice its natural frequency. Analytical formulas are given for the coupled-mode equations and frame deflections. A simple formula is derived for the mechanical-gain factor. For a 1-mm x 1.5-mm oblong scanning mirror, a 76. total optical scan angle is achieved at 21.8 kHz with 196-V peak-to-peak excitation voltages. [2009-0304]Publication Metadata only FRET-based nanoscale point-to-point and broadcast communications with multi-exciton transmission and channel routing(Ieee-Inst Electrical Electronics Engineers Inc, 2014) N/A; N/A; Department of Electrical and Electronics Engineering; Kuşcu, Murat; Akan, Özgür Barış; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; 316349; 6647Nanoscale communication based on Forster Resonance Energy Transfer (FRET) enables nanoscale single molecular devices to communicate with each other utilizing excitons generated on fluorescentmolecules as information carriers. Based on the point-to-point single-exciton FRET-based nanocommunication model, we investigate the multiple-exciton case for point-to-point and broadcast communications following an information theoretical approach and conducting simulations through Monte Carlo approach. We demonstrate that the multi-exciton transmission significantly improves the channel reliability and the range of the communication up to tens of nanometers for immobile nanonodes providing high data transmission rates. Furthermore, our analyses indicate that multi-exciton transmission enables broadcasting of information from a transmitter nanonode to many receiver nanonodes pointing out the potential of FRET-based communication to extend over nanonetworks. In this study, we also propose electrically and chemically controllable routing mechanisms exploiting the strong dependence of FRET rate on spectral and spatial characteristics of fluorescent molecules. We show that the proposed routing mechanisms enable the remote control of information flow in FRET-based nanonetworks. The high transmission rates obtained by multi-exciton scheme for point-to-point and broadcast communications, as well as the routing opportunities make FRET-based communication promising for future molecular computers.Publication Metadata only Layer-by-layer grown electrodes composed of cationic Fe 3 O 4 nanoparticles and graphene oxide nanosheets for electrochemical energy storage devices(Amer Chemical Soc, 2019) Erdem, Emre; Department of Chemistry; N/A; Department of Chemistry; Department of Chemistry; Öztuna, Feriha Eylül Saraç; Ünal, Özlem; Acar, Havva Funda Yağcı; Ünal, Uğur; Researcher; PhD Student; Faculty Member; Faculty Member; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Sciences; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; N/A; N/A; 178902; 42079Ultrathin electrodes composed of layer-by-layer assembled (3-aminopropyl)trimethoxysilane functionalized iron oxide nanoparticles and graphene oxide nanosheets were prepared by a simple and low-cost dip coating method without using any binders or conductive additives. The thickness of the Fe3O4/GO films was simply altered with the number of dip coating cycles. Multilayered films were chemically reduced with hydrazine vapor in order to increase the electrical conductivity. Characterization of multilayer films was performed with scanning transmission electron microscopy, UV-vis spectroscopy, atomic force microscopy, quartz crystal microbalance, X-ray photoelectron spectroscopy, and electron paramagnetic resonance spectroscopy. We have performed cyclic voltammetry and electrochemical impedance spectroscopy for the evaluation of Fe3O4/GO multilayers as possible electrochemical capacitor electrodes. Reduced Fe3O4/GO films exhibit high specific capacitances (varying between 200 and 350 F g(-1) at 5 mV s(-1)), Outperforming the layer-by-layer assembled iron oxides/carbon derivatives (carbon nanotube, graphene).Publication Metadata only Label-free and high-throughput detection of biomolecular interactions using a flatbed scanner biosensor(Amer Chemical Soc, 2017) Avci, Oguzhan; Seymour, Elif; Unlu, M. Selim; Ozkumur, Ayca Yalcin; N/A; Department of Electrical and Electronics Engineering; Aygün, Uğur; Ürey, Hakan; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; N/A; 8579Fluorescence based microarray detection systems provide sensitive measurements; however, variation of probe immobilization and poor repeatability negatively affect the final readout, and thus quantification capability of these systems. Here, we demonstrate a label-free and high-throughput optical biosensor that can be utilized for calibration of fluorescence microarrays. The sensor employs a commercial flatbed scanner, and we demonstrate transformation of this low cost (similar to 100 USD) system into an Interferometric Reflectance Imaging Sensor through hardware and software modifications. Using this sensor, we report detection of DNA hybridization and DNA directed antibody immobilization on label-free microarrays with a noise floor of similar to 30 pg/mm(2), and a scan speed of 5 s (50 s for 10 frames averaged) for a 2 mm X 2 mm area. This novel system may be used as a standalone label-free sensor especially in low-resource settings, as well as for quality control and calibration of microarrays in existing fluorescence-based DNA and protein detection platforms.