Publications without Fulltext
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
Browse
67 results
Search Results
Item Metadata only MNO2 nanoflower integrated optoelectronic biointerfaces for photostimulation of neurons(Wiley, 2023) 0000-0003-0394-5790; 0000-0002-7669-9589; 0000-0003-3682-6042; 0000-0002-4355-7592; 0000-0001-9885-5653; 0009-0002-2549-3983; 0000-0001-7789-8152; Vanalakar, Sharadrao Anandrao; Department of Electrical and Electronics Engineering; N/A; N/A; N/A; N/A; N/A; N/A; Nizamoğlu, Sedat; Karatüm, Onuralp; Önal, Asım; Kaleli, Humeyra Nur; Hasanreisoğlu, Murat; Balamur, Rıdvan; Kaya, Lokman; Faculty Member; PhD Student; PhD Student; PhD Student; Faculty Member; PhD Student; Master Student; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Health Sciences; School of Medicine; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; 130295; N/A; N/A; N/A; 182001; N/A; N/AOptoelectronic biointerfaces have gained significant interest for wireless and electrical control of neurons. Three-dimentional (3D) pseudocapacitive nanomaterials with large surface areas and interconnected porous structures have great potential for optoelectronic biointerfaces that can fulfill the requirement of high electrode-electrolyte capacitance to effectively transduce light into stimulating ionic currents. In this study, the integration of 3D manganese dioxide (MnO2) nanoflowers into flexible optoelectronic biointerfaces for safe and efficient photostimulation of neurons is demonstrated. MnO2 nanoflowers are grown via chemical bath deposition on the return electrode, which has a MnO2 seed layer deposited via cyclic voltammetry. They facilitate a high interfacial capacitance (larger than 10 mF cm(-2)) and photogenerated charge density (over 20 & mu;C cm(-2)) under low light intensity (1 mW mm(-2)). MnO2 nanoflowers induce safe capacitive currents with reversible Faradaic reactions and do not cause any toxicity on hippocampal neurons in vitro, making them a promising material for biointerfacing with electrogenic cells. Patch-clamp electrophysiology is recorded in the whole-cell configuration of hippocampal neurons, and the optoelectronic biointerfaces trigger repetitive and rapid firing of action potentials in response to light pulse trains. This study points out the potential of electrochemically-deposited 3D pseudocapacitive nanomaterials as a robust building block for optoelectronic control of neurons.Publication Metadata only Microfluidic pulse shaping methods for molecular communications(Elsevier, 2023) Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Kahvazi Zadeh, Maryam; Bolhassan, Iman Mokari; Kuşcu, Murat; Graduate School of Sciences and Engineering; College of EngineeringMolecular Communication (MC) is a bio-inspired communication modality that utilizes chemical signals in the form of molecules to exchange information between spatially separated entities. Pulse shaping is an important process in all communication systems, as it modifies the waveform of transmitted signals to match the characteristics of the communication channel for reliable and high-speed information transfer. In MC systems, the unconventional architectures of components, such as transmitters and receivers, and the complex, nonlinear, and time-varying nature of MC channels make pulse shaping even more important. While several pulse shaping methods have been theoretically proposed for MC, their practicality and performance are still uncertain. Moreover, the majority of recently proposed experimental MC testbeds that rely on microfluidics technology lack the incorporation of programmable pulse shaping methods, which hinders the accurate evaluation of MC techniques in practical settings. To address the challenges associated with pulse shaping in microfluidic MC systems, we provide a comprehensive overview of practical microfluidic chemical waveform generation techniques that have been experimentally validated and whose architectures can inform the design of pulse shaping methods for microfluidic MC systems and testbeds. These techniques include those based on hydrodynamic and acoustofluidic force fields, as well as electrochemical reactions. We also discuss the fundamental working mechanisms and system architectures of these techniques, and compare their performances in terms of spatiotemporal resolution, selectivity, system complexity, and other performance metrics relevant to MC applications, as well as their feasibility for practical MC applications.Publication Metadata only Stabilization and adiabatic control of antiferromagnetically coupled skyrmions without the topological hall effect(Royal Soc Chemistry, 2023) Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Yağan, Rawana; Cheghabouri, Arash Mousavi; Onbaşlı, Mehmet Cengiz; Graduate School of Sciences and Engineering; College of EngineeringSynthetic antiferromagnetically coupled (SAF) multilayers provide different physics of stabilizing skyrmions while eliminating the topological Hall effect (THE), enabling efficient and stable control. The effects of material parameters, external current drive, and a magnetic field on the skyrmion equilibrium and propagation characteristics are largely unresolved. Here, we present a computational and theoretical demonstration of the large window of material parameters that stabilize SAF skyrmions determined by saturation magnetization, uniaxial anisotropy, and Dzyaloshinskii-Moriya interaction. Current-driven SAF skyrmion velocities reach & SIM;200 m s(-1) without the THE. The SAF velocities are about 3-10 times greater than the typical ferromagnetic skyrmion velocities. The current densities needed for driving SAF skyrmions could be reduced to 10(8) A m(-2), while 10(11) A m(-2) or above is needed for ferromagnetic skyrmions. By reducing the SAF skyrmion drive current by 3 orders, Joule heating is reduced by 6 orders of magnitude. These results pave the way for new SAF interfaces with improved equilibrium, dynamics, and power savings in THE-free skyrmionics.Publication Metadata only Enhancement of resolution and propagation length by sources with temporal decay in plasmonic devices(Springer, 2020) Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Tetikol, Hüseyin Serhat; Aksun, M. İrşadi; PhD Student; Faculty Member; College of Engineering; College of Engineering; N/A; 28358Highly lossy nature of metals has severely limited the scope of practical applications of plasmonics. The conventional approach to circumvent this limitation has been to search for new materials with more favorable dielectric properties (e.g., reduced loss), or to incorporate gain media to overcome the inherent loss. In this study, however, we turn our attention to the source and show that the wealth of new SPP modes with simultaneous complex frequencies and complex wave vectors that are otherwise unreachable can be excited by imposing temporal decay on the excitation. Therefore, to understand the possible implications of these new modes and how to be able to tune them for specific applications, we propose a framework of pseudo-monochromatic modes that are generated by introducing exponential decays into otherwise monochromatic sources. Within this framework, the dispersion relation of complex SPPs is re-evaluated and cast to be a surface rather than a curve, depicting all possible omega-kpairs (both complex in general) that are supported by the given geometry. To demonstrate the potentials of the complex modes and the use of the framework to study them selectively, we have chosen two important, and somewhat limiting, features of SPPs to investigate; resolution in plasmonic lenses and propagation length in SPP waveguides. While the former is mainly used to validate the proposed method and the framework on the recent improvement of resolution in plasmonic superlenses, the latter provides a novel approach to extend the propagation length of the SPP modes in planar waveguides significantly. Since the improvement in propagation length due to the introduction of temporal decay to the excitation is rather counter-intuitive, the dispersion-based theoretical predictions (the proposed approach) have been validated via the FDTD simulations of Maxwell's equations in the same geometry without any a priori assumptions on the frequency or the wave vector.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; Department of Mechanical Engineering; 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; 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 Modeling and characterization of comb-actuated resonant microscanners(Iop Publishing Ltd, 2006) N/A; Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Ataman, Çağlar; Ürey, Hakan; PhD Student; Faculty Member; 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; Department of Electrical and Electronics Engineering; Baran, Utku; Holmstrom, Sven; Çakmak, Onur; Ürey, Hakan; Master Student; Researcher; PhD Student; Faculty Member; 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; Department of Electrical and Electronics Engineering; Arslan, Aslıhan; Holmstrom, Sven; Gökçe, Sertan Kutal; Ürey, Hakan; Researcher; Researcher; Master Student; Faculty Member; 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; Department of Electrical and Electronics Engineering; Kuşcu, Murat; Akan, Özgür Barış; PhD Student; Faculty Member; 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 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; Department of Electrical and Electronics Engineering; Aygün, Uğur; Ürey, Hakan; PhD Student; Faculty Member; 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.