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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/6
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Publication Open Access Fabrication and microfluidic analysis of graphene-based molecular communication receiver for Internet of Nano Things (IoNT)(Springer Nature, 2021) Ramezani, Hamideh; Dinç, Ergin; Akhavan, Shahab; Department of Electrical and Electronics Engineering; Akan, Özgür Barış; Kuşcu, Murat; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 6647; 316349Bio-inspired molecular communications (MC), where molecules are used to transfer information, is the most promising technique to realise the Internet of Nano Things (IoNT), thanks to its inherent biocompatibility, energy-efficiency, and reliability in physiologically-relevant environments. Despite a substantial body of theoretical work concerning MC, the lack of practical micro/nanoscale MC devices and MC testbeds has led researchers to make overly simplifying assumptions about the implications of the channel conditions and the physical architectures of the practical transceivers in developing theoretical models and devising communication methods for MC. On the other hand, MC imposes unique challenges resulting from the highly complex, nonlinear, time-varying channel properties that cannot be always tackled by conventional information and communication tools and technologies (ICT). As a result, the reliability of the existing MC methods, which are mostly adopted from electromagnetic communications and not validated with practical testbeds, is highly questionable. As the first step to remove this discrepancy, in this study, we report on the fabrication of a nanoscale MC receiver based on graphene field-effect transistor biosensors. We perform its ICT characterisation in a custom-designed microfluidic MC system with the information encoded into the concentration of single-stranded DNA molecules. This experimental platform is the first practical implementation of a micro/nanoscale MC system with nanoscale MC receivers, and can serve as a testbed for developing realistic MC methods and IoNT applications.Publication Open Access Modeling convection-diffusion-reaction systems for microfluidic molecular communications with surface-based receivers in Internet of Bio-Nano Things(Public Library of Science, 2018) Department of Electrical and Electronics Engineering; Kuşcu, Murat; Akan, Özgür Barış; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and EngineeringWe consider a microfluidic molecular communication (MC) system, where the concentration-encoded molecular messages are transported via fluid flow-induced convection and diffusion, and detected by a surface-based MC receiver with ligand receptors placed at the bottom of the microfluidic channel. The overall system is a convection-diffusion-reaction system that can only be solved by numerical methods, e.g., finite element analysis (FEA). However, analytical models are key for the information and communication technology (ICT), as they enable an optimisation framework to develop advanced communication techniques, such as optimum detection methods and reliable transmission schemes. In this direction, we develop an analytical model to approximate the expected time course of bound receptor concentration, i.e., the received signal used to decode the transmitted messages. The model obviates the need for computationally expensive numerical methods by capturing the nonlinearities caused by laminar flow resulting in parabolic velocity profile, and finite number of ligand receptors leading to receiver saturation. The model also captures the effects of reactive surface depletion layer resulting from the mass transport limitations and moving reaction boundary originated from the passage of finite-duration molecular concentration pulse over the receiver surface. Based on the proposed model, we derive closed form analytical expressions that approximate the received pulse width, pulse delay and pulse amplitude, which can be used to optimize the system from an ICT perspective. We evaluate the accuracy of the proposed model by comparing model-based analytical results to the numerical results obtained by solving the exact system model with COMSOL Multiphysics.Publication Open Access Modelling data for predicting new iron garnet thin films with perpendicular magnetic anisotropy(Elsevier, 2020) Department of Electrical and Electronics Engineering; N/A; Onbaşlı, Mehmet Cengiz; Zanjani, Saeedeh Mokarian; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and Engineering; 258783; N/AThese data include detailed calculations and graphs based on our manuscript submitted to Journal of Magnetism and Magnetic Materials, entitled “Predicting New Iron Garnet Thin Films with Perpendicular Magnetic Anisotropy”. These data are organized in two parts; first, we present the calculated plots of sensitivity of magnetic anisotropy field and anisotropy energy density for 49 epitaxial rare earth iron garnet (REIG) film/substrate pairs (a total of 98 plots, Figs. 1–15). In the second part, we present in Table 1 the complete details on the calculations for total magnetic anisotropy and all material constants used for each of 50 film/substrate pairs. The comparison with the previous experimental demonstrations is also shown in Table 1 (last column) and 2 with an accompanying discussion confirming the reliability of our model.Publication Open Access Bioabsorbable polymer optical waveguides for deep-tissue photomedicine(Nature Publishing Group (NPG), 2016) Gather, Malte C.; Humar, Matjaz; Choi, Myunghwan; Kim, Seonghoon; Kim, Ki Su; Hahn, Sei Kwang; Scarcelli, Giuliano; Randolph, Mark; Redmond, Robert W.; Yun, Seok Hyun.; Department of Electrical and Electronics Engineering; Nizamoğlu, Sedat; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 130295Advances in photonics have stimulated significant progress in medicine, with many techniques now in routine clinical use. However, the finite depth of light penetration in tissue is a serious constraint to clinical utility. Here we show implantable light-delivery devices made of bio-derived or biocompatible, and biodegradable polymers. In contrast to conventional optical fibres, which must be removed from the body soon after use, the biodegradable and biocompatible waveguides may be used for long-term light delivery and need not be removed as they are gradually resorbed by the tissue. As proof of concept, we demonstrate this paradigm-shifting approach for photochemical tissue bonding (PTB). Using comb-shaped planar waveguides, we achieve a full thickness ( 410 mm) wound closure of porcine skin, which represents similar to 10-fold extension of the tissue area achieved with conventional PTB. The results point to a new direction in photomedicine for using light in deep tissues.Publication Open Access Transmissive silicon photonic dichroic filters with spectrally selective waveguides(Nature Publishing Group (NPG), 2018) Li, Nanxi; Raval, Manan; Poulton, Christopher V.; Ruocco, Alfonso; Singh, Neetesh; Vermeulen, Diedrik; Ippen, Erich P.; Kolodziejski, Leslie A.; Watts, Michael R.; Department of Electrical and Electronics Engineering; Mağden, Emir Salih; Department of Electrical and Electronics Engineering; College of Engineering; 276368Many optical systems require broadband filters with sharp roll-offs for efficiently splitting or combining light across wide spectra. While free space dichroic filters can provide broadband selectivity, on-chip integration of these high-performance filters is crucial for the scalability of photonic applications in multi-octave interferometry, spectroscopy, and wideband wavelength-division multiplexing. Here we present the theory, design, and experimental characterization of integrated, transmissive, 1 x 2 port dichroic filters using spectrally selective waveguides. Mode evolution through adiabatic transitions in the demonstrated filters allows for single cutoff and flat-top responses with low insertion losses and octave-wide simulated bandwidths. Filters with cutoffs around 1550 and 2100 nm are fabricated on a silicon-on-insulator platform with standard complementary metal-oxide-semiconductor processes. A filter roll-off of 2.82 dB nm(-1) is achieved while maintaining ultra-broadband operation. This new class of nanophotonic dichroic filters can lead to new paradigms in on-chip communications, sensing, imaging, optical synthesis, and display applications.Publication Open Access Bridging the gap between RF and optical patch antenna analysis via the cavity model(Nature Publishing Group (NPG), 2015) Department of Electrical and Electronics Engineering; Ünal, Gül Seda; Aksun, M. İrşadi; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; N/A; 28358Although optical antennas with a variety of shapes and for a variety of applications have been proposed and studied, they are still in their infancy compared to their radio frequency (rf) counterparts. Optical antennas have mainly utilized the geometrical attributes of rf antennas rather than the analysis tools that have been the source of intuition for antenna engineers in rf. This study intends to narrow the gap of experience and intuition in the design of optical patch antennas by introducing an easy-to-understand and easy-to-implement analysis tool in rf, namely, the cavity model, into the optical regime. The importance of this approach is not only its simplicity in understanding and implementation but also its applicability to a broad class of patch antennas and, more importantly, its ability to provide the intuition needed to predict the outcome without going through the trial-and-error simulations with no or little intuitive guidance by the user.Publication Open Access D-DSC: decoding delay-based distributed source coding for Internet of Sensing Things(Public Library of Science, 2018) Aktaş, Metin; Dinç, Ergin; Department of Electrical and Electronics Engineering; Kuşcu, Murat; Akan, Özgür Barış; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and EngineeringSpatial correlation between densely deployed sensor nodes in a wireless sensor network (WSN) can be exploited to reduce the power consumption through a proper source coding mechanism such as distributed source coding (DSC). In this paper, we propose the Decoding Delay-based Distributed Source Coding (D-DSC) to improve the energy efficiency of the classical DSC by employing the decoding delay concept which enables the use of the maximum correlated portion of sensor samples during the event estimation. In D-DSC, network is partitioned into clusters, where the clusterheads communicate their uncompressed samples carrying the side information, and the cluster members send their compressed samples. Sink performs joint decoding of the compressed and uncompressed samples and then reconstructs the event signal using the decoded sensor readings. Based on the observed degree of the correlation among sensor samples, the sink dynamically updates and broadcasts the varying compression rates back to the sensor nodes. Simulation results for the performance evaluation reveal that D-DSC can achieve reliable and energy-efficient event communication and estimation for practical signal detection/estimation applications having massive number of sensors towards the realization of Internet of Sensing Things (loST).Publication Open Access Rapid alleviation of Parkinson's disease symptoms via electrostimulation of intrinsic auricular muscle zones(Frontiers, 2017) Cakmak, Yusuf O.; Apaydin, Hulya; Kiziltan, Gunes; Gunduz, Aysegul; Ozsoy, Burak; Cakmak, Ozgur O.; Ozdemir, Yasemin G.; Ertan, Sibel; Department of Electrical and Electronics Engineering; Ölçer, Selim; Ürey, Hakan; Other; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; N/A; 8579Background: Deep brain stimulation of the subthalamic nucleus (STN-DBS) and the pedunculopontine nucleus (PPN) significantly improve cardinal motor symptoms and postural instability and gait difficulty, respectively, in Parkinson's disease (PD). Objective and Hypothesis: Intrinsic auricular muscle zones (IAMZs) allow the potential to simultaneously stimulate the C2 spinal nerve, the trigeminal nerve, the facial nerve, and sympathetic and parasympathetic nerves in addition to providing muscle feedback and control areas including the STN, the PPN and mesencephalic locomotor regions. Our aim was to observe the clinical responses to IAMZ stimulation in PD patients.Method: Unilateral stimulation of an IAMZ, which includes muscle fibers for proprioception, the facial nerve, and C2, trigeminal and autonomic nerve fibers, at 130 Hz was performed in a placebo-and sham-controlled, double-blinded, within design, two-armed study of 24 PD patients.Results: The results of the first arm (10 patients) of the present study demonstrated a substantial improvement in Unified Parkinson's Disease Ratings Scale (UPDRS) motor scores due to 10 min of IAMZ electrostimulation (p = 0.0003, power: 0.99) compared to the placebo control (p = 0.130). A moderate to large clinical difference in the improvement in UPDRS motor scores was observed in the IAMZ electrostimulation group. The results of the second arm (14 patients) demonstrated significant improvements with dry needling (p = 0.011) and electrostimulation of the IAMZ (p < 0.001) but not with sham electrostimulation (p = 0.748). In addition, there was a significantly greater improvement in UPDRS motor scores in the IAMZ electrostimulation group compared to the IAMZ dry needling group (p < 0.001) and the sham electrostimulation (p < 0.001) groups. The improvement in UPDRS motor scores of the IAMZ electrostimulation group (Delta UPDRS = 5.29) reached moderate to high clinical significance, which was not the case for the dry needling group (Delta UPDRS = 1.54). In addition, both arms of the study demonstrated bilateral improvements in motor symptoms in response to unilateral IAMZ electrostimulation. Conclusion: The present study is the first demonstration of a potential role of IAMZ electrical stimulation in improving the clinical motor symptoms of PD patients in the short term.Publication Open Access Author correction: label-free detection of nanoparticles using depth scanning correlation interferometric microscopy(Nature Publishing Group (NPG), 2019) Department of Electrical and Electronics Engineering; Aygün, Uğur; Ürey, Hakan; Faculty Member; Department of Electrical and Electronics Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; N/A; 8579Publication Open Access All optical control of magnetization in quantum confined ultrathin magnetic metals(Nature Publishing Group (NPG), 2021) Department of Physics; Department of Electrical and Electronics Engineering; N/A; Müstecaplıoğlu, Özgür Esat; Onbaşlı, Mehmet Cengiz; Naseem, Muhammad Tahir; Zanjani, Saeedeh Mokarian; Faculty Member; Faculty Member; Department of Physics; Department of Electrical and Electronics Engineering; College of Sciences; College of Engineering; Graduate School of Sciences and Engineering; 1674; 258783; N/A; N/AAll-optical control dynamics of magnetization in sub-10 nm metallic thin films are investigated, as these films with quantum confinement undergo unique interactions with femtosecond laser pulses. Our theoretical analysis based on the free electron model shows that the density of states at Fermi level (DOSF) and electron-phonon coupling coefficients (G(ep)) in ultrathin metals have very high sensitivity to film thickness within a few angstroms. We show that completely different magnetization dynamics characteristics emerge if DOSF and G(ep) depend on thickness compared with bulk metals. Our model suggests highly efficient energy transfer from femtosecond laser photons to spin waves due to minimal energy absorption by phonons. This sensitivity to the thickness and efficient energy transfer offers an opportunity to obtain ultrafast on-chip magnetization dynamics.