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Publication Metadata only 3D coffee stains(Royal Soc Chemistry, 2017) N/A; N/A; Department of Electrical and Electronics Engineering; N/A; N/A; N/A; Department of Molecular Biology and Genetics; Department of Chemistry; Department of Chemistry; Department of Electrical and Electronics Engineering; Doğru-Yüksel, Itır Bakış; Söz, Çağla Koşak; Press, Daniel Aaron; Melikov, Rustamzhon; Begar, Efe; Çonkar, Deniz; Karalar, Elif Nur Fırat; Yılgör, Emel; Yılgör, İskender; Nizamoğlu, Sedat; PhD Student; PhD Student; Researcher; PhD Student; PhD Student; PhD Student; PhD Student; Faculty Member; Researcher; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Department of Chemistry; Department of Electrical and Electronics Engineering; N/A; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); N/A; N/A; N/A; N/A; N/A; N/A; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; College of Sciences; College of Engineering; N/A; N/A; N/A; N/A; N/A; N/A; 206349; N/A; 24181; 130295When a liquid droplet (e.g., coffee, wine, etc.) is splattered on a surface, the droplet dries in a ring-shaped stain. This widely observed pattern in everyday life occurs due to the phenomenon known as a coffee stain (or coffee ring) effect. While the droplet dries, the capillary flow moves and deposits the particles toward the pinned edges, which shows a 2D ring-like structure. Here we demonstrate the transition from a 2D to a 3D coffee stain that has a well-defined and hollow sphere-like structure, when the substrate surface is switched from hydrophilic to superhydrophobic. The 3D stain formation starts with the evaporation of the pinned aqueous colloidal droplet placed on a superhydrophobic surface that facilitates the particle flow towards the liquid-air interface. This leads to spherical skin formation and a cavity in the droplet. Afterwards the water loss in the cavity due to pervaporation leads to bubble nucleation and growth, until complete evaporation of the solvent. In addition to the superhydrophobicity of the surface, the concentration of the solution also has a significant effect on 3D coffee stain formation. Advantageously, 3D coffee stain formation in a pendant droplet configuration enables the construction of all-protein lasers by integrating silk fibroin with fluorescent proteins. No tools, components and/or human intervention are needed after the construction process is initiated; therefore, 3D coffee-stains hold promise for building self-assembled and functional 3D constructs and devices from colloidal solutions.Publication Metadata only A blind fractionally spaced equalization algorithm with global convergence(IEEE, 2007) Department of Electrical and Electronics Engineering; Erdoğan, Alper Tunga; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 41624In this article we present a fractionally spaced extension of the SubGradient based Blind equalization Algorithm (SGBA). The basic features of the proposed algorithm are the non-linear constraint on the search vector and the selection of the weighting and step size applied to the search vector. It is proven that the algorithm is globally convergent to a perfect equalization point under the well known equalizability conditions for the fractionally spaced setting. The simulation results provided at the end of the article illustrates the relative merit of the proposed algorithm in comparison to the state of the art algorithms.Publication Open Access A cartridge based sensor array platform for multiple coagulation measurements from plasma(Royal Society of Chemistry (RSC), 2015) Bulut, Serpil; Yaralioglu, G. G.; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Çakmak, Onur; Ermek, Erhan; Kılınç, Necmettin; Barış, İbrahim; Kavaklı, İbrahim Halil; Ürey, Hakan; PhD Student; Other; Researcher; Teaching Faculty; Faculty Member; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; 109991; N/A; 111629; 40319; 8579This paper proposes a MEMS-based sensor array enabling multiple clot-time tests for plasma in one disposable microfluidic cartridge. The versatile LoC (Lab-on-Chip) platform technology is demonstrated here for real-time coagulation tests (activated Partial Thromboplastin Time (aPTT) and Prothrombin Time (PT)). The system has a reader unit and a disposable cartridge. The reader has no electrical connections to the cartridge. This enables simple and low-cost cartridge designs and avoids reliability problems associated with electrical connections. The cartridge consists of microfluidic channels and MEMS microcantilevers placed in each channel. The microcantilevers are made of electroplated nickel. They are actuated remotely using an external electro-coil and the read-out is also conducted remotely using a laser. The phase difference between the cantilever oscillation and the coil drive is monitored in real time. During coagulation, the viscosity of the blood plasma increases resulting in a change in the phase read-out. The proposed assay was tested on human and control plasma samples for PT and aPTT measurements. PT and aPTT measurements from control plasma samples are comparable with the manufacturer's datasheet and the commercial reference device. The measurement system has an overall 7.28% and 6.33% CV for PT and aPTT, respectively. For further implementation, the microfluidic channels of the cartridge were functionalized for PT and aPTT tests by drying specific reagents in each channel. Since simultaneous PT and aPTT measurements are needed in order to properly evaluate the coagulation system, one of the most prominent features of the proposed assay is enabling parallel measurement of different coagulation parameters. Additionally, the design of the cartridge and the read-out system as well as the obtained reproducible results with 10 mu l of the plasma samples suggest an opportunity for a possible point-of-care application.Publication Metadata only A class of bounded component analysis algorithms for the separation of both independent and dependent sources(IEEE-inst Electrical Electronics Engineers inc, 2013) Department of Electrical and Electronics Engineering; Erdoğan, Alper Tunga; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 41624Bounded Component analysis (BCa) is a recent approach which enables the separation of both dependent and independent signals from their mixtures. in this approach, under the practical source boundedness assumption, the widely used statistical independence assumption is replaced by a more generic domain separability assumption. This article introduces a geometric framework for the development of Bounded Component analysis algorithms. Two main geometric objects related to the separator output samples, namely Principal Hyper-Ellipsoid and Bounding Hyper-Rectangle, Are introduced. the maximization of the volume ratio of these objects, and its extensions, Are introduced as relevant optimization problems for Bounded Component analysis. the article also provides corresponding iterative algorithms for both real and complex sources. the numerical examples illustrate the potential advantage of the proposed BCa framework in terms of correlated source separation capability as well as performance improvement for short data records.Publication Open Access A hybrid architecture for federated and centralized learning(Institute of Electrical and Electronics Engineers (IEEE), 2022) Elbir, Ahmet M.; Papazafeiropoulos, Anastasios K.; Kourtessis, Pandelis; Chatzinotas, Symeon; Department of Electrical and Electronics Engineering; Ergen, Sinem Çöleri; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 7211Many of the machine learning tasks rely on centralized learning (CL), which requires the transmission of local datasets from the clients to a parameter server (PS) entailing huge communication overhead. To overcome this, federated learning (FL) has been suggested as a promising tool, wherein the clients send only the model updates to the PS instead of the whole dataset. However, FL demands powerful computational resources from the clients. In practice, not all the clients have sufficient computational resources to participate in training. To address this common scenario, we propose a more efficient approach called hybrid federated and centralized learning (HFCL), wherein only the clients with sufficient resources employ FL, while the remaining ones send their datasets to the PS, which computes the model on behalf of them. Then, the model parameters are aggregated at the PS. To improve the efficiency of dataset transmission, we propose two different techniques: i) increased computation-per-client and ii) sequential data transmission. Notably, the HFCL frameworks outperform FL with up to 20% improvement in the learning accuracy when only half of the clients perform FL while having 50% less communication overhead than CL since all the clients collaborate on the learning process with their datasets.Publication Metadata only A nanoscale communication channel with fluorescence resonance energy transfer (FRET)(IEEE, 2011) Department of Electrical and Electronics Engineering; N/A; Akan, Özgür Barış; Kuşcu, Murat; Faculty Member; Master Student; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and Engineering; 6647; 316349In this study, a novel and physically realizable nanoscale communication paradigm is introduced based on a well-known phenomenon, Fluorescence Resonance Energy Transfer (FRET) for the first time in the literature. FRET is a nonradiative energy transfer process between fluorescent molecules based on the dipole-dipole interactions of molecules. Energy is transferred rapidly from a donor to an acceptor molecule in a close proximity such as 0 to 10 nm without radiation of a photon. Low dependency on the environmental factors, controllability of its parameters and relatively wide transfer range make FRET a promising candidate to be used for a high rate nanoscale communication channel. In this paper, the simplest form of the FRET-based molecular communication channel for a single transmitter and a single receiver nanomachine is modeled. Furthermore, using the information theoretical approach, the capacity of the point-to-point communication channel is investigated and the dependency of the capacity on some environmental and intrinsic parameters is analyzed. It is shown that the capacity can be increased by appropriately selecting the donor-acceptor pair, the medium, the intermolecular distance and the orientation of the molecules.Publication Open Access A new RIS architecture with a single power amplifier: energy efficiency and error performance analysis(Institute of Electrical and Electronics Engineers (IEEE), 2022) Alexandropoulos, George C.; Department of Electrical and Electronics Engineering; Başar, Ertuğrul; Taşçı, Recep Akif; Kılınç, Fatih; Faculty Member; Master Student; Researcher; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; 149116; N/A; N/AMany electrochemical devices are based on the fundamental process of ion migration and accumulation on surfaces. Complex interplay of molecular properties of ions and device dimensions control the entire process and define the overall dynamics of the system. Particularly, for ionic liquid-based electrolytes it is often not clear which property, and to what extent, contributes to the overall performance of the device. Herein we use X-ray photoelectron spectroscopy (XPS) while the device is under electrical bias. Such a procedure reveals localized electrical potential developments, through binding energy shifts of the atomic core levels, in a chemically specific fashion. Combining it with square-wave AC modulation, the information can also be extended to time domain, and we investigate devices configured as a coplanar capacitor, with an ionic liquid as the electrolyte, in macro-dimensions. Our analysis reveals that a nonlinear voltage profile across the device emerges from spatially non-uniform electrical double layer formation on electrode surfaces. Interestingly the coplanar capacitor has an extremely slow time response which is particularly controlled by IL film thickness. XPS measurements can capture the ion dynamics in the tens of seconds to microseconds range, and reveal that ionic motion is all over the device, including on metallic electrode regions. This behavior can only be attributed to motion in more than one dimension. The ion dynamics can also be faithfully simulated by using a modified PNP equation, taking into account steric effects, and device dimensions. XPS measurements on two devices with different dimensions corroborated and validated the simulation results. The present results propose a new experimental approach and provide new insights into the dynamics of ions across electrochemical devices.Publication Open Access A novel NOMA solution with RIS partitioning(Institute of Electrical and Electronics Engineers (IEEE), 2022) Department of Electrical and Electronics Engineering; Başar, Ertuğrul; Khaleel, Aymen; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and Engineering; 149116; N/AReconfigurable intelligent surface (RIS) empowered communications with non-orthogonal multiple access (NOMA) has recently become an appealing research direction for nextgeneration wireless communications. In this paper, we propose a novel NOMA solution with RIS partitioning, where we aim to enhance the spectrum efficiency by improving the ergodic rate of all users, and to maximize the user fairness. In the proposed system, we distribute the physical resources among users such that the base station (BS) and RIS are dedicated to serve different clusters of users. Furthermore, we formulate an RIS partitioning optimization problem to slice the RIS elements between the users such that the user fairness is maximized. The formulated problem is shown to be a non-convex and non-linear integer programming (NLIP) problem with a combinatorial feasible set, which is challenging to solve. Therefore, we exploit the structure of the problem to bound its feasible set and obtain a sub-optimal solution by sequentially applying three efficient search algorithms. Furthermore, we derive exact and asymptotic expressions for the outage probability. Simulation results clearly indicate the superiority of the proposed system over the considered benchmark systems in terms of ergodic sum-rate, outage probability, and user fairness performance.Publication Metadata only A novel reconfigurable intelligent surface-supported code index modulation-based receive spatial modulation system(IEEE-Institute of Electrical and Electronics Engineers, 2024) Ozden, Burak Ahmet; Cogen, Fatih; Aydin, Erdogan; Ilhan, Haci; Wen, Miaowen; Department of Electrical and Electronics Engineering; Başar, Ertuğrul; Department of Electrical and Electronics Engineering; College of EngineeringToday's wireless communication networks have many requirements such as high data rate, high reliability, low latency, low error data transmission, and high energy efficiency. High-performance index modulation (IM) techniques and reconfigurable intelligent surface (RIS) technology, which has recently attracted the attention of researchers, are strong candidates to meet these requirements. This paper introduces a novel RIS-supported code IM-based receive spatial modulation (RIS-CIM-RSM) system. The proposed RIS-CIM-RSM system uses quadrature amplitude modulation (QAM) symbols, receive antenna indices, and spreading code indices for wireless data transmission. In the proposed system, an RIS applies a phase rotation that maximizes signal-to-noise ratio (SNR) to the signals coming to the reflecting elements and directs them to the selected receive antenna. Performance analyses of the proposed RIS-CIM-RSM system such as data rate, throughput, and energy saving are obtained. The results obtained show that the proposed RIS-CIM-RSM system is superior to the counterpart RIS-based IM systems in the literature in terms of data rate, throughput, energy saving, and error performance.Publication Open Access A practical approach for rate-distortion-perception analysis in learned image compression(Institute of Electrical and Electronics Engineers (IEEE), 2021) Department of Electrical and Electronics Engineering; Tekalp, Ahmet Murat; Kırmemiş, Ogün; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and Engineering; 26207; N/ARate-distortion optimization (RDO) of codecs, where distortion is quantified by the mean-square error, has been a standard practice in image/video compression over the years. RDO serves well for optimization of codec performance for evaluation of the results in terms of PSNR. However, it is well known that the PSNR does not correlate well with perceptual evaluation of images; hence, RDO is not well suited for perceptual optimization of codecs. Recently, rate-distortion-perception trade-off has been formalized by taking the Kullback-Leibler (KL) divergence between the distributions of the original and reconstructed images as a perception measure. Learned image compression methods that simultaneously optimize rate, mean-square loss, VGG loss, and an adversarial loss were proposed. Yet, there exists no easy approach to fix the rate, distortion or perception at a desired level in a practical learned image compression solution to perform an analysis of the trade-off between rate, distortion and perception measures. In this paper, we propose a practical approach to fix the rate to carry out perception-distortion analysis at a fixed rate in order to perform perceptual evaluation of image compression results in a principled manner. Experimental results provide several insights for practical rate-distortion-perception analysis in learned image compression.