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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 communication theoretical modeling of axonal propagation in hippocampal pyramidal neurons(IEEE-Inst Electrical Electronics Engineers Inc, 2017) N/A; N/A; Department of Electrical and Electronics Engineering; Ramezani, Hamideh; Akan, Özgür Barış; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 6647Understandingthe fundamentals of communication among neurons, known as neuro-spike communication, leads to reach bio-inspired nanoscale communication paradigms. In this paper, we focus on a part of neuro-spike communication, known as axonal transmission, and propose a realistic model for it. The shape of the spike during axonal transmission varies according to previously applied stimulations to the neuron, and these variations affect the amount of information communicated between neurons. Hence, to reach an accurate model for neuro-spike communication, the memory of axon and its effect on the axonal transmission should be considered, which are not studied in the existing literature. In this paper, we extract the important factors on the memory of axon and define memory states based on these factors. We also describe the transition among these states and the properties of axonal transmission in each of them. Finally, we demonstrate that the proposed model can follow changes in the axonal functionality properly by simulating the proposed model and reporting the root mean square error between simulation results and experimental data.Publication Open Access A new type of microphotoreactor with integrated optofluidic waveguide based on solid-air nanoporous aerogels(Royal Society of Chemistry (RSC), 2018) Jonas, Alexandr; Department of Chemistry; Department of Electrical and Electronics Engineering; Department of Physics; Özbakır, Yaprak; Erkey, Can; Kiraz, Alper; PhD Student; Faculty Member; Faculty Member; Department of Chemistry; Department of Electrical and Electronics Engineering; Department of Physics; College of Engineering; College of Sciences; N/A; 29633; 22542In this study, we developed a new type of microphotoreactor based on an optofluidic waveguide with aqueous liquid core fabricated inside a nanoporous aerogel. To this end, we synthesized a hydrophobic silica aerogel monolith with a density of 0.22 g cm(-3) and a low refractive index of 1.06 that-from the optical point of view-effectively behaves like solid air. Subsequently, we drilled an L-shaped channel within the monolith that confined both the aqueous core liquid and the guided light, the latter property arising due to total internal reflection of light from the liquid-aerogel interface. We characterized the efficiency of light guiding in liquid-filled channel and-using the light delivered by waveguiding-we carried out photochemical reactions in the channel filled with aqueous solutions of methylene blue dye. We demonstrated that methylene blue could be efficiently degraded in the optofluidic photoreactor, with conversion increasing with increasing power of the incident light. The presented optofluidic microphotoreactor represents a versatile platform employing light guiding concept of conventional optical fibres for performing photochemical reactions.Publication Open Access A silicon photonic data link with a monolithic erbium-doped laser(Nature Publishing Group (NPG), 2020) Li, Nanxi; Xin, Ming; Su, Zhan; Singh, Neetesh; Notaros, Jelena; Timurdoğan, Erman; Purnawirman, Purnawirman; Bradley, Jonathan D.B.; Watts, Michael R.; Department of Electrical and Electronics Engineering; Mağden, Emir Salih; Department of Electrical and Electronics Engineering; College of Engineering; 276368To meet the increasing demand for data communication bandwidth and overcome the limits of electrical interconnects, silicon photonic technology has been extensively studied, with various photonics devices and optical links being demonstrated. All of the optical data links previously demonstrated have used either heterogeneously integrated lasers or external laser sources. This work presents the first silicon photonic data link using a monolithic rare-earth-ion-doped laser, a silicon microdisk modulator, and a germanium photodetector integrated on a single chip. The fabrication is CMOS compatible, demonstrating data transmission as a proof-of-concept at kHz speed level, and potential data rate of more than 1 Gbps. This work provides a solution for the monolithic integration of laser sources on the silicon photonic platform, which is fully compatible with the CMOS fabrication line, and has potential applications such as free-space communication and integrated LIDAR.Publication Metadata only A stochastic framework for rate-distortion optimized video coding over error-prone networks(IEEE-Inst Electrical Electronics Engineers Inc, 2007) Harmanci, Oztan; Department of Electrical and Electronics Engineering; Tekalp, Ahmet Murat; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; 26207This paper proposes a complete stochastic framework for RD optimal encoder design for video over error-prone networks, which applies to any motion-compensated predictive video codec. The distortion measure has been taken as the mean square error over an ensemble of channels given an estimate of the instantaneous packet loss probability. We show that 1) the optimal motion compensated prediction, in the MSE sense, requires computation of the expected value of the reference frames, and 2) calculation of the MSE (distortion measure) requires computation of the second moment of the reference frames. We propose a recursive procedure for the computation of both the expected value and second moment of the reference frames, which are together called the stochastic frame buffer. Furthermore, we propose a stochastic RD optimization method for selection of the optimal macroblock mode and motion vectors given the instantaneous packet loss probability. If available, channel feedback can also be incorporated into the proposed stochastic framework. However, the proposed framework does not require a feedback channel to exist, and when it exists, it does not have to be lossless. In the absence of any packet losses, the proposed stochastic framework reduces to the well-known deterministic RD optimization procedures. One possible application of the optimal stochastic framework would be for multicast streaming to an ensemble of receivers. Experimental results indicate that the proposed framework outperforms other available error tracking and control schemes.Publication Metadata only Advanced imaging with dynamic focus and extended depth using integrated FR4 platform(Optical Society of America (OSA), 2009) Varghese, Samuel; Abdullah, Fahd; Augustine, Robin; Sprague, Randy B.; Andron, Voytek; N/A; Department of Electrical and Electronics Engineering; Işıkman, Serhan Ömer; Ürey, Hakan; Master Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 8579A two-degrees-of-freedom scanned beam imaging system with large dynamic range and dynamic focusing is demonstrated. The laser diode, photo-detector and the optical components are integrated on a moving platform that is made of FR4 (Flame-Retardant 4), a common polymeric substrate used in printed circuit boards. A scan angle of 52 degrees is demonstrated at 60Hz resonant frequency while the laser is moved 250um in the out-of-plane direction to achieve dynamic focusing. The laser is scanned by physically rotating the laser diode and the collection optics to achieve high signal-to-noise ratio and good ambient light rejection. The collection optics is engineered such that the collection efficiency decreases when collecting light from close distances to avoid detector saturation. The detection range is extended from contact distance up to 600mm while the collected power level varies only by a factor of 30 within this long range. Slight modifications will allow increasing the detection range up to one meter. This is the first demonstration of a laser scan engine with such a high degree of integration of electronics, optoelectronics, optics and micromechanics on the same platform.Publication Open Access Ai driven advanced internet of things (Iotx(2)): the future seems irreversibly connected in medicine(Turkish Society of Cardiology, 2019) Belcastro, Kristen D.; Department of Electrical and Electronics Engineering; Ergen, Onur; Department of Electrical and Electronics Engineering; College of Engineering; 272106Publication 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.Publication Open Access An easy-to-fabricate microfluidic shallow trench induced three-dimensional cell culturing and imaging (STICI3D) platform(American Chemical Society (ACS), 2022) Coşkun, Umut Can; Rehman, Ateeq Ur; Gülle, Merve; Erten, Ahmet; N/A; Department of Physics; Department of Electrical and Electronics Engineering; N/A; Başer, Hatice Nur; Baysal, Kemal; Kiraz, Alper; Kul, Demet; Kuş, Funda; Morova, Berna; Faculty Member; Faculty Member; Researcher; Department of Physics; 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; School of Medicine; College of Sciences; College of Engineering; N/A; 119184; 22542; N/A; N/A; N/ACompared to the established monolayer approach of two-dimensional cell cultures, three-dimensional (3D) cultures more closely resemble in vivo models; that is, the cells interact and form clusters mimicking their organization in native tissue. Therefore, the cellular microenvironment of these 3D cultures proves to be more clinically relevant. In this study, we present a novel easy-to-fabricate microfluidic shallow trench induced 3D cell culturing and imaging (STICI3D) platform, suitable for rapid fabrication as well as mass manufacturing. Our design consists of a shallow trench, within which various hydrogels can be formed in situ via capillary action, between and fully in contact with two side channels that allow cell seeding and media replenishment, as well as forming concentration gradients of various molecules. Compared to a micropillar-based burst valve design, which requires sophisticated microfabrication facilities, our capillary-based STICI3D can be fabricated using molds prepared with simple adhesive tapes and razors alone. The simple design supports the easy applicability of mass-production methods such as hot embossing and injection molding as well. To optimize the STICI3D design, we investigated the effect of individual design parameters such as corner radii, trench height, and surface wettability under various inlet pressures on the confinement of a hydrogel solution within the shallow trench using Computational Fluid Dynamics simulations supported with experimental validation. We identified ideal design values that improved the robustness of hydrogel confinement and reduced the effect of end-user dependent factors such as hydrogel solution loading pressure. Finally, we demonstrated cultures of human mesenchymal stem cells and human umbilical cord endothelial cells in the STICI3D to show that it supports 3D cell cultures and enables precise control of cellular microenvironment and real-time microscopic imaging. The easy-to-fabricate and highly adaptable nature of the STICI3D platform makes it suitable for researchers interested in fabricating custom polydimethylsiloxane devices as well as those who are in need of ready-to-use plastic platforms. As such, STICI3Ds can be used in imaging cell-cell interactions, angiogenesis, semiquantitative analysis of drug response in cells, and measurement of transport through cell sheet barriers.Publication Open Access An LED-Based structured illumination microscope using a digital micromirror device and GPU accelerated image reconstruction(Public Library of Science, 2022) Aydın, Musa; Doğan, Buket; Department of Physics; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Kiraz, Alper; Karalar, Elif Nur Fırat; Morova, Berna; Uysallı, Yiğit; Özgönül, Ekin; Faculty Member; Researcher; PhD Student; PhD Student; Department of Physics; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; 22542; 206349; N/A; N/A; N/AWhen combined with computational approaches, fluorescence imaging becomes one of the most powerful tools in biomedical research. It is possible to achieve resolution figures beyond the diffraction limit, and improve the performance and flexibility of high-resolution imaging systems with techniques such as structured illumination microscopy (SIM) reconstruction. In this study, the hardware and software implementation of an LED-based superresolution imaging system using SIM employing GPU accelerated parallel image reconstruction is presented. The sample is illuminated with two-dimensional sinusoidal patterns with various orientations and lateral phase shifts generated using a digital micromirror device (DMD). SIM reconstruction is carried out in frequency space using parallel CUDA kernel functions. Furthermore, a general purpose toolbox for the parallel image reconstruction algorithm and an infrastructure that allows all users to perform parallel operations on images without developing any CUDA kernel code is presented. The developed image reconstruction algorithm was run separately on a CPU and a GPU. Two different SIM reconstruction algorithms have been developed for the CPU as mono-thread CPU algorithm and multi-thread OpenMP CPU algorithm. SIM reconstruction of 1024 × 1024 px images was achieved in 1.49 s using GPU computation, indicating an enhancement by*28 and*20 in computation time when compared with mono-thread CPU computation and multi-thread OpenMP CPU computation, respectively.