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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 Metadata only A communication theoretical modeling of single-layer graphene photodetectors and efficient multireceiver diversity combining(Ieee-Inst Electrical Electronics Engineers Inc, 2012) N/A; Department of Electrical and Electronics Engineering; Gülbahar, Burhan; Akan, Özgür Barış; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; 234525; 6647Graphene with groundbreaking properties has tremendous impact on physical sciences as 2-D atomic layer carbon sheet. Its unique electronic and photonic properties lead to applications such as transistors, graphene photodetectors (GPDs), and electronic circuit components. Metal-graphene-metal (MGM) GPDs with single-or multilayer graphene sheets are promising for future nanoscale optical communication architectures because of wide range absorption from far infrared to visible spectrum, fast carrier velocity, and advanced production techniques due to planar geometry. In this paper, signal-to-noise ratio (SNR), bit-error rate (BER), and data rate performances of nanoscale single-layer symmetric MGM photodetectors are analyzed for intensity modulation and direct detection (IM/DD) modulation. Shot and thermal noise limited (NL) performances are analyzed emphasizing graphene layer width dependence and domination of thermal NL characteristics for practical power levels. Tens of Gbit/s data rates are shown to be achievable with very low BERs for single-receiver (SR) GPDs. Furthermore, multireceiver (MR) GPDs and parallel line-scan (PLS) network topology are defined improving the efficiency of symmetric GPDs. SNR performance of SR PLS channels are both improved and homogenized with MR devices having the same total graphene area by optimizing their positions with maxmin solutions and using maximal ratio and equal gain diversity combining techniques.Publication Metadata only A communication theoretical modeling of single-walled carbon nanotube optical nanoreceivers and broadcast power allocation(Ieee-Inst Electrical Electronics Engineers Inc, 2012) N/A; Department of Electrical and Electronics Engineering; Gülbahar, Burhan; Akan, Özgür Barış; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; 234525; 6647Carbon nanotube (CNT) with its ground-breaking properties is a promising candidate for future nanoscale communication networks. CNTs can be used as on-chip optical antenna for wireless interconnects. Carbon nanotube field-effect transistors (CNTFETs) show significant performance as photodetectors due to wide spectral region and tunable bandgap. In this paper, CNTFETs composed of semiconducting single-walled carbon nanotube (SWNT) and metal contacts (M-SWNT-M) are used as photodiode receivers in nanoscale optical communication by theoretically modeling diameter-dependent characteristics for shot-, dark-, and thermal-noise-limited cases. Bit error rate (BER), cutoff bit rate, and signal-to-noise ratio performance are analyzed for intensity modulation and direct detection modulation. The multireceiver CNT nanoscale network topology is presented for information broadcast and the minimum SNR is maximized solving NP-hard max-min power allocation problem with semidefinite programming relaxation and branch and bound framework. The significant performance improvement is observed compared with uniform power allocation. Derived model is compared with existing experiments and hundreds of Mb/s data rate is achievable with very low BERs. Furthermore, optimization gain is highest for thermal-noise-limited case while the shot-noise-limited case gives the highest data rate.Publication Metadata only A fast algorithm for analysis of molecular communication in artificial synapse(IEEE-Inst Electrical Electronics Engineers Inc, 2017) N/A; Department of Electrical and Electronics Engineering; Bilgin, Bilgesu Arif; Akan, Özgür Barış; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 6647In this paper, we analyze molecular communications (MCs) in a proposed artificial synapse (AS), whose main difference from biological synapses (BSs) is that it is closed, i.e., transmitter molecules cannot diffuse out from AS. Such a setup has both advantages and disadvantages. Besides higher structural stability, being closed, AS never runs out of transmitters. Thus, MC in AS is disconnected from outer environment, which is very desirable for possible intra-body applications. On the other hand, clearance of transmitters from AS has to be achieved by transporter molecules on the presynaptic membrane of AS. Except from these differences, rest of AS content is taken to be similar to that of a glutamatergic BS. Furthermore, in place of commonly used Monte Carlo-based random walk experiments, we derive a deterministic algorithm that attacks for expected values of desired parameters such as evolution of receptor states. To assess validity of our algorithm, we compare its results with average results of an ensemble of Monte Carlo experiments, which shows near exact match. Moreover, our approach requires significantly less amount of computation compared with Monte Carlo approach, making it useful for parameter space exploration necessary for optimization in design of possible MC devices, including but not limited to AS. Results of our algorithm are presented in case of single quantal release only, and they support that MC in closed AS with elevated uptake has similar properties to that in BS. In particular, similar to glutamatergic BSs, the quantal size and the density of receptors are found to be main sources of synaptic plasticity. On the other hand, the proposed model of AS is found to have slower decaying transients of receptor states than BSs, especially desensitized ones, which is due to prolonged clearance of transmitters from AS.Publication Metadata only A Fourier transform spectrometer using resonant vertical comb actuators(Institute of Physics (IOP) Publishing, 2006) Wolter, Alexander; 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 design, fabrication and characterization of a novel out-of-plane vertical comb-drive actuator based lamellar grating interferometer (LGI) is reported. The interferometer utilizes resonant mode vertical comb actuators, where comb fingers are simultaneously used for actuation and as a movable diffraction grating, making the device very compact. The Fourier transform of the zeroth order intensity pattern as a function of the optical path difference gives the spectrum of light. The main advantages offered by the proposed device are a long travel range (i.e. good spectral resolution), a large clear aperture (i.e. high light efficiency), and a very simple, robust and compact spectrometer structure. Peak-to-peak 106 mu m out-of-plane deflection is observed in ambient pressure and at 28 V, corresponding to a theoretical spectral resolution of about 0.4 nm in the visible band and 3.6 nm at 1.5 mu m. A simple CMOS compatible process based on bulk micromachining of a silicon-on-insulator wafer is used for the device fabrication.Publication Metadata only A mechanical transduction-based molecular communication receiver for ınternet of nano things (IoNT)(Assoc Computing Machinery, 2021) N/A; Department of Electrical and Electronics Engineering; Aktaş, Dilara; Akan, Özgür Barış; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 6647Molecular conununication (MC) is one of the most promising technology to enable nanonetworks. Despite many aspects of MC have been investigated broadly, the physical design of the MC receiver has gained little interest. High-performance MC receivers based on bioFETs are proposed and extensively analyzed. However, they have some challenges such as limited detection with charged molecules, Debye screening, and the need for reference electrodes. To overcome these shortcomings, we propose a mechanical-based transducing scheme. In particular, we focus on a Flexure field-effect transistor (FET)-based MC receiver architecture, which provides exponentially high sensitivity by utilizing a nonlinear electromechanical coupling. In addition, the detection of neutral molecules with much simpler instrumentation is possible. In this paper, we analyze its fundamental performance metrics; sensitivity, noise power, signal-to-noise ratio, and the symbol error probability, from an MC theoretical perspective.Publication Metadata only Analysis of information flow in miso neuro-spike communication channel with synaptic plasticity(Institute of Electrical and Electronics Engineers (IEEE), 2018) Ramezani H.; Muzio G.; N/A; Department of Electrical and Electronics Engineering; Khan, Tooba; Akan, Özgür Barış; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 6647Communication among neurons is the most promising technique for biocompatible nanonetworks. This necessitates the thorough communication theoretical analysis of information transmission among neurons. The information flow in neuro-spike communication channel is regulated by the ability of neurons to change their synaptic strengths over time, i.e. synaptic plasticity. Thus, the performance evaluation of the nervous nanonetwork is incomplete without considering the influence of synaptic plasticity. Hence, in this paper, we provide a comprehensive model for multiple-input single-output (MISO) neuro-spike communication by integrating the spike timing dependent plasticity (STDP) into existing channel model. We simulate this model for a realistic scenario with correlated inputs and varying spiking threshold. We show that plasticity is strengthening the correlated input synapses at the expense of weakening the synapses with uncorrelated inputs. Moreover, a nonlinear behavior in signal transmission is observed with changing spiking threshold.Publication Metadata only Anisotropic gold nanostructures: optimization via in silico modeling for hyperthermia(Amer Chemical Soc, 2018) Singh, Ajay Vikram; Jahnke, Timotheus; Wang, Shuo; Xiao, Yang; Alapan, Yunus; Kozielski, Kristen; David, Hilda; Richter, Gunther; Bill, Joachim; Laux, Peter; Luch, Andreas; Sitti, Metin; Department of Electrical and Electronics Engineering; N/A; Onbaşlı, Mehmet Cengiz; Kharratian, Soheila; Faculty Member; PhD Student; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and Engineering; 258783; N/AProtein- and peptide-based manufacturing of self-assembled supramolecular functional materials has been a formidable challenge for biomedical applications, being complex in structure and immunogenic in nature. In this context, self assembly of short amino acid sequences as simplified building blocks to design metal-biomolecule frameworks (MBioFs) is an emerging field of research. Here, we report a facile, bioinspired route of anisotropic nanostructure synthesis using gold binding peptides (10-15mers) secreted by cancer cells. The bioinformatics tool i-TASSER predicts the effect of amino acid sequences on metal binding sites and the secondary structures of the respective peptide sequence. Electron microscopy, X-ray, infrared, and Raman spectroscopy validated the versatile anisotropic gold nanostructures and the metal-bioorganic nature of this biomineralization. We studied the influence of precursor salt, pH, and peptide concentration on the evolution of nanoleaf, nanoflower, nanofiber, and dendrimer-like anisotropic MBioFs. Characterization of photothermal properties using infrared laser (785 nm) revealed excellent conversion of light into heat. Exposure of bacterial cells in culture exhibits high rate of photothermal death using lower laser power (1.9 W/cm(2)) compared with recent reports. The MBioF's self-assembly process shown here can readily be extended and adapted to superior plasmonic material synthesis with a promising photothermal effect for in vivo biofilm destruction and cancer hyperthermia applications.Publication Metadata only Batch fabrication of self-assembled nickel-iron nanowires by electrodeposition(IEEE, 2006) N/A; Department of Electrical and Electronics Engineering; Department of Mechanical Engineering; Şardan, Özlem; Yalçınkaya, Arda Deniz; Alaca, Burhanettin Erdem; Master Student; Researcher; Faculty Member; Department of Electrical and Electronics Engineering; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; 144523; 115108Lack of batch-compatible fabrication techniques can be considered as the most important challenge in the integration of nanostructures with microelectromechanical systems (MEMS). a solution to the micro-nano integration problem is offered by introducing a batch-compatible nanowire fabrication technique based on basic lithographic techniques and guided self-assembly. the basic principle is obtaining cracks at predetermined locations in a sacrificial SiO2 layer on Si and filling these cracks with a suitable metal by electrodeposition. the technique is demonstrated by using Nickel-Iron as the deposition material and verifying the magnetic behavior of resulting nanowires.Publication Metadata only Cantilever array oscillators with nonlinear optical readout(IEEE, 2015) Yaralıoğlu, Gökşen G.; Leblebici, Yusuf; N/A; N/A; Department of Electrical and Electronics Engineering; Lüleç, Sevil Zeynep; Adiyan, Ulaş; Ürey, Hakan; Researcher; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; N/A; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 8579MEMS array oscillators typically require a separate detector and feedback loop for each oscillator. We show that grating-based-optical-readout induces nonlinearity, which enables simultaneous operation of an array-of-oscillators using only one detector and single electronic feedback-loop.