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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 deformation-based approach to tuning of magnetic micromechanical resonators(2018) Yalçınkaya, Arda D.; Department of Mechanical Engineering; N/A; Department of Mechanical Engineering; Biçer, Mahmut; Esfahani, Mohammad Nasr; Alaca, Burhanettin Erdem; Researcher; PhD Student; Faculty Member; Department of Mechanical Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 115108Resonance frequency tuning in magnetic micromechanical resonators remains a primary field of study for frequency reference applications. The use of magnetic micromechanical resonators for innovative timing, oscillator and sensing applications necessitates a platform for the precise control of the resonance frequency. The present work addresses a deformation based technique for tuning the resonance frequency of nickel micromechanical resonators. Frequency response is measured through magnetic actuation and optical readout. The tuning approach is based on a combination of flexural deformation and uniaxial strain. The bending deformation is achieved by using a DC current through the microbeam. This magnetomotive mechanism reduces the resonance frequency by about 13% for a maximum DC current of 80 mA. A substrate bending method is used for applying uniaxial strain to increase the resonance frequency by about 8%. A bidirectional frequency modulation is thus demonstrated by utilizing both deformation techniques. The interpretation of results is carried out by finite element analysis and electromechanical analogy in an equivalent circuit. Using deformation techniques, this study provides a rigorous approach to control the resonance frequency of magnetic micromechanical resonators.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 Aerogel-copper nanocomposites prepared using the adsorption of a polyfluorinated complex from supercritical CO2(Springer, 2012) Kostenko, Svetlana O.; Kurykin, Michael A.; Khrustalev, Victor N.; Khokhlov, Alexei R.; Zhang, Lichun; Aindow, Mark; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Bozbağ, Selmi Erim; Erkey, Can; Researcher; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; College of Engineering; N/A; 29633A supercritical deposition method has been used to synthesize aerogel-copper nanocomposites. Carbon, resorcinol-formaldehyde, and silica aerogels (CAs, RFAs, and SAs) were impregnated with a new polyfluorinated copper precursor (CuDI6), which has a high solubility in supercritical carbon dioxide (scCO(2)). Adsorption isotherms of CuDI6 onto various aerogels from scCO(2) were determined at 35 degrees C and 10.6 MPa using a batch method which is based on the measurement of the fluid phase concentration. The relative affinity between CuDI6 and different aerogels changed in the following order: CA > RFA > SA. The effect of temperature on the adsorption isotherms for the CuDI6-CO2-CA system was also studied at 35 and 55 degrees C and at a CO2 density of 736.1 kg/m(3). The CuDI6 uptake at a particular CuDI6 concentration increased with increasing temperature. Adsorbed CuDI6 was found to convert into Cu and Cu/Cu2O nanoparticles on the aerogel supports after chemical or thermal treatments at ambient pressure and at temperatures ranging from 200 to 400 degrees C.Publication Metadata only Anticancer use of nanoparticles as nucleic acid carriers(Amer Scientific Publishers, 2014) Gozuacik, D.; Akkoc, Y.; Kosar, A.; Dogan-Ekici, A. Isin; Ekici, Sinan; Department of Chemistry; Acar, Havva Funda Yağcı; Faculty Member; Department of Chemistry; College of Sciences; 178902Advances in nanotechnology opened up new horizons in the field of cancer research. Nanoparticles made of various organic and inorganic materials and with different optical, magnetic and physical characteristics have the potential to revolutionize the way we diagnose, treat and follow-up cancers. Importantly, designs that might allow tumor-specific targeting and lesser side effects may be produced. Nanoparticles may be tailored to carry conventional chemotherapeutics or new generation organic drugs. Currently, most of the drugs that are commonly used, are small chemical molecules targeting disease-related enzymes. Recent progress in RNA interference technologies showed that, even proteins that are considered to be "undruggable" by small chemical molecules, might be targeted by small RNAs for the purpose of curing diseases, including cancer. In fact, small RNAs such as siRNAs, shRNAs and miRNAs can drastically change cellular levels of almost any given disease-associated protein or protein group, resulting in a therapeutic effect. Gene therapy attempts were failing mainly due to delivery viral vector-related side effects. Biocompatible, non-toxic and efficient nanoparticle carriers raise new hopes for the gene therapy of cancer. In this review article, we discuss new advances in nucleic acid and especially RNA carrier nanoparticles, and summarize recent progress about their use in cancer therapy.Publication Metadata only Modeling and characterization of comb-actuated resonant microscanners(Iop Publishing Ltd, 2006) 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 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 Monolithic technology for silicon nanowires in high-topography architectures(Elsevier, 2017) Wollschlager, Nicole; Rangelow, Ivo W.; Leblebici, Yusuf; Department of Mechanical Engineering; Esfahani, Mohammad Nasr; Yılmaz, Mustafa Akın; Alaca, Burhanettin Erdem; PhD Student; PhD Student; Faculty Member; Department of Mechanical Engineering; 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; N/A; N/A; 115108Integration of silicon nanowires (Si NWs) in three-dimensional (3D) devices including integrated circuits (ICs) and microelectromechanical systems (MEMS) leads to enhanced functionality and performance in diverse applications. The immediate challenge to the extensive use of Si NWs in modern electronic devices is their integration with the higher-order architecture. Topography-related limits of integrating Si NWs in the third dimension are addressed in this work. Utilizing a well-tuned combination of etching and protection processes, Si NWs are batch-produced in bulk Si with an extreme trench depth of 40 gm, the highest trench depth obtained in a monolithic fashion within the same Si crystal so far. The implications of the technique for the thick silicon-on-insulator (S01) technology are investigated. The process is transferred to SOI wafers yielding Si NWs with a critical dimension of 100 nm along with a trench aspect ratio of 50. Electrical measurements verify the prospect of utilizing such suspended Si NWs spanning deep trenches as versatile active components in ICs and MEMS. Introducing a new monolithic approach to obtaining Si NWs and the surrounding higher-order architecture within the same SOI wafer, this work opens up new possibilities for modem sensors and power efficient ICs. (C) 2017 Elsevier B.V. All rights reserved.Publication Metadata only N(4)sim: the first nervous NaNonetwork simulator with synaptic molecular communications(IEEE-Inst Electrical Electronics Engineers Inc, 2022) Bilgin, Bilgesu A.; N/A; Department of Electrical and Electronics Engineering; Turgut, Nafi Ahmet; Akan, Özgür Barış; Master Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 6647The unconventional nature of molecular communication necessitates contributions from a host of scientific fields making the simulator design for such systems to be quite challenging. The nervous system is one of the largest and most important nanonetworks of the body. Several molecular and nano communication simulators exist in literature along with a few neural network simulators, however, most existing simulators are not specific for the nervous system since they ignore the synaptic diffusion because of the computational complexity required to model it. Additionally, information and communication theoretical (ICT) analysis of the system is not directly supported by existing neural network simulators. In this work, we present and describe Neural NaNoNetwork Simulator, N(4)Sim, which can resolve these issues in existing simulators. We describe key components of the simulator and methods to solve the synaptic communication in a fast and efficient manner. Our model for the synaptic communication channel is comparable in accuracy to those achieved by Monte Carlo simulations while using a fraction of time and processing resources. The presented simulator opens a large set of design options for applications in nervous system.Publication Metadata only Nanoscale plasmonic devices for dynamically controllable beam focusing and scanning(Elsevier, 2010) Çetin, Arif Engin; Department of Physics; Department of Physics; Sennaroğlu, Alphan; Müstecaplıoğlu, Özgür Esat; Faculty Member; Faculty Member; Department of Physics; College of Sciences; College of Sciences; 23851; 1674We have performed simulations to investigate the variable focusing and scanning capability of metallic nano-slit configurations. In a symmetric nanorod configuration inside an aperture with adjustable offset of the center rod, the focal position is found to be variable in the 0.5-3.5 mu m range. In a ladder configuration of the rods, the transmitted beam is found to be deflected up to 23 degrees. Horizontal displacement of rods allows for finer control of angular scanning up to 4 degrees. Such slit geometries offer the potential to be controlled by using nano-positioning systems for applications in dynamic beam shaping and scanning on the nanoscale.Publication Metadata only On heat transfer at microscale with implications for microactuator design(Iop Publishing Ltd, 2009) Yalçınkaya, Arda D.; Zervas, Michalis; Leblebici, Yusuf; N/A; Department of Mechanical Engineering; N/A; Özsun, Özgür; Alaca, Burhanettin Erdem; Yılmaz, Mehmet; Master Student; Faculty Member; Master Student; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; N/A; 115108; N/AThe dominance of conduction and the negligible effect of gravity, and hence free convection, are verified in the case of microscale heat sources surrounded by air at atmospheric pressure. A list of temperature-dependent heat transfer coefficients is provided. In contrast to previous approaches based on free convection, supplied coefficients converge with increasing temperature. Instead of creating a new external function for the definition of boundary conditions via conductive heat transfer, convective thin film coefficients already embedded in commercial finite element software are utilized under a constant heat flux condition. This facilitates direct implementation of coefficients, i. e. the list supplied in this work can directly be plugged into commercial software. Finally, the following four-step methodology is proposed for modeling: (i) determination of the thermal time constant of a specific microactuator, (ii) determination of the boundary layer size corresponding to this time constant, (iii) extraction of the appropriate heat transfer coefficients from a list provided and (iv) application of these coefficients as boundary conditions in thermomechanical finite element simulations. An experimental procedure is established for the determination of the thermal time constant, the first step of the proposed methodology. Based on conduction, the proposed method provides a physically sound solution to heat transfer issues encountered in the modeling of thermal microactuators.