Publications without Fulltext
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
Browse
20 results
Search Results
Publication Metadata only Modeling and characterization of comb-actuated resonant microscanners(Iop Publishing Ltd, 2006) N/A; Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Ataman, Çağlar; Ürey, Hakan; PhD Student; Faculty Member; 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 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; Department of Electrical and Electronics Engineering; Ramezani, Hamideh; Akan, Özgür Barış; PhD Student; Faculty Member; 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 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; Department of Mechanical Engineering; Özsun, Özgür; Alaca, Burhanettin Erdem; Yılmaz, Mehmet; Master Student; Faculty Member; Master Student; 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.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; Department of Chemistry; Acar, Havva Funda Yağcı; Faculty Member; 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 Passive sorting of emulsion droplets with different interfacial properties using laser-patterned surfaces(Springer Heidelberg, 2019) Erten, Ahmet; Jonas, Alexandr; N/A; Department of Physics; Department of Mechanical Engineering; Department of Physics; Department of Mechanical Engineering; Department of Physics; Rashid, Muhammed Zeeshan; Morova, Berna; Muradoğlu, Metin; Kiraz, Alper; PhD Student; Researcher; Faculty Member; Faculty Member; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; College of Sciences; N/A; 152935; 22542We demonstrate passive sorting of emulsion microdroplets based on differences in their interfacial tension and contact angle. The sorted droplets are flowing inside a microfluidic channel featuring a shallow guiding track (depth similar to 0.6 mu m) defined by femtosecond laser micromachining in polydimethylsiloxane coating deposited on glass. Under these flow conditions, the droplets experience a confinement force that pulls them into the track; this force depends on the interfacial tension and the difference between the contact angles inside and outside the ablated track. The interplay between the confinement force, fluid drag, and wall friction then determines the trajectory of the droplet along the guiding track. We investigate experimentally the droplet trajectory as a function of droplet velocity and angle between the track and the channel axis and demonstrate precise control of droplet direction by adjusting the track angle. Moreover, we show that droplets of liquids with different interfacial tensions and contact angles travel different distances along the guiding track at a constant flow rate, which can be used for droplet sorting. We develop a theoretical model that incorporates the droplet position with respect to the ablated track, interfacial tension, and contact angles to predict the droplet trajectory under given experimental conditions. Thus, the dynamic behavior of the droplets leading to different guiding scenarios can be studied without the need of computationally expensive fluid dynamics simulations. The presented study paves the way for designing and optimizing new systems for advanced manipulation of droplets of different content using potentially reconfigurable guiding tracks.Publication Metadata only Sum rate of MISO neuro-spike communication channel with constant spiking threshold(IEEE-Inst Electrical Electronics Engineers Inc, 2018) N/A; N/A; N/A; Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Ramezani, Hamideh; Khan, Tooba; Akan, Özgür Barış; PhD Student; PhD Student; Faculty Member; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 6647Communication among neurons, known as neuro-spike communication, is the most promising technique for realization of a bio-inspired nanoscale communication paradigm to achieve biocompatible nanonetworks. In neuro-spike communication, the information, encoded into spike trains, is communicated to various brain regions through neuronal network. An output neuron needs to receive signal from multiple input neurons to generate a spike. Hence, in this paper, we aim to quantify the information transmitted through the multiple-input single-output (MISO) neuro-spike communication channel by considering models for axonal propagation, synaptic transmission, and spike generation. Moreover, the spike generation and propagation in each neuron requires opening and closing of numerous ionic channels on the cell membrane, which consumes considerable amount of ATP molecules called metabolic energy. Thus, we evaluate how applying a constraint on available metabolic energy affects the maximum achievable mutual information of this system. To this aim, we derive a closed form equation for the sum rate of the MISO neuro-spike communication channel and analyze it under the metabolic cost constraints. Finally, we discuss the impacts of changes in number of pre-synaptic neurons on the achievable rate and quantify the tradeoff between maximum achievable sum rate and the consumed metabolic energy.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; Department of Mechanical Engineering; Biçer, Mahmut; Esfahani, Mohammad Nasr; Alaca, Burhanettin Erdem; Researcher; PhD Student; Faculty Member; 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 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; Department of Electrical and Electronics Engineering; Turgut, Nafi Ahmet; Akan, Özgür Barış; Master Student; Faculty Member; 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 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; Department of Electrical and Electronics Engineering; Ataman, Çağlar; Ürey, Hakan; PhD Student; Faculty Member; 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 Rate of information flow across layered neuro-spike network in the spinal cord(IEEE-Inst Electrical Electronics Engineers Inc, 2020) N/A; Department of Electrical and Electronics Engineering; Department of Electrical and Electronics Engineering; Civaş, Meltem; Akan, Özgür Barış; PhD Student; Faculty Member; Graduate School of Sciences and Engineering; College of Engineering; N/A; 6647Spinal Cord Injury (SCI) is a severe condition that can result in loss of motor and sensory functions by disrupting communication among neurons, i.e., neuro-spike communication. Future information and communication technology (ICT) based treatment techniques for SCI are expected to rely on nano networks, deployed inside the body. In this respect, modeling neuro-spike communication channels in the spinal cord and revealing the relationship between channel metrics and SCI are required to realize these treatment techniques and diagnosis tools such as replacement neural implants, high-performance diagnosis tools, which are based on ICT metrics instead of large medical data. Therefore, in this study, we focus on a spinal cord network, namely the descending spinal cord pathway, which is responsible for the transmission of brain motor signals to the spinal cord. We aim to analyze the rate of motor information flow to the corresponding muscle. To this end, we model the spinal cord motor network as a layered network consisting of a cascade of two independent neuro-spike channels, which are brain-spinal cord network and spinal cord interneuron-spinal cord motoneuron network. We derive upper and lower bounds for the total rate across the brain-spinal cord network and interneuron-spinal cord network. Our evaluations demonstrate that the total rate in the case of upper motor neuron syndrome (UMNS), which manifests itself with muscle weakness, approaches zero, where the brain-spinal cord network becomes a bottleneck. In lower motor neuron syndrome (LMNS), which results in muscle atrophy, the total rate again approaches zero with the loss of spinal cord motoneurons (MN).