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Permanent URI for this communityhttps://hdl.handle.net/20.500.14288/2
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Publication Metadata only Microcantilever based disposable viscosity sensor for serum and blood plasma measurements(Academic Press Inc Elsevier Science, 2013) N/A; Department of Mechanical Engineering; Department of Mechanical Engineering; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Department of Mechanical Engineering; Department of Chemical and Biological Engineering; Çakmak, Onur; Elbüken, Çağlar; Ermek, Erhan; Mostafazadeh, Aref; Barış, İbrahim; Alaca, Burhanettin Erdem; Kavaklı, İbrahim Halil; Ürey, Hakan; PhD Student; Researcher; Faculty Member; Researcher; Teaching Faculty; Faculty Member; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Department of Mechanical Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; College of Engineering; N/A; N/A; N/A; N/A; 111629; 115108; 40319; 8579This paper proposes a novel method for measuring blood plasma and serum viscosity with a microcantilever-based MEMS sensor. MEMS cantilevers are made of electroplated nickel and actuated remotely with magnetic field using an electro-coil. Real-time monitoring of cantilever resonant frequency is performed remotely using diffraction gratings fabricated at the tip of the dynamic cantilevers. Only few nanometer cantilever deflection is sufficient due to interferometric sensitivity of the readout. The resonant frequency of the cantilever is tracked with a phase lock loop (PLL) control circuit. The viscosities of liquid samples are obtained through the measurement of the cantilever's frequency change with respect to a reference measurement taken within a liquid of known viscosity. We performed measurements with glycerol solutions at different temperatures and validated the repeatability of the system by comparing with a reference commercial viscometer. Experimental results are compared with the theoretical predictions based on Sader's theory and agreed reasonably well. Afterwards viscosities of different Fetal Bovine Serum and Bovine Serum Albumin mixtures are measured both at 23 degrees C and 37 degrees C, body temperature. Finally the viscosities of human blood plasma samples taken from healthy donors are measured. The proposed method is capable of measuring viscosities from 0.86 cP to 3.02 cP, which covers human blood plasma viscosity range, with a resolution better than 0.04 cP. The sample volume requirement is less than 150 mu l and can be reduced significantly with optimized cartridge design. Both the actuation and sensing are carried out remotely, which allows for disposable sensor cartridges. (C) 2013 Published by Elsevier Inc.Publication Metadata only Molecular communication transmitter architectures for the internet of bio-nano things(Institute of Electrical and Electronics Engineers Inc., 2022) Department of Electrical and Electronics Engineering; N/A; Akan, Özgür Barış; Civaş, Meltem; Faculty Member; PhD Student; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and Engineering; 6647; N/AIn this study, we investigate the nanomaterial-based approach for developing practical molecular communication transmitters (MC-Txs) for the Internet of Bio-Nano Things (IoBNT) applications, which are expected to be unconventional in many aspects. In particular, we focus on the most pressing challenges for MC-Tx architectures, namely controlling information molecule release and molecule replenishment, together with other aspects, selective molecule release and molecule leakage mitigation. We discuss promising nanomaterials and also identify potential challenges and research directions.Publication Metadata only Multiscale dynamics of lipid vesicles in polymeric microenvironment(Mdpi, 2022) N/A; N/A; N/A; N/A; N/A; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Karaz, Selcan; Han, Mertcan; Akay, Gizem; Önal, Asım; Nizamoğlu, Sedat; Kızılel, Seda; Şenses, Erkan; Master Student; Master Student; PhD Student; PhD Student; Faculty Member; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Department of Chemical and Biological 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; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; N/A; 130295; 28376; 280298Understanding dynamic and complex interaction of biological membranes with extracellular matrices plays a crucial role in controlling a variety of cell behavior and functions, from cell adhesion and growth to signaling and differentiation. Tremendous interest in tissue engineering has made it possible to design polymeric scaffolds mimicking the topology and mechanical properties of the native extracellular microenvironment; however, A fundamental question remains unanswered: that is, how the viscoelastic extracellular environment modifies the hierarchical dynamics of lipid membranes. in this work, we used aqueous solutions of poly(ethylene glycol) (PEG) with different molecular weights to mimic the viscous medium of cells and nearly monodisperse unilamellar DMPC/DMPG liposomes as a membrane model. Using small-angle X-ray scattering (SaXS), dynamic light scattering, temperature-modulated differential scanning calorimetry, bulk rheology, and fluorescence lifetime spectroscopy, we investigated the structural phase map and multiscale dynamics of the liposome-polymer mixtures. the results suggest an unprecedented dynamic coupling between polymer chains and phospholipid bilayers at different length/time scales. the microviscosity of the lipid bilayers is directly influenced by the relaxation of the whole chain, resulting in accelerated dynamics of lipids within the bilayers in the case of short chains compared to the polymer-free liposome case. at the macroscopic level, the gel-to-fluid transition of the bilayers results in a remarkable thermal-stiffening behavior of polymer-liposome solutions that can be modified by the concentration of the liposomes and the polymer chain length.Publication Metadata only Narrow escape problem in synaptic molecular communications(Association for Computing Machinery, Inc, 2022) Koca, Çağlar; Department of Electrical and Electronics Engineering; N/A; Akan, Özgür Barış; Civaş, Meltem; Faculty Member; PhD Student; Department of Electrical and Electronics Engineering; College of Engineering; Graduate School of Sciences and Engineering; 6647; N/AThe narrow escape problem (NEP) is a well-known problem with many applications in cellular biology. It is especially important to understand synaptic molecular communications. Active regions of synapses, also known as apposition zones, are connected to synaptic cleft through narrow slits, from which neurotransmitters can escape to or return from the cleft into the apposition zones. While neurotransmitters leakage into the cleft might be desired for the reuptake process, escaping neurotransmitters might trigger an undesired, i.e., false-positive or action potential in the post-synaptic terminal. Obtaining analytic solutions to NEPs is very challenging due to its geometry dependency. Slight alterations in either or both shape or the size of the hole and the outer volume may cause drastic changes in the solution. Thus, we need a simulation-based approach to solve NEPs. However, NEP also requires the size of the hole to be much smaller than the dimensions of the volume. Combined with the requirement for Brownian motion, where the step size is much smaller than the dimensions of the volume, simulations can be prohibitively long, even for modern computers. Therefore, in this work, we suggest a simulation algorithm that simultaneously satisfies the NEP and Brownian motion simulation requirements. Our simulation framework can be used to quantify the neurotransmitter leakage within synaptic clefts.Publication Metadata only ProteinAC: a frequency domain technique for analyzing protein dynamics(Iop Publishing Ltd, 2018) N/A; Department of Electrical and Electronics Engineering; Varolgüneş, Yasemin Bozkurt; Demir, Alper; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 3756It is widely believed that the interactions of proteins with ligands and other proteins are determined by their dynamic characteristics as opposed to only static, time-invariant processes. We propose a novel computational technique, called ProteinAC (PAC), that can be used to analyze small scale functional protein motions as well as interactions with ligands directly in the frequency domain. PAC was inspired by a frequency domain analysis technique that is widely used in electronic circuit design, and can be applied to both coarse-grained and all-atom models. It can be considered as a generalization of previously proposed static perturbation-response methods, where the frequency of the perturbation becomes the key. We discuss the precise relationship of PAC to static perturbation-response schemes. We show that the frequency of the perturbation may be an important factor in protein dynamics. Perturbations at different frequencies may result in completely different response behavior while magnitude and direction are kept constant. Furthermore, we introduce several novel frequency dependent metrics that can be computed via PAC in order to characterize response behavior. We present results for the ferric binding protein that demonstrate the potential utility of the proposed techniques.Publication Metadata only Three-dimensional neuron-astrocyte construction on matrigel enhances establishment of functional voltage-gated sodium channels(Wiley-Blackwell, 2021) N/A; N/A; N/A; N/A; Department of Electrical and Electronics Engineering; N/A; N/A; Karahüseyinoğlu, Serçin; Şekerdağ, Emine; Aria, Mohammad Mohammadi; Taş, Yağmur Çetin; Nizamoğlu, Sedat; Solaroğlu, İhsan; Özdemir, Yasemin Gürsoy; Faculty Member; Researcher; PhD Student; Researcher; Faculty Member; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; N/A; Graduate School of Sciences and Engineering; N/A; College of Engineering; School of Medicine; N/A; 110772; N/A; N/A; N/A; 130295; 102059; 170592This study aimed to investigate and compare cell growth manners and functional differences of primary cortical neurons cultured on either poly-d-lysine (PDL) and or Matrigel, to delineate the role of extracellular matrix on providing resemblance to in vivo cellular interactions in nervous tissue. Primary cortical neurons, obtained from embryonic day 15 mice pups, seeded either on PDL- or Matrigel-coated culture ware were investigated by DIC/bright field and fluorescence/confocal microscopy for their morphology, 2D and 3D structure, and distribution patterns. Patch clamp, western blot, and RT-PCR studies were performed to investigate neuronal firing thresholds and sodium channel subtypes Nav1.2 and Nav1.6 expression. Cortical neurons cultured on PDL coating possessed a 2D structure composed of a few numbers of branched and tortuous neurites that contacted with each other in one to one manner, however, neurons on Matrigel coating showed a more complicated dimensional network that depicted tight, linear axonal bundles forming a 3D interacted neuron-astrocyte construction. This difference in growth patterns also showed a significant alteration in neuronal firing threshold which was recorded between 80 < linj > 120 pA on PDL and 2 < linj > 160 pA on Matrigel. Neurons grown up on Matrigel showed increased levels of sodium channel protein expression of Nav1.2 and Nav1.6 compared to neurons on PDL. These results have demonstrated that a 3D interacted neuron-astrocyte construction on Matrigel enhances the development of Nav1.2 and Nav1.6 in vitro and decreases neuronal firing threshold by 40 times compared to conventional PDL, resembling in vivo neuronal networks and hence would be a better in vitro model of adult neurons.