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Department: search.filters.department.Department of Electrical and Electronics EngineeringSubject: search.filters.subject.Molecular biology

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    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; 8579
    This 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.
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    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; 280298
    Understanding 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.
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    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; 3756
    It 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.