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Publication Metadata only A magnetically actuated resonant mass sensor with integrated optical readout(Ieee-Inst Electrical Electronics Engineers Inc, 2008) N/A; N/A; Department of Electrical and Electronics Engineering; N/A; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; Öztürk, Alibey; Ocaklı, Hüseyin İlker; Özber, Natali; Ürey, Hakan; Kavaklı, İbrahim Halil; Alaca, Burhanettin Erdem; Master Student; Researcher; Master Student; Faculty Member; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; 8579; 40319; 115108Nickel cantilevers with integrated diffraction gratings are used as resonant mass sensors with a resolution of 500 femtograms. Their applicability to biosensing is demonstrated with human opioid receptors. The device is fabricated through a single-mask lithographic process. The microoptical readout provides a simple measurement platform with one external photodiode. Thanks to its ac operation principle, the device is immune to environmental noise and entails a high tolerance to fabrication defects. Obtained signal-to-noise ratio is comparable to that of a high-end Doppler vibrometer. The device with these aspects for systems integration and microarray technology is a candidate for low-cost portable sensors.Publication Metadata only Advances in constraint theories of rubber-like elasticity of polymers(Pergamon-Elsevier Science Ltd, 2010) Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997Advances in the constraint theories of rubber elasticity during the past few years, based on the constrained junction, tube, and slip-link models, are cited and discussed. (C) 2009 Elsevier Ltd. All rights reserved.Publication Metadata only Aerogels for optofluidic waveguides(MDPI, 2017) Jonas, Alexandr; N/A; Department of Physics; Department of Chemical and Biological Engineering; Özbakır, Yaprak; Erkey, Can; Kiraz, Alper; PhD Student; Faculty Member; Faculty Member; Department of Physics; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; N/A; 29633; 22542Aerogels-solid materials keeping their internal structure of interconnected submicron-sized pores intact upon exchanging the pore liquid with a gas-were first synthesized in 1932 by Samuel Kistler. Overall, an aerogel is a special form of a highly porous material with a very low solid density and it is composed of individual nano-sized particles or fibers that are connected to form a three-dimensional network. The unique properties of these materials, such as open pores and high surface areas, are attributed to their high porosity and irregular solid structure, which can be tuned through proper selection of the preparation conditions. Moreover, their low refractive index makes them a remarkable solid-cladding material for developing liquid-core optofluidic waveguides based on total internal reflection of light. This paper is a comprehensive review of the literature on the use of aerogels for optofluidic waveguide applications. First, an overview of different types of aerogels and their physicochemical properties is presented. Subsequently, possible techniques to fabricate channels in aerogel monoliths are discussed and methods to make the channel surfaces hydrophobic are described in detail. Studies in the literature on the characterization of light propagation in liquid-filled channels within aerogel monoliths as well as their light-guiding characteristics are discussed. Finally, possible applications of aerogel-based optofluidic waveguides are described.Publication Open Access Dielectric response and tunability of a dielectric-paraelectric composite(American Institute of Physics (AIP) Publishing, 2008) Zhou, K.; Boggs, S. A.; Ramprasad, R.; Aindow, M.; Alpay, S. P.; Department of Chemical and Biological Engineering; Erkey, Can; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 29633A theoretical study was carried out to determine the dielectric response and tunability of a composite consisting of a linear, low-loss dielectric matrix with uniformly sized, randomly distributed paraelectric Ba0.60Sr0.40TiO3 (BST 60/40) particles as functions of the volume fraction and size of the particles. The field dependence of the polarization and the dielectric response of the inclusions are specified through a nonlinear thermodynamic model and then incorporated into a two-dimensional finite element analysis. Near the percolation threshold for BST particles (similar to 27% to 45% depending on the particle size), high dielectric tunabilities with a lower effective permittivity than monolithic BST can be realized. (C) 2008 American Institute of Physics. American Institute of Physics.Publication Metadata only Enhancing biocompatibility of NiTi shape memory alloys by simple NH3 treatments(Elsevier, 2020) N/A; N/A; N/A; Department of Chemical and Biological Engineering; Department of Chemistry; Department of Mechanical Engineering; Öztulum, Samira Fatma Kurtoğlu; Yağcı, Mustafa Barış; Uzun, Alper; Ünal, Uğur; Canadinç, Demircan; PhD Student; Researcher; Faculty Member; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Chemistry; Department of Mechanical Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; N/A; College of Engineering; College of Sciences; College of Engineering; 384798; N/A; 59917; 42079; 23433This paper presents the treatment of NiTi shape memory alloys (SMAs) in flowing ammonia at 700 degrees C as a simple and cost-effective nitriding process to provide a protective surface layer hindering Ni ion release in biological environments. Experimental results demonstrated that a smooth protective TiN layer on the NiTi SMAs along with TiOxNy and TiO2 formed on the surface upon treating the as-received NiTi SMA in ammonia at 700 degrees C. The protective TiN layer and the smooth surface hinder the amount of Ni ion release to artificial saliva (AS) after 28 days of immersion, while the dry air treatment at similar conditions results in a significantly rough surface, leading to about 20 times higher Ni ion release. Overall, the findings presented herein demonstrate that NH3 nitriding is an effective method to eliminate the Ni presence from the surface and to obtain a smooth final surface, which, in turn, restricts the Ni ion release from the NiTi SMA into AS. Consequently, nitriding the surface of NiTi under NH3 at 700 degrees C turned out as a promising method to lower Ni ion release and thereby contribute to the biocompatibility of NiTi SMAs, which, however; needs to be further validated through further experimentation.Publication Open Access Optimum folding pathways of proteins: their determination and properties(American Institute of Physics (AIP) Publishing, 2006) Department of Chemical and Biological Engineering; Güner, Pınar Tatar; Arkun, Yaman; Erman, Burak; Teaching Faculty; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 188227; 108526; 179997We develop a dynamic optimization technique for determining optimum folding pathways of proteins starting from different initial configurations. A coarse-grained Go model is used. Forces acting on each bead are (i) the friction force, (ii) forces from bond length constraints, (iii) excluded volume constraints, and (iv) attractive forces between residue pairs that are in contact in the native state. An objective function is defined as the total attractive energy between nonbonded residues, which are neighbors in the native state. The objective function is minimized over all feasible paths, satisfying bond length and excluded volume constraints. The optimization problem is nonconvex and contains a large number of constraints. An augmented Lagrangian method with a penalty barrier function was used to solve the problem. The method is applied to a 36-residue protein, chicken villin headpiece. Sequences of events during folding of the protein are determined for various pathways and analyzed. The relative time scales are compared and scaled according to experimentally measured events. Formation times of the helices, turn, and the loop agree with experimental data. We obtain the overall folding time of the protein in the range of 600 ns-1.2 mu s that is smaller than the experimental result of 4-5 mu s, showing that the optimal folding times that we obtain may be possible lower bounds. Time dependent variables during folding and energies associated with short- and long-range interactions between secondary structures are analyzed in modal space using Karhunen-Loeve expansion.Publication Open Access Optofluidic waveguides written in hydrophobic silica aerogels with a femtosecond laser(Society of Photo-optical Instrumentation Engineers (SPIE), 2015) Yalızay, B.; Morova, Y.; Jonas, A.; Aktürk, S.; Department of Physics; Department of Chemical and Biological Engineering; Kiraz, Alper; Erkey, Can; Özbakır, Yaprak; Faculty Member; Faculty Member; Department of Physics; Department of Chemical and Biological Engineering; College of Sciences; 22542; 29633; N/AWe present a new method to form liquid-core optofluidic waveguides inside hydrophobic silica aerogels. Due to their unique material properties, aerogels are very attractive for a wide variety of applications; however, it is very challenging to process them with traditional methods such as milling, drilling, or cutting because of their fragile structure. Therefore, there is a need to develop alternative processes for formation of complex structures within the aerogels without damaging the material. In our study, we used focused femtosecond laser pulses for high-precision ablation of hydrophobic silica aerogels. During the ablation, we directed the laser beam with a galvo-mirror system and, subsequently, focused the beam through a scanning lens on the surface of bulk aerogel which was placed on a three-axis translation stage. We succeeded in obtaining high-quality linear microchannels inside aerogel monoliths by synchronizing the motion of the galvo-mirror scanner and the translation stage. Upon ablation, we created multimode liquid-core optical waveguides by filling the empty channels inside low-refractive index aerogel blocks with high-refractive index ethylene glycol. In order to demonstrate light guiding and measure optical attenuation of these waveguides, we coupled light into the waveguides with an optical fiber and measured the intensity of transmitted light as a function of the propagation distance inside the channel. The measured propagation losses of 9.9 dB/cm demonstrate the potential of aerogel-based waveguides for efficient routing of light in optofluidic lightwave circuits.Publication Open Access Statistical thermodynamics of residue fluctuations in native proteins(American Institute of Physics (AIP) Publishing, 2009) Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Yoğurtçu, Osman Nuri; Gür, Mert; Erman, Burak; PhD Student; Faculty Member; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; College of Engineering; N/A; N/A; 179997Statistical thermodynamics of residue fluctuations of native proteins in a temperature, pressure, and force reservoir is formulated. The general theory is discussed in terms of harmonic and anharmonic fluctuations of residues. The two elastic network models based on the harmonic approximation, the anisotropic network and the Gaussian network models are discussed as the limiting cases of the general theory. The heat capacity and the correlations between the energy fluctuations and residue fluctuations are obtained for the harmonic approximation. The formulation is extended to large fluctuations of residues in order to account for effects of anharmonicity. The fluctuation probability function is constructed for this purpose as a tensorial Hermite series expansion with higher order moments of fluctuations as coefficients. Evaluation of the higher order moments using the proposed statistical thermodynamics model is explained. The formulation is applied to a hexapeptide and the fluctuations of residues obtained by molecular dynamics simulations are characterized in the framework of the model developed. In particular, coupling of two different modes in the nonlinear model is discussed in detail.