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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 Open Access A multi-state coarse grained modeling approach for an intrinsically disordered peptide(American Institute of Physics (AIP) Publishing, 2017) Department of Chemical and Biological Engineering; N/A; Sayar, Mehmet; Dalgıçdır, Cahit; Ramezanghorbani, Farhad; Faculty Member; PhD Student; Department of Chemical and Biological Engineering; College of Engineering; Graduate School of Sciences and Engineering; 109820; N/A; N/AMany proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LK alpha 14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LK alpha 14 is disordered in dilute solutions; however, it strictly adopts the alpha-helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an alpha-helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results.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 An integrated computational-experimental hierarchical approach for the rational design of an IL/UiO-66 composite offering infinite CO2 selectivity(Wiley, 2022) Department of Chemical and Biological Engineering; Department of Chemistry; Zeeshan, Muhammad; Gülbalkan, Hasan Can; Durak, Özce; Haşlak, Zeynep Pınar; Ünal, Uğur; Keskin, Seda; Uzun, Alper; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Chemistry; 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); College of Engineering; College of Sciences; Graduate School of Sciences and Engineering; N/A; N/A; N/A; N/A; 42079; 40548; 59917Owing to the possibility of generating theoretically unlimited numbers of ionic liquid (IL)-metal-organic framework (MOF) combinations, experimental studies on IL/MOF composites for gas separation applications are mostly conducted on a trial-and-error basis. To address this problem, an integrated computational-experimental hierarchical approach is presented for selecting the best IL-MOF combination for a target gas separation application. For this purpose, UiO-66 and pyrrolidinium-based ILs are chosen as the parent MOF and IL family, respectively, and three powerful computational tools, Conductor-like Screening Model for Realistic Solvents calculations, density functional theory calculations, and grand canonical Monte Carlo simulations, are integrated to identify the most promising IL-UiO-66 combination as 1-n-butyl-1-methylpyrrolidinium dicyanamide/UiO-66, [BMPyrr][DCA]/UiO-66. Then, this composite is synthesized, characterized in deep detail, and tested for CO2/N-2, CO2/CH4, and CH4/N-2 separations. Results demonstrate that [BMPyrr][DCA]/UiO-66 offers an extraordinary gas separation performance, with practically infinite CO2 and CH4 selectivities over N-2 at 15 degrees C and at low pressures. The integrated hierarchical approach proposed in this work paves the way for the rational design and development of novel IL/MOF composites offering exceptional performance for any desired gas separation application.Publication Open Access Band alignment engineers faradaic and capacitive photostimulation of neurons without surface modification(American Physical Society (APS), 2019) Department of Electrical and Electronics Engineering; N/A; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Srivastava, Shashi Bhushan; Melikov, Rustamzhon; Aria, Mohammad Mohammadi; Dikbaş, Uğur Meriç; Kavaklı, İbrahim Halil; Nizamoğlu, Sedat; Researcher; PhD Student; Master Student; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; College of Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; N/A; 40319; 130295Photovoltaic substrates have attracted significant attention for neural photostimulation. The control of the Faradaic and capacitive (non-Faradaic) charge transfer mechanisms by these substrates are critical for safe and effective neural photostimulation. We demonstrate that the intermediate layer can directly control the strength of the capacitive and Faradaic processes under physiological conditions. To resolve the Faradaic and capacitive stimulations, we enhance photogenerated charge density levels by incorporating PbS quantum dots into a poly(3-hexylthiophene-2,5-diyl):([6,6]-Phenyl-C61-butyric acid methyl ester (P3HT:PCBM) blend. This enhancement stems from the simultaneous increase of absorption, well matched band alignment of PbS quantum dots with P3HT:PCBM, and smaller intermixed phase-separated domains with better homogeneity and roughness of the blend. These improvements lead to the photostimulation of neurons at a low light intensity level of 1 mW cm(-2), which is within the retinal irradiance level. These findings open up an alternative approach toward superior neural prosthesis.Publication Open Access Biocompatible quantum funnels for neural photostimulation(American Chemical Society (ACS), 2019) N/A; Department of Chemical and Biological Engineering; N/A; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; N/A; Jalali, Houman Bahmani; Doğru-Yüksel, Itır Bakış; Eren, Güncem Özgün; Nizamoğlu, Sedat; Karatüm, Onuralp; Melikov, Rustamzhon; Dikbaş, Uğur Meriç; Kavaklı, İbrahim Halil; Sadeghi, Sadra; Yıldız, Erdost; Ergün, Çağla; Şahin, Afsun; PhD Student; Faculty Member; PhD Student; Master Student; Faculty Member; PhD Student; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; School of Medicine; N/A; N/A; N/A; 130295; N/A; N/A; N/A; 40319; N/A; N/A; N/A; 171267Neural photostimulation has high potential to understand the working principles of complex neural networks and develop novel therapeutic methods for neurological disorders. A key issue in the light-induced cell stimulation is the efficient conversion of light to bioelectrical stimuli. In photosynthetic systems developed in millions of years by nature, the absorbed energy by the photoabsorbers is transported via nonradiative energy transfer to the reaction centers. Inspired by these systems, neural interfaces based on biocompatible quantum funnels are developed that direct the photogenerated charge carriers toward the bionanojunction for effective photostimulation. Funnels are constructed with indium-based rainbow quantum dots that are assembled in a graded energy profile. Implementation of a quantum funnel enhances the generated photoelectrochemical current 215% per unit absorbance in comparison with ungraded energy profile in a wireless and free-standing mode and facilitates optical neuromodulation of a single cell. This study indicates that the control of charge transport at nanoscale can lead to unconventional and effective neural interfaces.Publication Open Access Bulk-heterojunction photocapacitors with high open-circuit voltage for low light intensity photostimulation of neurons(Royal Society of Chemistry (RSC), 2021) Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; N/A; Department of Chemical and Biological Engineering; N/A; Srivastava, Shashi Bhushan; Melikov, Rustamzhon; Yıldız, Erdost; Dikbaş, Uğur Meriç; Sadeghi, Sadra; Kavaklı, İbrahim Halil; Şahin, Afsun; Nizamoğlu, Sedat; Researcher; PhD Student; PhD Student; Master Student; PhD Student; Faculty Member; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; School of Medicine; N/A; N/A; N/A; N/A; N/A; 40319; 171267; 130295High-level transduction control of light to bioelectricity is an important goal for the realization of superior neuron-device interfaces that can be used for regulating fundamental cellular processes to cure neurological disorders. In this study, a single-junction, wireless, and capacitive-charge-injecting optoelectronic biointerface with negligible faradaic reactions by using a high open-circuit voltage (0.75 V) bulk heterojunction of PTB7-Th:PC71BM is designed and demonstrated. The biointerface generates a 2-fold higher photocurrent in comparison with P3HT:PC61BM having an open-circuit voltage of 0.55 V. Furthermore, we observed that light intensity is logarithmically correlated with the open-circuit voltage of solar cells, and the photovoltage of the biointerfaces varies the switching speed of capacitive charge-transfer. Finally, pulse trains of capacitive stimuli at a low light intensity of 20 mW cm−2elicit action potential generation in primary hippocampal neurons extracted from E15-E17 Wistar Albino rats. These findings show the great promise of high open-circuit voltage bulk heterojunction biointerfaces for non-genetic, all-optical and safe modulation of neurons.Publication Open Access Calculating the local solvent chemical potential in crystal hydrates(American Physical Society (APS), 2000) Mezei, M.; Department of Chemical and Biological Engineering; Reşat, Haluk; Faculty Member; Department of Chemical and Biological Engineering; College of EngineeringDetermining solvation patterns in biological systems is crucial in investigating the functional role water may play in structural stabilization and molecular recognition. Determining whether a particular position would be occupied by a solvent molecule requires the local thermodynamics to be known. In this work we introduce a simple and inexpensive approach based on grand canonical molecular simulations to determine the occupancy factors of the cavities. The method is applied to the test case of the sodium salt of hyaluronic acid. The results agree very well with experimental results and demonstrate the success of the method.Publication Metadata only Computational screening of ZIFs for CO2 separations(Taylor & Francis Ltd, 2015) N/A; N/A; Department of Chemical and Biological Engineering; Yılmaz, Gamze; Özcan, Aydın; Keskin, Seda; Master Student; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 40548Using molecular simulations, we studied a diverse collection of zeolite-imidazolate frameworks (ZIFs) to evaluate their performances in adsorption- and membrane-based gas separations. Molecular simulations were performed for both single-component gases (CH4, CO2, H-2 and N-2) and binary gas mixtures (CO2/CH4, CO2/N-2, CO2/H-2 and CH4/H-2) to predict the intrinsic and mixture selectivities of ZIFs. These two selectivities were compared to discuss the importance of multi-component mixture effects on making predictions about the separation performance of a material. Gas separation performances of ZIFs were compared with other nanoporous materials and our results showed that several ZIFs can outperform well-known zeolites and metal-organic frameworks in CO2 separations. Several other properties of ZIFs such as gas permeability, working capacity and sorbent selection parameter were computed to identify the most promising materials in adsorption- and membrane-based separation of CO2/CH4, CO2/N-2, CO2/H-2 and CH4/H-2.