Researcher:
Kiraz, Alper

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Alper

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Now showing 1 - 10 of 144
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    Motion of single terrylene molecules in confined channels of poly(butadiene)-poly(ethylene oxide) diblock copolymer
    (Amer Chemical Soc, 2009) N/A; Department of Physics; Department of Chemistry; Yorulmaz, Mustafa; Kiraz, Alper; Demirel, Adem Levent; Master Student; Faculty Member; Faculty Member; Department of Physics; Department of Chemistry; Graduate School of Sciences and Engineering; College of Sciences; College of Sciences; N/A; 22542; 6568
    The motion of terrylene probe molecules in confined PB channels of an asymmetric PB-PEO diblock copolymer has been investigated by single molecule tracking. The one-dimensional diffusion coefficients were found to be significantly smaller and had a narrower distribution compared to two-dimensional diffusion coefficients in PB. The trajectories of some single molecules showed unusual behavior of directed motion where mean square displacement had a parabolic dependence oil lag time. The likely origin of this behavior is discussed in terms of local variations in the PB channel width and the resulting change in the local density. The results show the effect of nonuniformities and heterogeneities in the channels on the motion of single molecules and demonstrate the sensitivity of single molecule tracking in characterizing self-assembled block copolymer morphologies.
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    FRET lasing from self-assembled DNA tetrahedral nanostructures suspended in optofluidic droplet resonators
    (Springer, 2014) Jonas, A.; Liu, H.; Fan, C.; Chen, Q.; Fan, X.; Department of Physics; N/A; N/A; Kiraz, Alper; Özelci, Ersan; Aas, Mehdi; Faculty Member; PhD Student; PhD Student; Department of Physics; College of Sciences; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; 22542; N/A; N/A
    We demonstrate Förster resonance energy transfer (FRET) lasing from self-assembled tetrahedral DNA complexes labeled with Cy3 and Cy5 dyes and suspended as a gain medium in aqueous microdroplet cavities deposited on a superhydrophobic surface. Threshold fluence and differential efficiency are characterized for DNA complexes containing 1Cy3-3Cy5 and 3Cy3-1Cy5. We demonstrate that at a constant Cy5 concentration, average threshold fluence is reduced 3 to 8 times and average differential efficiency is enhanced 6 to 30 times for 3Cy3-1Cy5 as compared to 1Cy3-3Cy5. Using 3Cy3-1Cy5 nanostructures, FRET lasing is observed at very low concentrations down to ∼ 1 μM. This work shows that optofluidic microlasers based on droplet resonators can be combined with DNA nanotechnology to explore applications in bio/chemical sensing and novel photonic devices.
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    Reversible switching of wetting properties and erasable patterning of polymer surfaces using plasma oxidation and thermal treatment
    (Elsevier Science Bv, 2018) Soydan, Seren; Jonas, Alexander; N/A; Department of Chemistry; N/A; Department of Chemistry; Department of Physics; Department of Chemistry; Rashid, Muhammed Zeeshan; Atay, İpek; Yağcı, Mustafa Barış; Yılgör, Emel; Kiraz, Alper; Yılgör, İskender; PhD Student; Post Doctorate Student; Researcher; Researcher; Faculty Member; Faculty Member; Department of Physics; Department of Chemistry; 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 Sciences; College of Sciences; College of Sciences; College of Sciences; N/A; N/A; N/A; N/A; 40527; 22542; 24181
    Polymer surfaces reversibly switchable from superhydrophobic to superhydrophilic by exposure to oxygen plasma and subsequent thermal treatment are demonstrated. Two inherently different polymers, hydrophobic segmented polydimethylsiloxane-urea copolymer (TPSC) and hydrophilic poly(methyl methacrylate) (PMMA) are modified with fumed silica nanoparticles to prepare superhydrophobic surfaces with roughness on nanometer to micrometer scale. Smooth TPSC and PMMA surfaces are also used as control samples. Regardless of their chemical structure and surface topography, all surfaces display completely reversible wetting behavior changing from hydrophobic to hydrophilic and back for many cycles upon plasma oxidation followed by thermal annealing. Influence of plasma power, plasma exposure time, annealing temperature and annealing time on the wetting behavior of polymeric surfaces are investigated. Surface compositions, textures and topographies are characterized by X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and white light interferometry (WLI), before and after oxidation and thermal annealing. Wetting properties of the surfaces are determined by measuring their static, advancing and receding water contact angle. We conclude that the chemical structure and surface topography of the polymers play a relatively minor role in reversible wetting behavior, where the essential factors are surface oxidation and migration of polymer molecules to the surface upon thermal annealing. Reconfigurable water channels on polymer surfaces are produced by plasma treatment using a mask and thermal annealing cycles. Such patterned reconfigurable hydrophilic regions can find use in surface microfluidics and optofluidics applications. (C) 2018 Elsevier B.V. All rights reserved.
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    Versatile liquid-core optofluidic waveguides fabricated in hydrophobic silica aerogels by femtosecond-laser ablation
    (Elsevier, 2015) Yalizay, Berna; Morova, Yagiz; Dincer, Koray; Jonas, Alexandr; Akturk, Selcuk; N/A; Department of Chemical and Biological Engineering; Department of Physics; Özbakır, Yaprak; Erkey, Can; Kiraz, Alper; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Physics; Graduate School of Sciences and Engineering; College of Engineering; College of Science; N/A; 29633; 22542
    We report on the fabrication and characterization of versatile light waveguides exploiting filaments of a polar liquid confined within hydrophobic silica aerogels. Aerogels are highly porous materials with extremely low refractive index which makes them suitable as rigid cladding of liquid-core optofluidic waveguides based on total internal reflection of light. In this article, we introduce a new microfabrication technique that allows direct and precise processing of monolithic silica aerogels by ablation with femtosecond laser pulses. Using fast scanning of the focused laser ablation beam synchronized with the motion of the processed aerogel sample, we created high-quality straight microchannels of similar to 5 mm length with controlled cross-sections inside monolithic aerogels. After the ablation, we filled the channels with high-refractive index ethylene glycol, forming multimode liquid core - solid cladding optofluidic waveguides. Subsequently, we carried out light-guiding experiments to measure overall optical attenuation of these waveguides. The characterization of waveguide transmission yielded values of propagation losses lower than 10 dB cm(-1), demonstrating that the liquid-core waveguides with laser-ablated aerogel cladding represent an attractive alternative in optofluidic applications targeting controlled routing of light along arbitrary three-dimensional paths.
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    A micropillar-based microfluidic viscometer for newtonian and non-newtonian fluids
    (Elsevier, 2020) Tanyeri, Melikhan; Erten, Ahmet; Department of Physics; N/A; N/A; N/A; N/A; Kiraz, Alper; Yalçın, Özlem; Mustafa, Adil; Aksu, Ali Cenk; Eser, Ayşenur; Faculty Member; Faculty Member; PHD Student; PHD Student; Master Student; Department of Physics; College of Sciences; School of Medicine; Graduate School of Sciences and Engineering; School of Medicine; Graduate School of Sciences and Engineering; 22542; 218440; N/A; N/A; N/A
    In this study, a novel viscosity measurement technique based on measuring the deflection of flexible (poly) dimethylsiloxane (PDMS) micropillars is presented. The experimental results show a nonlinear relationship between fluid viscosity and the deflection of micropillars due to viscoelastic properties of PDMS. A calibration curve, demonstrating this nonlinear relationship, is generated, and used to determine the viscosity of an unknown fluid. Using our method, viscosity measurements for Newtonian fluids (glycerol/water solutions) can be performed within 2-100 cP at shear rates gamma = 60.5-398.4 s(-1). We also measured viscosity of human whole blood samples (non-Newtonian fluid) yielding 2.7-5.1 cP at shear rates gamma = 120-345.1 s(-1), which compares well with measurements using conventional rotational vis-cometers (3.6-5.7 cP). With a sensitivity better than 0.5 cP, this method has the potential to be used as a portable microfluidic viscometer for real-time rheological studies. (C) 2020 Elsevier B.V. All rights reserved.
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    Total internal reflection-based optofluidic waveguides fabricated in aerogels
    (Springer, 2017) Jona, Alexandr; Department of Physics; Department of Chemical and Biological Engineering; N/A; Kiraz, Alper; Erkey, Can; Özbakır, Yaprak; Faculty Member; Faculty Member; PhD Student; Department of Physics; Department of Chemical and Biological Engineering; College of Sciences; College of Engineering; Graduate School of Sciences and Engineering; 22542; 29633; N/A
    Liquid-core optofluidic waveguides based on total internal reflection of light were built in water-filled cylindrical microchannels fabricated in hydrophobic silica aerogels. Silica aerogels with densities ranging from 0.15 to 0.39 g/cm(3) were produced by aging of alcogels in tetraethylorthosilicate solution for various time periods, followed by supercritical extraction of the solvent from the alcogel network. Subsequently, the resulting hydrophilic aerogel samples were made hydrophobic by hexamethyldisilazane vapor treatment. The synthesized samples retained their low refractive index (below similar to 1.09) and, hence, they could serve as suitable optical cladding materials for aqueous waveguide cores (refractive index n(core) = 1.33). Hydrophobic silica aerogel samples produced by the above technique also had low absorption coefficients in the visible part of the spectrum. Fabrication of microchannels in aerogel blocks by manual drilling preserving nanoporous and monolithic structure of aerogels was demonstrated for the first time. Long channels (up to similar to 7.5 cm) with varying geometries such as straight and inclined L-shaped channels could be fabricated. Multimode optofluidic waveguides prepared by filling the channels in the drilled aerogel monoliths with water yielded high numerical aperture values (similar to 0.8). Efficient guiding of light by total internal reflection in the water-filled channels in aerogels was visually revealed and characterized by monitoring the channel output. The presented technique is expected to open up further possibilities for creating three-dimensional networks of liquid channels in aerogels for optofluidic applications.
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    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; Rashid, Muhammed Zeeshan; Morova, Berna; Muradoğlu, Metin; Kiraz, Alper; PhD Student; Researcher; Faculty Member; Faculty Member; Department of Mechanical Engineering; Department of Physics; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; College of Sciences; N/A; 152935; 22542
    We 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.
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    Bypassing pro-survival and resistance mechanisms of autophagy in EGFR-positive lung cancer cells by targeted delivery of 5FU using theranostic Ag2S quantum dots
    (Royal Soc Chemistry, 2019) Akkoç, Yunus; Gözüaçık, Devrim; N/A; N/A; N/A; N/A; Department of Physics; Department of Chemistry; Demirci, Gözde; Duman, Fatma Demir; Bavili, Nima; Kiraz, Alper; Acar, Havva Funda Yağcı; PhD Student; Master Student; PhD Student; Faculty Member; Faculty Member; Department of Physics; Department of Chemistry; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; School of Medicine; College of Sciences; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); N/A; N/A; N/A; 22542; 178902
    Targeted drug delivery systems that combine imaging and therapeutic functions in a single structure have become very popular in nanomedicine. Near-infrared (NIR) emitting Ag2S quantum dots (QDs) are excellent candidates for this task. Here, we have developed PEGylated Ag2S QDs functionalized with Cetuximab (Cet) antibody and loaded with an anticancer drug, 5-fluorouracil (5FU). These theranostic QDs were used for targeted NIR imaging and treatment of lung cancer using low (H1299) and high (A549) Epidermal Growth Factor Receptor (EGFR) overexpressing cell lines. The Cet conjugated QDs effectively and selectively delivered 5FU to A549 cells and provided significantly enhanced cell death associated with apoptosis. Interestingly, while treatment of cells with free 5FU activated autophagy, a cellular mechanism conferring resistance to cell death, these EGFR targeting multimodal QDs significantly overcame drug resistance compared to 5FU treatment alone. The improved therapeutic outcome of 5FU delivered to A549 cells by Cet conjugated Ag2S QDs is suggested as the synergistic outcome of enhanced receptor mediated uptake of nanoparticles, and hence the drug, coupled with suppressed autophagy even in the absence of addition of an autophagy suppressor.
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    FRET optofluidic microlasers enhance biological sensing
    (Pennwell Publ. Co., 2016) Karadağ, Yasin; Jonas, Alexandr; Department of Physics; Kiraz, Alper; Faculty Member; Department of Physics; College of Sciences; 22542
    The marriage of liquid-based optical microcavities with engineered biological gain media using fluorescence resonance energy transfer (FRET) creates unique miniature lasers capable of ultra-sensitive biochemical detection.
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    Vibronic excitation of single molecules: a new technique for studing low-temperature dynamics
    (Wiley-Blackwell, 2005) Ehrl, Moritz; Hellriegel, Christian; Bräuchle, Christoph; Zumbusch, Andreas; Department of Physics; Kiraz, Alper; Faculty Member; Department of Physics; College of Sciences; 22542
    Herein, we present vibronic excitation and detection of purely electronic zero-phonon lines (ZPL) of single molecules as a new tool for investigating dynamics at cryogenic temperatures. Applications of this technique to study crystalline and amorphous matrix materials are presented. In the crystalline environment, spectrally stable ZPLs are observed at moderate excitation powers. By contrast, investigations at higher excitation intensities reveal the opening of local degrees of freedom and spectral jumps, which we interpret as the observation of elementary steps in the melting of a crystal. We compare these results to spectral single-molecule trajectories recorded in a polymer, The way in which much more complicated spectral features can be analysed is shown. Surprisingly, pronounced spectral shifts on a previously not accessible large energy scale are observed, which are hard to reconcile with the standard two-level model system used to describe low-temperature dynamics in disordered systems.