Researcher:
Şanlı, Deniz

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Deniz

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Şanlı

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Şanlı, Deniz

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2011 - 201512

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    Structural cooperativity in histone H3 tail modifications
    (Wiley, 2011) N/A; Department of Chemical and Biological Engineering; Department of Computer Engineering; Department of Chemical and Biological Engineering; Şanlı, Deniz; Keskin, Özlem; Gürsoy, Attila; Erman, Burak; Researcher; Faculty Member; Faculty Member; Faculty Member; Department of Computer Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; 26605; 8745; 179997
    Post-translational modifications of histone H3 tails have crucial roles in regulation of cellular processes. There is cross-regulation between the modifications of K4, K9, and K14 residues. The modifications on these residues drastically promote or inhibit each other. In this work, we studied the structural changes of the histone H3 tail originating from the three most important modifications; tri-methylation of K4 and K9, and acetylation of K14. We performed extensive molecular dynamics simulations of four types of H3 tails: (i) the unmodified H3 tail having no chemical modification on the residues, (ii) the tri-methylated lysine 4 and lysine 9 H3 tail (K4me3K9me3), (iii) the tri-methylated lysine 4 and acetylated lysine 14 H3 tail (K4me3K14ace), and (iv) tri-methylated lysine 9 and acetylated lysine 14 H3 tail (K9me3K14ace). Here, we report the effects of K4, K9, and K14 modifications on the backbone torsion angles and relate these changes to the recognition and binding of histone modifying enzymes. According to the Ramachandran plot analysis; (i) the dihedral angles of K4 residue are significantly affected by the addition of three methyl groups on this residue regardless of the second modification, (ii) the dihedral angle values of K9 residue are similarly altered majorly by the tri-methylation of K4 residue, (iii) different combinations of modifications (tri-methylation of K4 and K9, and acetylation of K14) have different influences on phi and psi values of K14 residue. Finally, we discuss the consequences of these results on the binding modes and specificity of the histone modifying enzymes such as DIM-5, GCN5, and JMJD2A.
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    Synthesis of nanostructured materials using supercritical CO2: Part I. Physical transformations
    (Springer, 2012) N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Şanlı, Deniz; Bozbağ, Selmi Erim; Erkey, Can; Researcher; Researcher; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; 29633
    Nanostructured materials have been attracting increased attention for a wide variety of applications due to their superior properties compared to their bulk counterparts. Current methods to synthesize nanostructured materials have various drawbacks such as difficulties in control of the nanostructure and morphology, excessive use of solvents, abundant energy consumption, and costly purification steps. Supercritical fluids especially supercritical carbon dioxide (scCO(2)) is an attractive medium for the synthesis of nanostructured materials due to its favorable properties such as being abundant, inexpensive, non-flammable, non-toxic, and environmentally benign. Furthermore, the thermophysical properties of scCO(2) can be adjusted by changing the processing temperature and pressure. The synthesis of nanostructured materials in scCO(2) can be classified as physical and chemical transformations. In this article, Part I of our review series, synthesis of nanostructured materials using physical transformations is described where scCO(2) functions as a solvent, an anti-solvent or as a solute. The nanostructured materials, which can be synthesized by these techniques include nanoparticles, nanowires, nanofibers, foams, aerogels, and polymer nanocomposites. scCO(2) based processes can also be utilized in the intensification of the conventional processes by elimination of some of the costly purification or separation steps. The fundamental aspects of the processes, which would be beneficial for further development of the technologies, are also reviewed.
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    Bubble point pressures and densities of hexamethyldisiloxane-carbon dioxide binary mixture using a constant volume view cell
    (Elsevier Science Bv, 2013) N/A; Department of Chemical and Biological Engineering; Şanlı, Deniz; Erkey, Can; Researcher; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; College of Engineering; N/A; 29633
    The phase behavior of hexamethyldisiloxane (HMDS)-carbon dioxide (CO2) binary mixture was investigated using a constant volume view cell. The accuracy of the measurement technique was inspected against the bubble point pressure data in the literature for ethanol (C2H5OH)-carbon dioxide (CO2) binary mixture. The bubble point pressures for C2H5OH-CO2 agreed well with the literature values. The bubble point pressures of HMDS-CO2 binary mixture were determined at five different temperatures (T=298.2 K, 308.2 K, 3132 K, 323.2 K, 333.2 K) and at various compositions. The bubble point pressures increased with increasing temperature and CO2 mole fraction in the binary mixture. The phase behavior of the binary mixture was modeled using the Peng-Robinson Stryjek-Vera equation of state (PRSVEoS). The binary interaction parameters were regressed from experimental bubble point pressures at each temperature and were found to exhibit a linear dependency on temperature. The HMDS-CO2 binary mixture was also found to exhibit Type II phase behavior. Additionally, P-T-rho measurements for the same binary system were conducted and excess molar volumes were calculated.
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    Effect of polymer molecular weight and deposition temperature on the properties of silica aerogel/hydroxy-terminated poly(dimethylsiloxane) nanocomposites prepared by reactive supercritical deposition
    (Elsevier Science Bv, 2015) N/A; N/A; Department of Chemical and Biological Engineering; Şanlı, Deniz; Erkey, Can; Researcher; Faculty Member; Department of Chemical and Biological Engineering; N/A; College of Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); N/A; 29633
    Monolithic nanocomposites of silica aerogels with hydroxy-terminated poly(dimethylsiloxane) (PDMS(OH)) were prepared by reactive supercritical deposition technique. The depositions were performed by using PDMS(OH) having two different molecular weights (M-n = 2750 g/mol and 18,000 g/mol) and at three different temperatures (313.2 K, 323.2 K, 333.2 K) and the effects of deposition temperature and polymer molecular weight on the properties of nanocomposites were investigated. The polymer uptake of the nanocomposites was found to increase with increasing deposition temperature indicating faster reaction rates at higher temperatures. PDMS(OH) molecules with lower molecular weight were homogenously distributed throughout the cylindrical composites. On the other hand, the samples that were deposited with high molecular weight PDMS(OH) were not homogenous with a higher polymer concentration near the surface than at the center. The pore volumes and BET surface areas of the nanocomposites decreased upon deposition of the polymer. The reductions in pore volumes were higher by a factor of two than the volume of the deposited polymer indicative of blocking of pores. Moreover, the compressive modulus of the nanocomposite was found to be more than three times greater than the compressive modulus of the native silica aerogel.
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    Frequency response of microcantilevers immersed in gaseous, liquid, and supercritical carbon dioxide
    (Elsevier, 2013) N/A; Department of Chemical and Biological Engineering; Department of Physics; N/A; Department of Physics; Department of Mechanical Engineering; Department of Physics; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Uzunlar, Erdal; Beykal, Burcu; Ehrlich, Katjana; Şanlı, Deniz; Jonas, Alexandr; Alaca, Burhanettin Erdem; Kiraz, Alper; Ürey, Hakan; Erkey, Can; Master Student; Undergraduate Student; N/A; Researcher; Other; Faculty Member; Faculty Member; Faculty Member; Faculty Member; Department of Mechanical Engineering; Department of Physics; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; College of Engineering; College of Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; N/A; N/A; 115108; 22542; 8579; 29633
    The frequency response of ferromagnetic nickel microcantilevers with lengths ranging between 200 mu m and 400 mu m immersed in gaseous, liquid and supercritical carbon dioxide (CO2) was investigated. the resonant frequency and the quality factor of the cantilever oscillations in CO2 were measured for each cantilever length in the temperature range between 298 K and 323 K and the pressure range between 0.1 MPa and 20.7 MPa. at a constant temperature, both the resonant frequency and the quality factor were found to decrease with increasing pressure as a result of the increasing CO2 density and viscosity. very good agreement was found between the measured cantilever resonant frequencies and predictions of a model based on simplified hydrodynamic function of a cantilever oscillating harmonically in a viscous fluid valid for Reynolds numbers in the range of [1;1000] (average deviation of 2.40%). at high pressures of CO2, the experimental Q-factors agreed well with the predicted ones. at low CO2 pressures, Additional internal mechanisms of the cantilever oscillation damping caused lowering of the measured Q-factor with respect to the hydrodynamic model predictions.
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    Three-dimensional optofluidic waveguides in hydrophobic silica aerogels via supercritical fluid processing
    (Elsevier, 2013) Jonas, Alexandr; Department of Chemical and Biological Engineering; N/A; N/A; Department of Chemical and Biological Engineering; Department of Physics; Department of Physics; Department of Chemical and Biological Engineering; Eris, Gamze; Şanlı, Deniz; Ülker, Zeynep; Bozbağ, Selmi Erim; Kiraz, Alper; Erkey, Can; Researcher; Researcher; PhD Student; Researcher; Other; Faculty Member; Faculty Member; Department of Physics; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); College of Engineering; N/A; Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; College of Sciences; College of Engineering; N/A; N/A; 262388; N/A; N/A; 22542; 29633
    Optofluidic components enable flexible routing and transformations of light beams in integrated lab-on-a-chip systems with the use of carefully shaped fluid parcels. For structural integrity reasons, the working fluid is typically contained within a solid-material chip. One of the outstanding challenges in optofluidics is the preparation and processing of optofluidic waveguides. These require solid cladding materials that are sufficiently strong to contain the fluid while possessing optical properties that allow efficient confinement of light within fluidic channels. Here, we report on a new technique to obtain liquid-core optofluidic waveguides based on total internal reflection of light in three-dimensional water-filled channels embedded in hydrophobic silica aerogel. To form the channels, we employ a fiber made of cage-like silicon-oxygen compound - trifluoropropyl polyhedral oligomeric silsesquioxane (trifluoropropyl PUSS) - which has high solubility in supercritical CO2 (scCO(2)). A U-shaped fiber made of trifluoropropyl PUSS is obtained by melt/freeze processing of PUSS powder and subsequently placed in a silicate sol. After gelation of the sol and aging of the gel, scCO(2) extraction is used to dry the wet gel and extract the POSS fiber, yielding a dry silica aerogel with a U-shaped empty channel inside it. Finally, the silanol groups at the surface of the aerogel are reacted with hexamethyldisilazane (HMDS) in the presence of scCO(2) to render the aerogel surface hydrophobic and the channel is filled with water. We demonstrate efficient waveguiding by coupling light into the water-filled channel and monitoring the channel output. The presented procedure opens up new possibilities for creating complex three-dimensional networks of liquid channels in aerogels for optofluidic applications. (C) 2012 Elsevier B.V. All rights reserved.
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    Demixing pressures of hydroxy-terminated poly(dimethylsiloxane)-carbon dioxide binary mixtures at 313.2 K, 323.2 K and 333.2 K
    (Elsevier Science Bv, 2014) N/A; Department of Chemical and Biological Engineering; Şanlı, Deniz; Erkey, Can; Researcher; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; College of Engineering; N/A; 29633
    The phase behavior of PDMS(OH)-CO2 binary mixtures was investigated. Two different molecular weight PDMS(OH) were utilized and the demixing pressures were determined at three temperatures for a wide composition range. Both of these polymers were found to form miscible mixtures with CO2 at all compositions at pressures lower than 31 MPa in the temperature range 313.2-333.2 K. Depending on the composition of the binary mixtures, two types of phase separation was observed during depressurization; the bubble point and the cloud point. In addition, at specific weight fractions a color change was also observed which was attributed to the mixture critical point. The demixing pressures were observed to increase with temperature and decrease with increasing polymer weight fraction. In addition, higher demixing pressures were obtained for the higher molecular weight polymer mixtures. The bubble point data were modeled by using Sanchez-Lacombe equation of state (SLEoS) and the binary interaction parameters were regressed at the studied temperatures. It was observed that the binary interaction parameters decreased with increasing temperature.
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    Synthesis of nanostructured materials using supercritical CO2: part II. chemical transformations
    (Springer, 2012) Department of Chemical and Biological Engineering; N/A; Department of Chemical and Biological Engineering; Bozbağ, Selmi Erim; Şanlı, Deniz; Erkey, Can; Researcher; Researcher; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); College of Engineering; N/A; College of Engineering; N/A; N/A; 29633
    This article, the second part of our review series on the use of supercritical carbon dioxide (scCO(2)) for synthesis of nanostructured material deals with the production techniques that involve chemical transformations. Taking advantage of both solvent and anti-solvent tunable properties of scCO(2), many nanostructured materials including supported/unsupported nanoparticles, quantum nanodots, nanofilms, nanorods, nanofoams, and nanowires can be prepared. Furthermore, material surfaces can be functionalized using scCO(2). scCO(2) can also be used as a carbon source for the controlled synthesis of carbon nanotubes and fullerenes or as an oxygen source for metal oxide nanostructures. Moreover, materials produced using scCO(2) does not usually need additional purification or drying steps. Depending on surface properties, the morphology of the final material can be adjusted by tuning the process conditions and the reactant concentrations.
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    Applications of aerogels and their composites in energy-related technologies
    (Elsevier, 2014) N/A; N/A; Department of Chemical and Biological Engineering; Ülker, Zeynep; Şanlı, Deniz; Erkey, Can; PhD 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; 262388; N/A; 29633
    Aerogels were first synthesized in 1932 and are promising materials for a variety of energy-related applications. Their intriguing and adjustable properties such as high surface areas, sharp pore size distributions, low thermal conductivities, and high sorption capacities will continue to make these materials attractive for scientists and researchers from a wide variety of disciplines.
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    Monolithic composites of silica aerogels by reactive supercritical deposition of hydroxy-terminated poly(dimethylsiloxane)
    (amer Chemical Soc, 2013) N/A; Department of Chemical and Biological Engineering; Şanlı, Deniz; Erkey, Can; Researcher; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); Graduate School of Sciences and Engineering; College of Engineering; N/A; 29633
    Monolithic composites of silica aerogels with hydroxyl-terminated poly(dimethylsiloxane) (PDMS(OH)) were developed with a novel reactive supercritical deposition technique. the method involves dissolution of PDMS(OH) in supercritical CO2 (scCO(2)) and then exposure of the aerogel samples to this single phase mixture of PDMS(OH)-CO2. the demixing pressures of the PDMS(OH)-CO2 binary mixtures determined in this study indicated that PDMS(OH) forms miscible mixtures with CO2 at a wide composition range at easily accessible pressures. Upon supercritical deposition, the polymer molecules were discovered to react with the hydroxyl groups on the silica aerogel surface and form a conformal coating on the surface. the chemical attachment of the polymer molecules on the aerogel surface were verified by prolonged extraction with pure scCO(2), simultaneous deposition with superhydrophobic and hydrophilic silica aerogel samples and aTR-FTIR analysis. all of the deposited silica aerogel samples were obtained as monoliths and retained their transparency up to around 30 wt % of mass uptake. PDMS(OH) molecules were found to penetrate all the way to the center of the monoliths and were distributed homogenously throughout the cylindrical aerogel samples. Polymer loadings as high as 75.4 wt % of the aerogel mass could be attained. It was shown that the polymer uptake increases with increasing exposure time, As well as the initial polymer concentration in the vessel.