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Publication Metadata only 2d -> 3d polycatenated and 3d -> 3d interpenetrated metal-organic frameworks constructed from thiophene-2,5-dicarboxylate and rigid bis(imidazole) ligands(Elsevier, 2014) Erer, Hakan; Yesilel, Okan Zafer; Arici, Mursel; Buyukgungor, Orhan; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548Hydrothermal reactions of rigid 1,4-bis(imidazol-1-yl)benzene (dib) and 1,4-bis(imidazol-1-yl)-2, 5-dimethylbenzene (dimb) with deprotonated thiophene-2,5-dicarboxylic acid (H(2)tdc) in the presence of Zn(II) and Cd(II) salts in H2O produced three new metal-organic frameworks, namely, [Zn(mu-tdc)(H2O) (mu-dib)](n) (1), [Cd(mu-tdc)(H2O)(mu-dib)(n) (2), and {[Cd-2(mu(3)-tdc)(2)(mu-dimb)(2)] center dot (H2O)}(n) (3). These MOFs were characterized by FT-IR spectroscopy, elemental, thermal (TG, DTA, DTG and DSC), and single-crystal X-ray diffraction analyses. Isomorphous complexes 1 and 2 reveal polycatenated 2D+2D -> 3D framework based on an undulated (4,4)-sql layer. Complex 3 exhibits a new 4-fold interpenetrating 3D framework with the point symbol of 6(6). Molecular simulations were used to assess the potentials of the complexes for H-2 storage application. Moreover, these coordination polymers exhibit blue fluorescent emission bands in the solid state at room temperature.Publication Open Access A comparative molecular dynamics study of methylation state specificity of JMJD2A(Public Library of Science, 2011) Bozfakioğlu S.; Uğurel, Elif; Sinan, M.; Department of Chemical and Biological Engineering; Keskin, Özlem; Erman, Burak; Gürsoy, Attila; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; College of Sciences; College of Engineering; 26605; 179997; N/AHistone modifications have great importance in epigenetic regulation. JMJD2A is a histone demethylase which is selective for di- and trimethyl forms of residues Lys9 and Lys36 of Histone 3 tail (H3K9 and H3K36). We present a molecular dynamics simulations of mono-, di- and trimethylated histone tails in complex with JMJD2A catalytic domain to gain insight into how JMJD2A discriminates between the methylation states of H3K9. The methyl groups are located at specific distances and orientations with respect to Fe(II) in methylammonium binding pocket. For the trimethyllysine the mechanism which provides the effectual orientation of methyl groups is the symmetry, whereas for the dimethyllysine case the determining factors are the interactions between methyllysine head and its environment and subsequently the restriction on angular motion. The occurrence frequency of methyl groups in a certain proximity of Fe(II) comes out as the explanation of the enzyme activity difference on di-and tri-methylated peptides. Energy analysis suggests that recognition is mostly driven by van der Waals and followed by Coulombic interactions in the enzyme-substrate interface. The number (mono, di or tri) and orientations of methyl groups and water molecules significantly affect the extent of van der Waals interaction strengths. Hydrogen bonding analysis suggests that the interaction between JMJD2A and its substrates mainly comes from main chain-side chain interactions. Binding free energy analysis points out Arg8 as an important residue forming an intra-substrate hydrogen bond with tri and dimethylated Lys9 of the H3 chain. Our study provides new insights into how JMJD2A discriminates between its substrates from both a structural and dynamical point of view.Publication Metadata only A new approach to defining a dynamic relative gain(Elsevier Sci Ltd, 2003) Mc Avoy, T.; Chen, R.; Robinson, D.; Schnelle, P.D.; Department of Chemical and Biological Engineering; Arkun, Yaman; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 108526A new approach to defining a dynamic RGA (DRGA) is presented. The approach assumes the availability of a dynamic process model which is used to design a proportional output optimal controller. The new DRGA is defined based on the resulting controller gain matrix. Two examples in which the traditional RGA gives the wrong pairings and an inaccurate indication of the amount of interaction present are discussed. One example involves transfer function models and the other an industrial recycle/reactor system. In both cases the new DRGA indicates the best pairings to use and it accurately assesses the extent of interaction present.Publication Metadata only A new dataset of non-redundant protein/protein interfaces(Biophysical Society, 2003) Tsai, CJ; Wolfson, H; Nussinov, R; Department of Chemical and Biological Engineering; Keskin, Özlem; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 26605Publication Metadata only A new dataset of protein-protein interfaces(Cell Press, 2007) Güney, Emre; Nussinov, Ruth; Tsai, C. J.; Department of Computer Engineering; Department of Chemical and Biological Engineering; Gürsoy, Attila; Keskin, Özlem; Tunçbağ, Nurcan; Faculty Member; Faculty Member; PhD Student; Department of Computer Engineering; Department of Chemical and Biological Engineering; College of Engineering; College of Engineering; 8745; 26605; 245513Publication Metadata only A novel BHLHE41 variant is associated with short sleep and resistance to sleep deprivation in humans(Oxford University Press (OUP), 2014) Pellegrino, Renata; Goel, Namni; Cardinale, Christopher J.; Dinges, David F.; Kuna, Samuel T.; Maislin, Greg; Van Dongen, Hans P. A.; Tufik, Sergio; Hogenesch, John B.; Hakonarson, Hakon; Pack, Allan I.; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Kavaklı, İbrahim Halil; Faculty Member; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; College of Engineering; 40319Study Objectives: Earlier work described a mutation in DEC2 also known as BHLHE41 (basic helix-loop-helix family member e41) as causal in a family of short sleepers, who needed just 6 h sleep per night. We evaluated whether there were other variants of this gene in two well-phenotyped cohorts. Design: Sequencing of the BHLHE41 gene, electroencephalographic data, and delta power analysis and functional studies using cell-based luciferase. Results: We identified new variants of the BHLHE41 gene in two cohorts who had either acute sleep deprivation (n = 200) or chronic partial sleep deprivation (n = 217). One variant, Y362H, at another location in the same exon occurred in one twin in a dizygotic twin pair and was associated with reduced sleep duration, less recovery sleep following sleep deprivation, and fewer performance lapses during sleep deprivation than the homozygous twin. Both twins had almost identical amounts of non rapid eye movement (NREM) sleep. This variant reduced the ability of BHLHE41 to suppress CLOCK/BMAL1 and NPAS2/BMAL1 transactivation in vitro. Another variant in the same exome had no effect on sleep or response to sleep deprivation and no effect on CLOCK/BMAL1 transactivation. Random mutagenesis identified a number of other variants of BHLHE41 that affect its function. Conclusions: There are a number of mutations of BHLHE41. Mutations reduce total sleep while maintaining NREM sleep and provide resistance to the effects of sleep loss. Mutations that affect sleep also modify the normal inhibition of BHLHE41 of CLOCK/BMAL1 transactivation. Thus, clock mechanisms are likely involved in setting sleep length and the magnitude of sleep homeostasis.Publication Metadata only A novel composite of alginate aerogel with PET nonwoven with enhanced thermal resistance(Elsevier, 2018) Ülker, Zeynep; N/A; Department of Chemical and Biological Engineering; Ahmad, Faheem; Erkey, Can; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 29633There is a need to develop new composite fabrics with improved thermal properties. Aerogels are highly porous materials with low thermal conductivities and can be used to develop new composites with standard nonwoven fabrics. In this study, a new composite of alginate aerogel with polyester (PET) nonwoven was synthesized by a sol-gel method. A needle punched PET nonwoven was soaked with an alginate solution and then immersed in an aqueous CaCl2 solution which resulted in the formation of a gel inside the PET nonwoven. The gel was dried with supercritical CO2 after solvent exchange with ethanol leading to alginate aerogel-PET nonwoven composite. The aerogels were porous and were in the form of blocks in between the PET fibers as evident from SEM images. The thermal properties of the composite were measured using a heat flow meter. The thermal diffusivity of the composite was significantly lower than the thermal diffusivity of the pure PET nonwoven. The composite also had a higher thermal resistance and also a higher tensile strength than the pure PET nonwoven. Experiments using a thermal imaging camera indicated that the heat flux in the composite is much lower than in pure PET nonwoven due to the presence of alginate aerogel. The results show that the new composite material is promising for use in thermal clothing applications.Publication Open Access A novel hybrid material: an inorganic silica aerogel core encapsulated with a tunable organic alginate aerogel layer(Royal Society of Chemistry (RSC), 2014) Department of Chemical and Biological Engineering; Ülker, Zeynep; Erkey, Can; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 29633A novel layered material consisting of a silica aerogel core encapsulated by an alginate aerogel layer was developed. The components of the hybrid aerogel had the high surface area and high porosity of pure aerogels which should lead to development of new layered systems for a wide variety of applications.Publication Metadata only A phytochemical-containing metal-organic framework: synthesis, characterization and molecular simulations for hydrogen adsorption(Elsevier Science Sa, 2015) Demir, Selcuk; Cepni, H. Merve; Topcu, Yildiray; Holynska, Malgorzata; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548As a result of involvement of all carboxylato/methoxo/oxo donor oxygen atoms of a phytochemical ferulic acid with zinc ions, a Zn-ferulate metal-organic framework (PhytoMOF-1), {[Zn-2(fer)(2)]}(n) is formed. The structure of PhytoMOF-1 was characterized by single crystal X-ray diffraction studies. PhytoMOF-1 contains channels with a considerable diameter of 15.1(1) x 17.2(1) angstrom. The total void volume of PhytoMOF-1 is similar to 3517 angstrom(3). N-2 adsorption/desorption analyses indicate that the PhytoMOF-1 is porous. Molecular simulations show that PhytoMOF-1 might store hydrogen. The luminescent properties of PhytoMOF-1 are quenched upon the adsorption of toluene and nitrobenzene.Publication Open Access A promising catalyst for the dehydrogenation of perhydro-dibenzyltoluene: Pt/Al2O3 prepared by supercritical CO2 deposition(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Modisha, Phillimon; Garidzirai, Rudaviro; Rommel, Sarshad; Uzunlar, Erdal; Aindow, Mark; Bessarabov, Dmitri; Department of Chemical and Biological Engineering; Bozbağ, Selmi Erim; Erkey, Can; Güneş, Hande; 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; 29633; N/APt/Al2O3 catalysts prepared via supercritical deposition (SCD), with supercritical CO2, wet impregnation (WI) methods and a selected benchmark catalyst, were evaluated for the dehydrogenation of perhydro-dibenzyltoluene (H18-DBT) at 300 degrees C in a batch reactor. After ten dehydrogenation runs, the average performance of the catalyst prepared using SCD was the highest compared to the benchmark and WI-prepared catalysts. The pre-treatment of the catalysts with the product (dibenzyltoluene) indicated that the deactivation observed is mainly due to the adsorbed H0-DBT blocking the active sites for the reactant (H18-DBT). Furthermore, the SCD method afforded a catalyst with a higher dispersion of smaller sized Pt particles, thus improving catalytic performance towards the dehydrogenation of H18-DBT. The particle diameters of the SCD- and WI-prepared catalysts varied in the ranges of 0.6-2.2 nm and 0.8-3.4 nm and had average particle sizes of 1.1 nm and 1.7 nm, respectively. Energy dispersive X-ray spectroscopy analysis of the catalysts after ten dehydrogenation runs revealed the presence of carbon. In this study, improved catalyst performance led to the production of more liquid-based by-products and carbon material compared to catalysts with low catalytic performance.