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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 Metadata only 3D printed poly(lactic acid) scaffolds modified with chitosan and hydroxyapatite for bone repair applications(Elsevier, 2020) N/A; N/A; N/A; N/A; Department of Chemistry; Department of Chemical and Biological Engineering; Department of Chemistry; Nazeer, Muhammad Anwaar; Önder, Özgün Can; Sevgili, İlkem; Yılgör, Emel; Kavaklı, İbrahim Halil; Yılgör, İskender; PhD Student; PhD Student; PhD Student; Researcher; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Chemistry; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; College of Sciences; N/A; N/A; N/A; N/A; 40319; 241813D printed poly(lactic acid) (PLA) scaffolds surface modified with chitosan (CS) and hydroxyapatite (HA) to produce a novel bioactive composite scaffold is reported. Excellent mechanical properties of PLA, the bioactivity of CS, and osteogenic characteristics of HA are combined to fabricate composite scaffolds using a simple desktop 3D printer. Scaffolds were characterized through attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy, scanning electron microscopy (SEM), energy dispersive X-ray (EDX) spectroscopy, X-ray diffraction (XRD) and water contact angle measurements before and after modification. Formic acid was used as a solvent to prepare stable CS/HA dispersions and was found to be a suitable solvent for producing PLA/CS/HA composites. Surface properties of modified scaffolds were superior in terms of hydrophilicity and bioactivity, which resulted in enhanced attachment and proliferation of human osteosarcoma cells in vitro compared to the unmodified PLA scaffolds.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 dynamic non-isothermal model for a hydrocracking reactor: model development by the method of continuous lumping and application to an industrial unit(Elsevier Sci Ltd, 2012) Çakal, Berna; Gökçe, Dila; Kuzu, Emre; N/A; Department of Chemical and Biological Engineering; Şıldır, Hasan; Arkun, Yaman; Phd Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; 242076; 108526Hydrocracking is an important refinery process which is carried out in catalytic reactors to convert heavy petroleum fractions into valuable products. Because of the large number of species and complex reactions involved, modeling of hydrocracking is a challenging task. In this paper a dynamic, non-isothermal reactor model has been constructed using the method of continuous lumping which treats the complex reactive mixture as a continuum. In doing so concentrations are characterized in terms of reactivity which is a monotonic function of the true boiling point of the mixture. The material and energy balances are developed in the form of integro-differential equations. The significant modeling parameters are identified and estimated using data from an industrial reactor. Steady-state and dynamic predictions of the model outputs such as reactor temperature, product yields and hydrogen consumption are shown to be in good agreement with plant data.Publication Metadata only A fast approximate method of identifying paths of allosteric communication in proteins(Wiley, 2013) Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997Fluctuations of the distance between a pair of residues i and j may be correlated with the fluctuations of the distance between another pair k and l. In this case, information may be transmitted among these four residues. Allosteric activity is postulated to proceed through such correlated paths. In this short communication a fast method for calculating correlations among all possible pairs ij and kl leading to a pathway of correlated residues of a protein is proposed. The method is based on the alpha carbon centered Gaussian Network Model. The model is applied to Glutamine Amidotransferase and pathways of allosteric activity are identified and compared with literature. Proteins 2013; 81:1097-1101. (c) 2013 Wiley Periodicals, Inc.Publication Open Access A mixed-integer linear programming based training and feature selection method for artificial neural networks using piece-wise linear approximations(Elsevier, 2022) Şıldır, Hasan; Department of Chemical and Biological Engineering; Aydın, Erdal; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); College of EngineeringArtificial Neural Networks (ANNs) may suffer from suboptimal training and test performance related issues not only because of the presence of high number of features with low statistical contributions but also due to their non-convex nature. This study develops piecewise-linear formulations for the efficient approximation of the non-convex activation and objective functions in artificial neural networks for optimal, global and simultaneous training and feature selection in regression problems. Such formulations include binary variables to account for the existence of the features and piecewise-linear approximations, which in turn, after one exact linearization step, calls for solving a mixed-integer linear programming problem with a global optimum guarantee because of convexity. Suggested formulation is implemented on two industrial case studies. Results show that efficient approximations are obtained through the usage of the method with only a few number of breakpoints. Significant feature space reduction is observed bringing about notable improvement in test accuracy.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 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 new venue toward predicting the role of hydrogen embrittlement on metallic materials(Springer, 2016) N/A; N/A; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; Bal, Burak; Şahin, İbrahim; Uzun, Alper; Canadinç, Demircan; PhD Student; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; 59917; 23433This paper presents a new crystal plasticity formulation to predict the role of hydrogen embrittlement on the mechanical behavior of metallic materials. Specifically, a series of experiments were carried out to monitor the role of hydrogen interstitial content on the uniaxial tensile deformation response of iron alloyed with hydrogen, and the classical Voce hardening scheme was modified to account for the shear stresses imposed on arrested dislocations due to the surrounding hydrogen interstitials. The proposed set of physically grounded crystal plasticity formulations successfully predicted the deformation response of iron in the presence of different degrees of hydrogen embrittlement. Moreover, the combined experimental and modeling effort presented herein opens a new venue for predicting the alterations in the performance of metallic materials, where the hydrogen embrittlement is unavoidable.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.