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Publication Metadata only 1.07 - Rubberlike elasticity(Elsevier, 2012) Mark, J.E.; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997Molecular structure, molecular and phenomenological theories, and computer simulations of amorphous rubberlike polymeric networks of rubber elasticity are discussed. Behavior of responsive gels, multimodal, liquid-crystalline, and reinforced elastomers in the state of thermodynamic equilibrium are outlined. Characterization of structure and properties based on stress–strain experiments, optical and spectroscopic techniques, scanning tunneling microscopy, atomic force microscopy, nuclear magnetic resonance, small-angle and Brillouin scattering, and pulse wave propagation are outlined. © 2012 Elsevier B.V. All rights reserved.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 Metadata only 3D printing of cytocompatible gelatin-cellulose-alginate blend hydrogels(Wiley-V C H Verlag Gmbh, 2020) Erkoc, Pelin; Uvak, Ileyna; Odeh, Yazan Nitham; Akdogan, Ozan; Odeh, Yazan Nitham; Akdogan, Ozan; N/A; Department of Chemistry; Department of Chemical and Biological Engineering; Nazeer, Muhammad Anwaar; Batool, Syeda Rubab; Kızılel, Seda; PhD Student; Researcher; Faculty Member; Department of Chemistry; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; N/A; N/A; 283763D bioprinting of hydrogels has gained great attention due to its potential to manufacture intricate and customized scaffolds that provide favored conditions for cell proliferation. Nevertheless, plain natural hydrogels can be easily disintegrated, and their mechanical strengths are usually insufficient for printing process. Hence, composite hydrogels are developed for 3D printing. This study aims to develop a hydrogel ink for extrusion-based 3D printing which is entirely composed of natural polymers, gelatin, alginate, and cellulose. Physicochemical interactions between the components of the intertwined gelatin-cellulose-alginate network are studied via altering copolymer ratios. The structure of the materials and porosity are assessed using infrared spectroscopy, swelling, and degradation experiments. The utility of this approach is examined with two different crosslinking strategies using glutaraldehyde or CaCl2. Multilayer cylindrical structures are successfully 3D printed, and their porous structure is confirmed by scanning electron microscopy and Brunauer-Emmett-Teller surface area analyses. Moreover, cytocompatibility of the hydrogel scaffolds is confirmed on fibroblast cells. The developed material is completely natural, biocompatible, economical, and the method is facile. Thus, this study is important for the development of advanced functional 3D hydrogels that have considerable potential for biomedical devices and artificial tissues.Publication Metadata only [BMIM] [PF6] incorporation doubles CO2 selectivity of ZIF-8: elucidation of interactions and their consequences on performance(Amer Chemical Soc, 2016) N/A; N/A; N/A; N/A; N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Kınık, Fatma Pelin; Altıntaş, Çiğdem; Balcı, Volkan; Koyutürk, Burak; Uzun, Alper; Keskin, Seda; Master Student; Researcher; PhD Student; Master Student; Faculty Member; 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; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; N/A; 59917; 40548Experiments were combined with atomically detailed simulations and density functional theory (DFT) calculations to understand the effect of incorporation of an ionic liquid (IL), 1-n-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]), into a metal organic framework (MOF with a zeolitic imidazolate framework), ZIF-8, on the CO2 separation performance. The interactions between [BMIM] [PF6] and ZIF-8 were examined in deep detail, and their consequences on CO2/CH4, CO2/N-2, and CH4/N-2 separation have been elucidated by using experimental measurements complemented by DFT calculations and atomically detailed simulations. Results suggest that IL-MOF interactions strongly affect the gas affinity of materials at low pressure, whereas available pore volume plays a key role for gas adsorption at high pressures. Direct interactions between IL and MOF lead to at least a doubling of CO2/CH4 and CO2/N-2 selectivities of ZIF-8. These results provide opportunities for rational design and development of IL-incorporated MOFs with exceptional selectivity for target gas separation applications.Publication Metadata only [BMIM][OAc] coating layer makes activated carbon almost completely selective for CO2(Elsevier Science Sa, 2022) N/A; N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Durak, Özce; Zeeshan, Muhammad; Keskin, Seda; Uzun, Alper; Master Student; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; 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); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; 40548; 59917Tuning the molecular affinity of porous materials towards desired gases is important to achieve superior selectivity for a target separation. Herein, we report a novel composite, prepared by coating an ordinary activated carbon (AC) with an ionic liquid (IL) (1-butyl-3-methylimidazolium acetate, [BMIM][OAc]) offering an almost complete CO2 selectivity over N-2 and CH4. Data indicated that pore blockage by the IL accompanied with the enhancement in polarity and reduction in the hydrophobic character of the surface hindered the sorption of N-2 and CH4. For CO2, on the other hand, new chemisorption and physisorption sites became available associated with the IL layer on the surface, making the composite material significantly selective. Newly formed chemisorption sites attributed to the cation's acidic C2H sites, which become available with bi-layer formation. Presence of multiple competitive sorption sites with different energies was further proven with thermal analysis and detailed spectroscopic analysis. Data showed that CO2/CH4 and CO2/N-2 ideal selectivities boosted from 3.3 to 688.3 (2.3 to 54.7) and from 15.6 to 903.7 (7.1 to 74.3) at 0.1 (1) bar and 25 degrees C, respectively, upon the deposition of IL layer. Especially at lower pressures, the IL/AC material became almost fully selective for CO2 offering ideal selectivities in the order of several tens of thousands. To the best of our knowledge, the remarkable enhancement in the ideal CO2 selectivity by a straightforward post-synthesis modification of an ordinary AC, as reported here, sets a new benchmark in high-performance and efficient gas separation for similar porous materials.Publication Metadata only A CLOCK-binding small molecule disrupts the interaction between CLOCK and BMAL1 and enhances circadian rhythm amplitude(Elsevier, 2020) Akyel, Yasemin Kübra; Yılmaz, Fatma; Öztürk, Nuri; Öztürk, Narin; Okyar, Alper; N/A; N/A; Department of Chemical and Biological Engineering; N/A; Department of Molecular Biology and Genetics; Department of Industrial Engineering; Department of Chemical and Biological Engineering; Doruk, Yağmur Umay; Yarparvar, Darya; Gül, Şeref; Taşkın, Ali Cihan; Barış, İbrahim; Türkay, Metin; Kavaklı, İbrahim Halil; Master Student; PhD Student; Researcher; Other; Teaching Faculty; Faculty Member; Faculty Member; Department of Molecular Biology and Genetics; Department of Industrial Engineering; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; College of Sciences; College of Engineering; College of Engineering; N/A; N/A; N/A; 291296; 111629; 24956; 40319Proper function of many physiological processes requires a robust circadian clock. Disruptions of the circadian clock can result in metabolic diseases, mood disorders, and accelerated aging. Therefore, identifying small molecules that specifically modulate regulatory core clock proteins may potentially enable better management of these disorders. In this study, we applied a structure-based molecular-docking approach to find small molecules that specifically bind to the core circadian regulator, the transcription factor circadian locomotor output cycles kaput (CLOCK). We identified 100 candidate molecules by virtual screening of ?2 million small molecules for those predicted to bind closely to the interface in CLOCK that interacts with its transcriptional co-regulator, Brain and muscle Arnt-like protein-1 (BMAL1). Using a mammalian two-hybrid system, real-time monitoring of circadian rhythm in U2OS cells, and various biochemical assays, we tested these compounds experimentally and found one, named CLK8, that specifically bound to and interfered with CLOCK activity. We show that CLK8 disrupts the interaction between CLOCK and BMAL1 and interferes with nuclear translocation of CLOCK both in vivo and in vitro. Results from further experiments indicated that CLK8 enhances the amplitude of the cellular circadian rhythm by stabilizing the negative arm of the transcription/translation feedback loop without affecting period length. Our results reveal CLK8 as a tool for further studies of CLOCK's role in circadian rhythm amplitude regulation and as a potential candidate for therapeutic development to manage disorders associated with dampened circadian rhythms.Publication Metadata only A computational model for controlling conformational cooperativity and function in proteins(Wiley, 2018) Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997We present a computational model that allows for rapid prediction of correlations among a set of residue pairs when the fluctuations of another set of residues are perturbed. The simple theory presented here is based on the knowledge of the fluctuation covariance matrix only. In this sense, the theory is model independent and therefore universal. Perturbation of any set of fluctuations and the resulting response of the remaining set are calculated using conditional probabilities of a multivariate normal distribution. The model is expected to rapidly and accurately map the consequences of mutations in proteins, as well as allosteric activity and ligand binding. Knowledge of triple correlations of fluctuations of residues i, j, and k, 〈ΔRiΔRjΔRk〉 emerges as the necessary source of information for controlling residue pairs by perturbing a distant residue. Triple correlations have not received wide attention in literature. Perturbation–response–function relations for ubiquitin (UBQ) are discussed as an example. Covariance matrix for UBQ obtained from the Gaussian Network Model combined with the present computational algorithm is able to reflect the millisecond molecular dynamics correlations and observed NMR results.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 facile method for cross-linking of methacrylated wood fibers for engineered wood composites(Elsevier B.V., 2023) Bengü, Başak; Biçer, Aziz; Yarıcı, Tugay; N/A; N/A; N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Sarıoğlu, Ebru; Turhan, Emine Ayşe; Karaz, Selcan; Erkey, Can; Şenses, Erkan; PhD Student; PhD Student; Master Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM), Koç University Boron and Advanced Materials Application and Research Center (KUBAM) / Koç Üniversitesi Bor ve İleri Malzemeler Uygulama ve Araştırma Merkezi (KUBAM); Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; 29633; 280298Chemical modifications are widely used to enhance the properties of wood composites and create a strong bonding mechanism for enhancing the dimensional stability, water resistance as well as decreasing carcinogenic formaldehyde emission. Esterification is the most-known modification way to enhance the durability of wood composites, but it does not improve mechanical performance. In this work, we demonstrated a two-step, easy and quick wood surface modification strategy based on microwave heating and UV crosslinking. Firstly, the fiber surface was reacted with methacrylic anhydride, then using methacrylated groups on wood, the fibers are covalently linked. As a proof-of-concept the fibers cross-linked within five minutes under UV radiation using benzophenone solution. Then, the effect of crosslinked wood fiber on the properties of mechanical and swelling of fiberboard were studied. Using SEM, FTIR-ATR, and swelling tests, we investigated the wood-based products' reaction mechanism, morphology, and internal bonding strength. The chemical cross-linking gives stronger bonding, compared to hydrogen bonding, between fibers even in wet conditions, resulting in a cross-linked foam-like structure. Also, wood panels were fabricated, compared to unmodified fibers, the internal bond strength and dimensional stability of fiberboards increased slightly. Overall, these results show that chemical cross-linking of wood fibers can be a fast and promising way to produce multi-functional wood composites.