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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 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.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 Metadata only A magnetically actuated resonant mass sensor with integrated optical readout(Ieee-Inst Electrical Electronics Engineers Inc, 2008) N/A; N/A; Department of Electrical and Electronics Engineering; N/A; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; Öztürk, Alibey; Ocaklı, Hüseyin İlker; Özber, Natali; Ürey, Hakan; Kavaklı, İbrahim Halil; Alaca, Burhanettin Erdem; Master Student; Researcher; Master Student; Faculty Member; Faculty Member; Faculty Member; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; 8579; 40319; 115108Nickel cantilevers with integrated diffraction gratings are used as resonant mass sensors with a resolution of 500 femtograms. Their applicability to biosensing is demonstrated with human opioid receptors. The device is fabricated through a single-mask lithographic process. The microoptical readout provides a simple measurement platform with one external photodiode. Thanks to its ac operation principle, the device is immune to environmental noise and entails a high tolerance to fabrication defects. Obtained signal-to-noise ratio is comparable to that of a high-end Doppler vibrometer. The device with these aspects for systems integration and microarray technology is a candidate for low-cost portable sensors.Publication Metadata only A model to predict maximum tolerable temperatures of metal-oxide-supported 1-n-butyl-3-methylimidazolium based ionic liquids(Elsevier, 2015) N/A; N/A; N/A; Department of Chemical and Biological Engineering; Akçay, Aslı; Babucci, Melike; Balci, Volkan; Uzun, Alper; Master Student; PhD Student; PhD Student; 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; College of Engineering; N/A; N/A; N/A; 59917The thermal stability limits of metal-oxide-supported ionic liquids (Its) with 1-n-butyl-3-methylimidazolium cation, [BMIM](+), on most commonly used metal-oxides, SiO2, TiO2, gamma-Al2O3, and MgO are determined. Data show that stability limits of bulk and metal-oxide-supported ILs linearly increase with increasing acidity of C2 proton on imidazolium ring, controlling the inter-ionic interaction strength. Moreover, data also show that the presence of metal-oxide lowers the stability limits considerably. This effect becomes more significant as the surface acidity of the metal-oxide decreases from SiO2 to MgO This decrease in stability limits with increasing point of zero charge (PZC) of metal-oxide indicates that the interaction between IL and metal-oxide becomes the dominant factor rather than the inter-ionic interactions. Based on these findings a simple mathematical expression was developed as a function of PZC and inter-ionic interaction strength probed by nu(C2H) to predict the stability limits of [BMIM](+)-based ILs immobilized on metal-oxides. Performance of the model was tested on several different ILs supported on different metal-oxides, including Fe2O3 and CeO2. Results show that the model successfully predicts the maximum operating or tolerable temperatures of supported-[BMIM](+)-based ILs with an average relative error less than 4.3%. We suggest that the model developed here can help to choose proper ILs that can tolerate the operating conditions of systems including ILs immobilized on metal oxides, such as in solid catalysts with ionic liquid layer (SCILL) or in supported ionic liquid phase (SILP) catalysts. (C) 2014 Elsevier Ltd. All rights reserved.Publication Metadata only A molecular dynamics study of allosteric transitions in Leishmania mexicana pyruvate kinase(Cell Press, 2015) Naithani, Ankita; Taylor, Paul; Walkinshaw, Malcolm D.; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997A comparative molecular dynamics analysis of the pyruvate kinase from Leishmania mexicana is presented in the absence and presence of the allosteric effector fructose 2,6-bisphosphate. Comparisons of the simulations of the large 240 kDa apo and holo tetramers show that binding of fructose 2,6-bisphosphate cools the enzyme and reduces dynamic movement, particularly of the B-domain. The reduced dynamic movement of the holo form traps the pyruvate kinase tetramer in its enzymatically active state with the B-domain acting as a lid to cover the active site. The simulations are also consistent with a transition of the mobile active-site alpha 6' helix, which would adopt a helical conformation in the active R-state and a less structured coil conformation in the inactive T-state. Analysis of the rigid body motions over the trajectory highlights the concerted anticorrelated rigid body rocking motion of the four protomers, which drives the T to R transition. The transitions predicted by these simulations are largely consistent with the Monod-Wyman-Changeux model for allosteric activation but also suggest that rigidification or cooling of the overall structure upon effector binding plays an additional role in enzyme activation.Publication Metadata only A new approach for predicting gas separation performances of MOF membranes(Elsevier Science Bv, 2016) N/A; Department of Chemical and Biological Engineering; Gürdal, Yeliz; Keskin, Seda; Master Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 40548Metal organic framework (MOF) membranes are widely used for gas separations. Permeability and selectivity of MOF membranes can be accurately calculated using 'the detailed method' which computes transport diffusivities of gases in MOFs' pores. However, this method is computationally demanding therefore not suitable to screen large numbers of MOFs. Another approach is to use the approximate method' which uses self-diffusivities of gases to predict gas permeabilities of MOF membranes. The approximate method requires fewer amounts of time compared to the detailed method but significantly underestimates gas permeabilities since mixture correlation effects are ignored in this method. In this work, we first used computationally demanding detailed method to calculate permeabilities and selectivities of 8 different MOF membranes for Xe/Kr and Xe/Ar separations. We then compared these results with the predictions of the approximate method. After observing significant underestimation of the gas permeabilities by the approximate method, we proposed a new computational method to accurately predict gas separation properties of MOF membranes. This new method requires the same computational time and resources with the approximate method but makes much more accurate predictions for gas permeabilities. The new method that we proposed in this work will be very useful for large-scale screening of MOFs to identify the most promising membrane materials prior to extensive computational calculations and experimental efforts. (C) 2016 Elsevier B.V. All rights reserved.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 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 Metadata only A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications(Wiley, 2004) 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; 26605Here, we present a diverse, structurally nonredundant data set of two-chain protein–protein interfaces derived from the PDB. Using a sequence order-independent structural comparison algorithm and hierarchical clustering, 3799 interface clusters are obtained. These yield 103 clusters with at least five nonhomologous members. We divide the clusters into three types. In Type I clusters, the global structures of the chains from which the interfaces are derived are also similar. This cluster type is expected because, in general, related proteins associate in similar ways. In Type II, the interfaces are similar; however, remarkably, the overall structures and functions of the chains are different. The functional spectrum is broad, from enzymes/inhibitors to immunoglobulins and toxins. The fact that structurally different monomers associate in similar ways, suggests “good” binding architectures. This observation extends a paradigm in protein science: It has been well known that proteins with similar structures may have different functions. Here, we show that it extends to interfaces. In Type III clusters, only one side of the interface is similar across the cluster. This structurally nonredundant data set provides rich data for studies of protein–protein interactions and recognition, cellular networks and drug design. In particular, it may be useful in addressing the difficult question of what are the favorable ways for proteins to interact.Publication Metadata only A novel alkali activated magnesium silicate as an effective and mechanically strong adsorbent for methylene blue removal(Elsevier, 2022) Kaya Özkiper, Kardelen; Soyer Uzun, Sezen; Department of Chemical and Biological Engineering; Uzun, Alper; 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); College of Engineering; 59917A novel, cheap, and easy-to-synthesize sepiolite-based alkali-activated material (Sep-AAM), synthesized by the reaction of a magnesium silicate source, sepiolite, with sodium silicate solution, demonstrating high mechanical strength and methylene blue (MB) removal performance is introduced. Kinetics data indicated that MB adsorption occurs through pseudo-second-order adsorption kinetics model, while the Langmuir isotherm model provided a better fit to adsorption isotherms. The Sep-AAM provided a removal capacity of 99.92 mg g-1 at 50 degrees C, setting a new benchmark value among the materials used for this purpose. Thermodynamical parameters indicated that the adsorption of MB onto Sep-AAM was endothermic and the interaction between Sep-AAM and MB included weak chemical bonding. Regenerability of the Sep-AAM in powder and monolith forms was confirmed up to four-cycles. Structural parameters determined by several characterization tools demonstrated that the surface hydroxyl groups are responsible for the superior MB adsorption performance. The mechanical strength measurements showed that Sep-AAM in monolith form displayed a remarkable compressive strength value of 40 MPa. To establish a new approach forward on the development of AAMs for wastewater treatment, this study shows that sepiolite can effectively be utilized and Sep-AAM provides a sustainable solution for dye removal with advanced mechanical properties.Publication 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.