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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Publication Metadata only Physics-informed neural network based modeling of an industrial wastewater treatment unit(Elsevier B.V., 2023) Esenboğa, Elif Ecem; Cosgun, Ahmet; Kuşoğlu, Gizem; Aydın, Duygu; Department of Chemical and Biological Engineering; Asrav, Tuse; Köksal, Ece Serenat; Aydın, Erdal; 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 EngineeringWastewater treatment units consist of biological treatment with activated sludge and are subject to many disturbances such as influent flowrate, pollutant load and weather conditions bringing about many challenges for the modeling of such plants. Data-driven models may respond to these challenges at the cost of issues such as overfitting or poor fitting due to the lack of high-quality data. To benefit from the available physics-based knowledge and to eliminate the drawbacks of suboptimal and poor training, physics informed neural networks might be quite promising. In this work, artificial, recurrent and physics-informed neural network models are utilized for the wastewater plant in Tüpraş İzmit Refinery. For recurrent models with selected features based on correlation technique, test mean squared error is up to 82% smaller compared to the standard artificial neural network models. Physics-informed trained neural network models with selected features improved the test performance by decreasing mean squared error up to 87% with acceptable decreases in training performance which addresses its strength compared to fully data-driven models.Publication Metadata only Modeling of an industrial delayed coker unit(Elsevier B.V., 2023) Firstauthor, Anne; Secondauthor, Tim B.; Thirdauthora, James Q.; Department of Chemical and Biological Engineering; Kuşoğlu, Gizem Kaya; Arkun, Yaman; Department of Chemical and Biological Engineering; College of EngineeringDelayed Coker Unit (DCU) converts the vacuum residual feedstock to lighter and more valuable products such as motor fuels and eliminates the low-order and environment-damaging streams. Thus, optimal operation of this unit provides great economic return. In this direction, we have modeled an industrial DCU which exists in the TUPRAS Refinery. The steady-state model consists of the furnace and coke drums and implemented using MATLAB. Physical properties are determined by Aspen HYSYS. The obtained model was used for predicting the coke level in the coke drums where the reaction takes place and the distribution of the products. Both furnace and coke drum models were verified by comparing obtained results with actual plant data. © 2023 Elsevier B.V.Publication Metadata only Structure of mono- and bimetallic heterogeneous catalysts based on noble metals obtained by means of fluid technology and metal-vapor synthesis(Maik Nauka/Interperiodica/Springer, 2012) Said-Galiev, E. E.; Vasil'kov, A. Yu.; Nikolaev, A. Yu.; Lisitsyn, A. I.; Naumkin, A. V.; Volkov, I. O.; Abramchuk, S. S.; Lependina, O. L.; Khokhlov, A. R.; Shtykova, E. V.; Dembo, K. A.; Department of Chemical and Biological Engineering; Erkey, Can; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 29633Monometallic nanocomposites are obtained with the use of supercritical carbon dioxide (fluid technique) and metal-vapor synthesis (MVS), while bimetallic nanocomposites of Pt and Au noble metals and gamma-Al2O3 oxide matrix are synthesized by a combination of these two methods. The structures, concentrations, and chemical states of metal atoms in composites are studied by means of small-angle X-ray scattering (SAXS), transparent electron microscopy (TEM), X-ray fluorescent analysis (XFA), and X-ray photoelectron spectroscopy (XPS). The neutral state of metal atoms in clusters is shown by XPS and their size distribution is found according to SAXS; as is shown, it is determined by the pore sizes of the oxide matrices and lies in the range of 1 to 50 nm. The obtained composites manifest themselves as effective catalysts in the oxidation of CO to CO2.Publication Metadata only Comparative biological network analysis for differentially expressed proteins as a function of bacilysin biosynthesis in Bacillus subtilis(2022) Kutnu, Meltem; İşlerel, Elif Tekin; Özcengiz, Gülay; Department of Chemical and Biological Engineering; Tunçbağ, Nurcan; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 245513The Gram-positive bacterium Bacillus subtilis produces a diverse range of secondary metabolites with different structures and activities. Among them, bacilysin is an enzymatically synthesized dipeptide that consists of L-alanine and L-anticapsin. Previous research by our group has suggested bacilysin’s role as a pleiotropic molecule in its producer, B. subtilis PY79. However, the nature of protein interactions in the absence of bacilysin has not been defined. In the present work, we constructed a protein–protein interaction subnetwork by using Omics Integrator based on our recent comparative proteomics data obtained from a bacilysin-silenced strain, OGU1. Functional enrichment analyses on the resulting networks pointed to certain putatively perturbed pathways such as citrate cycle, quorum sensing and secondary metabolite biosynthesis. Various molecules, which were absent from the experimental data, were included in the final network. We believe that this study can guide further experiments in the identification and confirmation of protein–protein interactions in B. subtilis.Publication Metadata only Improved coating of pancreatic islets with regulatory T cells to create local immunosuppression by using the biotin-polyethylene glycol-succinimidyl valeric acid ester molecule(Elsevier Science Inc, 2014) Golab, K.; Hara, M.; Zielinski, M.; Grose, R.; Savari, O.; Wang, X. -J.; Wang, L. -J.; Tibudan, M.; Krzystyniak, A.; Marek-Trzonkowska, N.; Millis, J. M.; Trzonkowski, P.; Witkowski, P.; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Kızılel, Seda; Bal, Tuğba; Faculty Member; PhD. Student; Department of Chemical and Biological Engineering; College of Engineering; Graduate School of Sciences and Engineering; 28376; N/ABackground. We showed that T regulatory (Treg) cells can be attached to the surface of pancreatic islets providing local immunoprotection. Further optimization of the method can improve coating efficiency, which may prolong graft survival. In this study, we compared the effectiveness of two different molecules used for binding of the Tregs to the surface of pancreatic islets. Our aim was to increase the number of Treg cells attached to islets without compromising islets viability and function. Methods. The cell surface of human Treg cells and pancreatic islets was modified using biotin-polyethylene glycol-N-hydroxylsuccinimide (biotin-PEG-NHS) or biotin-PEG-succinimidyl valeric acid ester (biotin-PEG-SVA). Then, islets were incubated with streptavidin as islet/Treg cells binding molecule. Treg cells were stained with Cell Tracker CM-DiL dye and visualized using a Laser Scanning Confocal Microscope. The number of Treg cells attached per islets surface area was analyzed by Imaris software. The effect of coating on islet functionality was determined using the glucose-stimulated insulin response (GSIR) assay. Results. The coating procedure with biotin-PEG-SVA allowed for attaching 40% more Treg cells per 1 mu m(2) of islet surface. Although viability was comparable, function of the islets after coating using the biotin-PEG-SVA molecule was better preserved than with NHS molecule. GSIR was 62% higher for islets coated with biotin-PEG-SVA compared to biotin-PEG-NHS. Conclusion. Coating of islets with Treg cells using biotin-PEG-SVA improves effectiveness with better preservation of the islet function. Improvement of the method of coating pancreatic islets with Treg cells could further facilitate the effectiveness of this novel immunoprotective approach and translation into clinical settings.Publication Metadata only Competitive hydrogen bonding in aspirin-aspirin and aspirin-leucine interactions(Scientific Technical Research Council Turkey-Tubitak, 2012) Department of Chemistry; Department of Chemical and Biological Engineering; Department of Chemistry; Yurtsever, Zeynep; Erman, Burak; Yurtsever, İsmail Ersin; Undergraduate Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Chemistry; College of Sciences; College of Engineering; College of Sciences; N/A; 179997; 7129Aspirin-aspirin and aspirin-leucine interactions are studied by the density functional theory (DFT) and high level ab initio calculations with second order Moller-Plesset perturbation theory (MP2). The rotational isomers of aspirin are identified by their relative stability both in gaseous phase and in water using the polarizable continuum method (PCM). Local minima of aspirin monomers in water are found to be all highly populated compared to the gas phase behavior. Homodimers of aspirin form hydrogen bonds with bond energies of 10 kcal/mol. Weak hydrogen bonds utilizing phenyl and methyl groups are also found. The interaction between aspirin and leucine is stronger with relatively short bond lengths compared to homodimeric aspirin interactions. The potential energy surface has several minima with comparable stability. This study shows the significance of diverse bonding schemes, which are important for understanding complete interaction mechanisms of aspirin.