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Publication Open Access Database for CO2 separation performances of MOFs based on computational materials screening(American Chemical Society (ACS), 2018) Eruçar, İlknur; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Altıntaş, Çiğdem; Avcı, Gökay; Harman, Hilal Dağlar; Azar, Ayda Nemati Vesali; Velioğlu, Sadiye; Keskin, Seda; Researcher; Post Doctorate Student; College of Engineering; N/A; N/A; N/A; N/A; N/A; 40548Metal-organic frameworks (MOFs) are potential adsorbents for CO2 capture. Because thousands of MOFs exist, computational studies become very useful in identifying the top performing materials for target applications in a time-effective manner. In this study, molecular simulations were performed to screen the MOF database to identify the best materials for CO2 separation from flue gas (CO2/N-2) and landfill gas (CO2/CH4) under realistic operating conditions. We validated the accuracy of our computational approach by comparing the simulation results for the CO2 uptakes, CO2/N-2 and CO2/CH4 selectivities of various types of MOFs with the available experimental data. Binary CO2/N-2 and CO2/CH4 mixture adsorption data were then calculated for the entire MOF database. These data were then used to predict selectivity, working capacity, regenerability, and separation potential of MOFs. The top performing MOF adsorbents that can separate CO2/N-2 and CO2/CH4 with high performance were identified. Molecular simulations for the adsorption of a ternary CO2/N-2/CH4 mixture were performed for these top materials to provide a more realistic performance assessment of MOF adsorbents. The structure-performance analysis showed that MOFs with Delta Q(st)(0) > 30 kJ/mol, 3.8 angstrom < pore-limiting diameter < 5 angstrom, 5 angstrom < largest cavity diameter < 7.5 angstrom, 0.5 < phi < 0.75, surface area < 1000 m(2)/g, and rho > 1 g/cm(3) are the best candidates for selective separation of CO2 from flue gas and landfill gas. This information will be very useful to design novel MOFs exhibiting high CO2 separation potentials. Finally, an online, freely accessible database https://cosmoserc.ku.edu.tr was established, for the first time in the literature, which reports all of the computed adsorbent metrics of 3816 MOFs for CO2/N-2, CO2/CH4, and CO2/N-2/CH4 separations in addition to various structural properties of MOFs.Publication Open Access Improving CO2 separation performance of MIL-53(Al) by incorporating 1-N-Butyl-3-methylimidazolium methyl sulfate(Wiley, 2019) Department of Chemical and Biological Engineering; N/A; Department of Chemical and Biological Engineering; Kulak, Harun; Polat, Hüsamettin Mert; Kavak, Safiyye; Keskin, Seda; Uzun, Alper; Faculty Member; 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; N/A; N/A; N/A; 40548; 599171-n-Butyl-3-methylimidazolium methyl sulfate is incorporated into MIL-53(Al). Detailed characterization is done by X-ray fluorescence, Brunauer-Emmett-Teller surface area, scanning electron microscopy, X-ray diffraction, Fourier-transform infrared spectroscopy, and thermogravimetric analysis. Results show that ionic liquid (IL) interacts directly with the framework, significantly modifying the electronic environment of MIL-53(Al). Based on the volumetric gas adsorption measurements, CO2, CH4, and N-2 adsorption capacities decreased from 112.0, 46.4, and 19.6 cc (STP) g(MIL-53(Al))(-1) to 42.2, 13.0, and 4.3 cc (STP) g(MIL-53(Al))(-1) at 5 bar, respectively, upon IL incorporation. Data show that this postsynthesis modification leads to more than two and threefold increase in the ideal selectivity for CO2 over CH4 and N-2 separations, respectively, as compared with pristine MIL-53(Al). The isosteric heat of adsorption (Qst) values show that IL incorporation increases CO2 affinity and decreases CH4 and N-2 affinities. Cycling adsorption-desorption measurements show that the composite could be regenerated with almost no decrease in the CO2 adsorption capacity for six cycles and confirm the lack of any significant IL leaching. The results offer MIL-53(Al) as an excellent platform for the development of a new class of IL/MOF composites with exceptional performance for CO2 separation.Publication Open Access Engineering human stellate cells for beta cell replacement therapy promotes in vivo recruitment of regulatory T cells(Elsevier, 2019) N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Oran, Dilem Ceren; Lokumcu, Tolga; Bal, Tuğba; İnceoğlu, Yasemin; Albayrak, Özgür; Erkan, Murat Mert; Kurtoğlu, Metin; Can, Füsun; Önder, Tuğba Bağcı; Kızılel, Seda; Akolpoğlu, Mükrime Birgül; Faculty Member; Faculty Member; Master Student; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; Graduate School of Health Sciences; College of Engineering; School of Medicine; N/A; N/A; N/A; N/A; N/A; N/A; N/A; 103165; 184359; 28376; N/AType 1 diabetes (T1D) is an autoimmune disease characterized by destruction of pancreatic β cells. One of the promising therapeutic approaches in T1D is the transplantation of islets; however, it has serious limitations. To address these limitations, immunotherapeutic strategies have focused on restoring immunologic tolerance, preventing transplanted cell destruction by patients’ own immune system. Macrophage-derived chemokines such as chemokine-ligand-22 (CCL22) can be utilized for regulatory T cell (Treg) recruitment and graft tolerance. Stellate cells (SCs) have various immunomodulatory functions: recruitment of Tregs and induction of T-cell apoptosis. Here, we designed a unique immune-privileged microenvironment around implantable islets through overexpression of CCL22 proteins by SCs. We prepared pseudoislets with insulin-secreting mouse insulinoma-6 (MIN6) cells and human SCs as a model to mimic naive islet morphology. Our results demonstrated that transduced SCs can secrete CCL22 and recruit Tregs toward the implantation site in vivo. This study is promising to provide a fundamental understanding of SC-islet interaction and ligand synthesis and transport from SCs at the graft site for ensuring local immune tolerance. Our results also establish a new paradigm for creating tolerable grafts for other chronic diseases such as diabetes, anemia, and central nervous system (CNS) diseases, and advance the science of graft tolerance.Publication Open Access The epidemiological and molecular characterization of vancomycin-resistant enterococci Isolated from rectal swab samples of hospitalized patients in Turkey(Clinical Laboratory, 2014) Çakırlar, Fatma Köksal; Karakullukçu, Asiye; Sirekbasan, Serhat; Bağdatlı, Yaşar; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Barış, İbrahim; Kavaklı, İbrahim Halil; Teaching Faculty; College of Engineering; 111629; 40319Background: Vancomycin-resistant enterococci (VRE) are a serious problem all over the world. The present study was conducted to investigate antimicrobial resistance patterns, genotypes, clonal relationship, and virulence factors of VRE species isolated from rectal swab samples of hospitalized patients, patient's relatives, and medical staff at Istanbul University Cerrahpasa Medical School hospital. Methods: The VRE isolates were typed with an automated VITEK system and their antibiotic sensibilities were analysed by disc diffusion and Etest (R) method. The molecular characterization and clonal relationships were performed using a PCR method and virulence genes by sequence typing. Results: A total of 100 (10.3%) of the 971 patients were colonized with VRE. None of the investigated 25 patient's relatives and 45 medical staff carried VRE. All VRE strains were identified as E. faecium. They were vanA geno-type and originated from a single clone. VRE strains exhibited multi-drug resistance. High-level gentamicin-resistance was 93%. However, lower resistance rates were found for linezolid (40%) and quinopristin-dalfopristin (11%). The enterococcal surface protein gene esp was found positive in 87 of 100 isolates, and four strains were positive for the cylB (cytolysin) gene. Conclusions: The identification of VRE strains to the species level and detection of virulence genes will assist in infection control practices.Publication Open Access Analysis of correlations between energy and residue fluctuations in native proteins and determination of specific sites for binding(American Physical Society (APS), 2009) Haliloğlu, Turkan; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; College of Engineering; 179997The Gaussian network model is used to derive the correlations between energy and residue fluctuations in native proteins. Residues are identified that respond strongly to energy fluctuations and that display correlations with the remaining residues of the protein at the highest modes. We postulate that these residues are located at specific sites for drug binding. We test the validity of this postulate on a data set of 33 structurally distinct proteins in the unbound state. Detailed results are presented for drug binding to the HIV protease.Publication Open Access Large-scale computational screening of MOF membranes and MOF-based polymer membranes for H2/N2 separations(American Chemical Society (ACS), 2019) Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Azar, Ayda Nemati Vesali; Velioğlu, Sadiye; Keskin, Seda; Graduate School of Sciences and Engineering; N/A; 200650; 40548Several thousands of metal organic frameworks (MOFs) have been reported to date, but the information on H-2/N-2 separation performances of MOF membranes is currently very limited in the literature. We report the first large-scale computational screening study that combines state-of-the-art molecular simulations, grand canonical Monte Carlo (GCMC) and molecular dynamics (MD), to predict H-2 permeability and H-2/N-2 selectivity of 3765 different types of MOF membranes. Results showed that MOF membranes offer very high H-2 permeabilities, 2.5 x 10(3) to 1.7 x 10(6) Barrer, and moderate H-2/N-2 membrane selectivities up to 7. The top 20 MOF membranes that exceed the polymeric membranes' upper bound for H-2/N-2 separation were identified based on the results of initial screening performed at infinite dilution condition. Molecular simulations were then carried out considering binary H-2/N-2 and quaternary H-2/N-2/CO2/CO mixtures to evaluate the separation performance of MOF membranes under industrial operating conditions. Lower H-2 permeabilities and higher N-2 permeabilities were obtained at binary mixture conditions compared to the ones obtained at infinite dilution due to the absence of multicomponent mixture effects in the latter. Structure performance relations of MOFs were also explored to provide molecular-level insights into the development of new MOF membranes that can offer both high H-2 permeability and high H-2/N-2 selectivity. Results showed that the most promising MOF membranes generally have large pore sizes (>6 A) as well as high surface areas (>3500 m(2)/g) and high pore volumes (>1 cm(3)/g). We finally examined H-2/N-2 separation potentials of the mixed matrix membranes (MMMs) in which the best MOF materials identified from our high-throughput screening were used as fillers in various polymers. Results showed that incorporation of MOFs into polymers almost doubles H-2 permeabilities and slightly enhances H-2/N-2 selectivities of polymer membranes, which can advance the current membrane technology for efficient H-2 purification.Publication Open Access Predicting important residues and ınteraction pathways in proteins using Gaussian network model: binding and stability of HLA proteins(Public Library of Science, 2010) Haliloğlu, Türkan; Gül, Ahmet; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; College of Engineering; 179997A statistical thermodynamics approach is proposed to determine structurally and functionally important residues in native proteins that are involved in energy exchange with a ligand and other residues along an interaction pathway. The structure-function relationships, ligand binding and allosteric activities of ten structures of HLA Class I proteins of the immune system are studied by the Gaussian Network Model. Five of these models are associated with inflammatory rheumatic disease and the remaining five are properly functioning. In the Gaussian Network Model, the protein structures are modeled as an elastic network where the inter-residue interactions are harmonic. Important residues and the interaction pathways in the proteins are identified by focusing on the largest eigenvalue of the residue interaction matrix. Predicted important residues match those known from previous experimental and clinical work. Graph perturbation is used to determine the response of the important residues along the interaction pathway. Differences in response patterns of the two sets of proteins are identified and their relations to disease are discussed.Publication Open Access Investigation of hydrodynamic behavior of alginate aerogel particles in a laboratory scale Wurster fluidized bed(Multidisciplinary Digital Publishing Institute (MDPI), 2019) Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Erkey, Can; Akgün, Işık Sena; Faculty Member; Researcher; Graduate School of Sciences and Engineering; 29633; N/AThe effects of design and operating parameters on the superficial velocity at the onset of circulatory motion and the residence time of alginate aerogel particles in a laboratory scale Wurster fluidized bed were investigated. Several sets of experiments were conducted by varying Wurster tube diameter, Wurster tube length, batch volume and partition gap height. The superficial velocities for Wurster tube with 10 cm diameter were lower than the tube with 8 cm diameter. Superficial velocities increased with increasing batch volume and partition gap height. Moreover, increasing batch volume and partition gap height led to a decrease in the particle residence time in the Wurster tube. The results showed that there is an upper limit for each parameter in order to obtain a circulatory motion of the particles. It was found that the partition gap height should be 2 cm for proper particle circulation. Maximum batch volume for the tube with 10 cm diameter was found as 500 mL whereas maximum batch volume was 250 mL for the tube with 8 cm diameter. The fluidization behavior of the aerogel particles investigated in this study could be described by the general fluidization diagrams in the literature.Publication Open Access Observation of the correlations between pair wise interaction and functional organization of the proteins, in the protein ınteraction network of saccaromyces cerevisiae(World Academy of Science, Engineering and Technology (WASET), 2008) Haliloğlu, T.; Department of Computer Engineering; Department of Chemical and Biological Engineering; Department of Computer Engineering; Department of Chemical and Biological Engineering; Tunçbağ, Nurcan; Keskin, Özlem; Faculty Member; College of Engineering; N/A; 26605Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins.Publication Open Access Experimental verification of gap metric as a tool for model selection in multi-linear model-based control(Elsevier, 2004) Galan, O.; Romagnoli, J. A.; Palazoğlu, A.; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Arkun, Yaman; Faculty Member; College of Engineering; 108526A nonlinear system can be modeled using a set of linear models that cover the range of operation. A model-based control strategy then can be employed that uses the local models in a cooperative manner to control the nonlinear system. The decision of how many models are sufficient for effective control can be tackled by the use of the gap metric that quantifies the distance between two linear operators. A pH control experiment is used to demonstrate the effectiveness of gap metric as a tool for model selection.