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Publication Open Access Simple and green process for silk fibroin production by water degumming(American Chemical Society, 2025-01-05) N/A; KUYTAM (Koç University Surface Science and Technology Center); College of Sciences; College of Engineering; Department of Chemistry; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Atay, İpek; Yağcı, Mustafa Barış; Sürme, Saliha; Kavaklı, İbrahim Halil; Yılgör, Emel; Yılgör, İskender; N/ASilk fibroin (SF), a natural polymer with very desirable physicochemical and biological properties, is an ideal material for crafting biocompatible scaffolds in tissue engineering. However, conventional methods for removing the sericin layer and dissolving SF often involve environmentally harmful reagents and processes, requiring extensive dialysis procedures to purify the fibers produced. Such processes may also damage the surface and bulk properties of the SF produced. Here, we report a simple, green water degumming method, in which almost complete sericin removal of 30% by weight is achieved in 6 h in boiling water. The SF produced is easily dissolved in formic acid/orthophosphoric acid (90/10, 85/15, and 70/30) mixtures, eliminating the need for salts like LiBr and CaCl2 followed by dialysis and freeze-drying, thus simplifying the process significantly. Additionally, our findings demonstrate significantly enhanced cell viability in electrospun poly(lactic acid)/SF blends. Overall, SF production via water degumming offers an eco-friendly pathway for generating bioactive scaffolds in tissue engineering applications.Publication Open Access Multifunctional alginate-based hydrogel with reversible crosslinking for controlled therapeutics delivery(Elsevier, 2020) Ekinci, Duygu; N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Batool, Syeda Rubab; Nazeer, Muhammad Anwaar; Kızılel, Seda; Şahin, Afsun; PhD Student; Faculty Member; Faculty Member; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); Graduate School of Sciences and Engineering; College of Engineering; School of Medicine; N/A; N/A; 28376; 171267Glycan-based alginate hydrogels have great potential in creating new vehicles with responsive behavior and tunable properties for biomedicine. However, precise control and tunability in properties present major barrier for clinical translation of these materials. Here, we report the synthesis of pH responsive anthracene modified glycan-based hydrogels for selective release of therapeutic molecules. Hydrogels were crosslinked through simultaneous photopolymerization of vinyl groups and photodimerization of anthracene. Incorporation of anthracene into these gels leads to reversible control on crosslinking and transition between gel/sol states through dimerization/dedimerization of anthracene groups. Chemotherapeutic drug doxorubicin-loaded hydrogels were then tested in a cancer mimetic microenvironment where 85% of the drug was released from anthracene-conjugated hydrogels at pH 2 for 6 days. Control on gelation with anthracene incorporation was observed through alterations in modulus, where storage modulus was increased two-fold with anthracene conjugation during photopolymerization and photodimerization. Furthermore, cell survival analysis revealed that anthracene conjugation could selectively compromise cancer cell viability without inducing significant toxicity on healthy fibroblasts. This study combines light-induced control of crosslink density due to anthracene and pH-triggered therapeutics delivery with alginate. The approach would be applicable for systems where multiple control is required with high precision.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 SimMBM channel simulator for media-based modulation systems(Institute of Electrical and Electronics Engineers (IEEE), 2021) Yiğit Zehra; Altunbaş, İbrahim; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Başar, Ertuğrul; Faculty Member; College of Engineering; 149116Media-based modulation (MBM), exploiting rich scattering properties of transmission environments via different radiation patterns of a single reconfigurable antenna (RA), has brought new insights into future communication systems. In this study, considering this innovative transmission principle, we introduce the realistic, two-dimensional (2D), and open-source SimMBM channel simulator to support various applications of MBM systems at sub-6 GHz frequency band in different environments.Publication Open Access Hypothetical yet effective: computational identification of high-performing MOFs for CO2 capture(Elsevier, 2022) Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Demir, Hakan; Keskin, Seda; Faculty Member; College of Engineering; N/A; 40548With the advances in computational resources and algorithms, computer simulations are being increasingly used to tackle the most challenging problems of the world. Among them, CO2 capture is a topic that needs imminent attention as the presence of high levels of CO2 in the air can lead to drastic shifts in global climate. Here, a recently developed hypothetical metal-organic framework (MOF) database comprised of anion-pillared (AP) MOFs is computationally screened for the separation of CO2/CO, CO2/H-2, and CO2/N-2 gas mixtures at room temperature. The best performing MOFs are identified using three performance metrics, adsorption selectivity, working capacity, and regenerability, in conjunction. In these top materials, the preferential adsorption sites are illustrated, which will be useful in guiding the experimental design of new MOFs with extraordinarily high CO2 selectivities. The favorable separation performances of AP MOFs suggest that efficient gas separations can be conducted using MOFs without open metal sites.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 Synchronous and asynchronous response in dynamically perturbed proteins(American Chemical Society (ACS), 2021) Erkip, Albert; Erman, Batu; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Hacısüleyman, Aysima; Erman, Burak; Faculty Member; Graduate School of Sciences and Engineering; College of Engineering; N/A; 179997We present a dynamic perturbation-response model of proteins based on the Gaussian Network Model, where a residue is perturbed periodically, and the dynamic response of other residues is determined. The model shows that periodic perturbation causes a synchronous response in phase with the perturbation and an asynchronous response that is out of phase. The asynchronous component results from the viscous effects of the solvent and other dispersive factors in the system. The model is based on the solution of the Langevin equation in the presence of solvent, noise, and perturbation. We introduce several novel ideas: The concept of storage and loss compliance of the protein and their dependence on structure and frequency; the amount of work lost and the residues that contribute significantly to the lost work; new dynamic correlations that result from perturbation; causality, that is, the response of j when i is perturbed is not equal to the response of i when j is perturbed. As examples, we study two systems, namely, bovine rhodopsin and the class of nanobodies. The general results obtained are (i) synchronous and asynchronous correlations depend strongly on the frequency of perturbation, their magnitude decreases with increasing frequency, (ii) time-delayed mean-squared fluctuations of residues have only synchronous components. Asynchronicity is present only in cross correlations, that is, correlations between different residues, (iii) perturbation of loop residues leads to a large dissipation of work, (iv) correlations satisfy the hypothesis of pre-existing pathways according to which information transfer by perturbation rides on already existing equilibrium correlations in the system, (v) dynamic perturbation can introduce a selective response in the system, where the perturbation of each residue excites different sets of responding residues, and (vi) it is possible to identify nondissipative residues whose perturbation does not lead to dissipation in the protein. Despite its simplicity, the model explains several features of allosteric manipulation.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.