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Publication Open Access A multi-state coarse grained modeling approach for an intrinsically disordered peptide(American Institute of Physics (AIP) Publishing, 2017) Department of Chemical and Biological Engineering; N/A; Sayar, Mehmet; Dalgıçdır, Cahit; Ramezanghorbani, Farhad; Faculty Member; PhD Student; Department of Chemical and Biological Engineering; College of Engineering; Graduate School of Sciences and Engineering; 109820; N/A; N/AMany proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LK alpha 14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LK alpha 14 is disordered in dilute solutions; however, it strictly adopts the alpha-helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an alpha-helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results.Publication Open Access A new class of porous materials for efficient CO2 separation: ionic liquid/graphene aerogel composites(Elsevier, 2021) Department of Chemical and Biological Engineering; N/A; Department of Chemistry; Zeeshan, Muhammad; Yalçın, Kaan; Keskin, Seda; Uzun, Alper; Öztuna, Feriha Eylül Saraç; Ünal, Uğur; PhD Student; Faculty Member; Faculty Member; Department of Chemical and Biological Engineering; Department of Chemistry; 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; College of Engineering; College of Sciences; N/A; N/A; 40548; 59917; N/A; 42079Here, we report a new post-synthesis modification strategy for functionalizing reduced graphene aerogels (rGAs) towards an exceptional CO2 separation performance. 1-N-butyl-3-methylimidazolium hexafluorophosphate ([BMIM][PF6]) was impregnated on a rGA, prepared by reducing GA at 700 degrees C, at various ionic liquid (IL) loadings of 5, 10, 30, and 50 wt%. The resulting composites were characterized in deep detail by X-ray photoelectron spectroscopy, X-ray diffraction, N-2 physical adsorption measurements, scanning electron microscopy, Fourier transform infrared and Raman spectroscopies, and thermogravimetric analysis. Results indicated the presence of interactions between the rGA surface and the anion of the IL, potentially improving the CO2 affinity. Volumetric gas adsorption measurements using these materials showed that the deposition of [BMIM][PF6] on rGA surface at an IL loading of 50 wt% boosts the CO2/CH4 selectivity by more than 20-times, exceeding an absolute value of 120, a remarkably higher CO2/CH4 selectivity compared to that of other functionalized materials under similar operating conditions. Tunability of both the IL structure and the surface characteristics of rGA offer a tremendous degree of flexibility for the rational design of these IL/rGA composites towards high performance in gas separation applications.Publication Open Access A novel method for PEGylation of chitosan nanoparticles through photopolymerization(Royal Society of Chemistry (RSC), 2019) Department of Chemical and Biological Engineering; Bozüyük, Uğur; Gökulu, İpek Simay; Doğan, Nihal Olcay; Kızılel, Seda; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; N/A; N/A; N/A; 28376An ultrafast and convenient method for PEGylation of chitosan nanoparticles has been established through a photopolymerization reaction between the acrylate groups of PEG and methacrylated-chitosan nanoparticles. The nanoparticle characteristics under physiological pH conditions were optimized through altered PEG chain length, concentration and duration of UV exposure. The method developed here has potential for clinical translation of chitosan nanoparticles. It also allows for the scalable and fast synthesis of nanoparticles with colloidal stability.Publication Open Access A promising catalyst for the dehydrogenation of perhydro-dibenzyltoluene: Pt/Al2O3 prepared by supercritical CO2 deposition(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Modisha, Phillimon; Garidzirai, Rudaviro; Rommel, Sarshad; Uzunlar, Erdal; Aindow, Mark; Bessarabov, Dmitri; Department of Chemical and Biological Engineering; Bozbağ, Selmi Erim; Erkey, Can; Güneş, Hande; Researcher; Faculty Member; Department of Chemical and Biological Engineering; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); College of Engineering; N/A; 29633; N/APt/Al2O3 catalysts prepared via supercritical deposition (SCD), with supercritical CO2, wet impregnation (WI) methods and a selected benchmark catalyst, were evaluated for the dehydrogenation of perhydro-dibenzyltoluene (H18-DBT) at 300 degrees C in a batch reactor. After ten dehydrogenation runs, the average performance of the catalyst prepared using SCD was the highest compared to the benchmark and WI-prepared catalysts. The pre-treatment of the catalysts with the product (dibenzyltoluene) indicated that the deactivation observed is mainly due to the adsorbed H0-DBT blocking the active sites for the reactant (H18-DBT). Furthermore, the SCD method afforded a catalyst with a higher dispersion of smaller sized Pt particles, thus improving catalytic performance towards the dehydrogenation of H18-DBT. The particle diameters of the SCD- and WI-prepared catalysts varied in the ranges of 0.6-2.2 nm and 0.8-3.4 nm and had average particle sizes of 1.1 nm and 1.7 nm, respectively. Energy dispersive X-ray spectroscopy analysis of the catalysts after ten dehydrogenation runs revealed the presence of carbon. In this study, improved catalyst performance led to the production of more liquid-based by-products and carbon material compared to catalysts with low catalytic performance.
Publication Metadata only A strategy based on protein-protein interface motifs may help in identifying drug off-targets(American Chemical Society (ACS), 2012) Nussinov, Ruth; Department of Chemical and Biological Engineering; Department of Computer Engineering; Keskin, Özlem; Gürsoy, Attila; Ergin, Billur Çelebi; Faculty Member; Faculty Member; Teaching Faculty; Department of Chemical and Biological Engineering; Department of Computer Engineering; The Center for Computational Biology and Bioinformatics (CCBB); College of Engineering; College of Engineering; 26605; 8745; 261792Networks are increasingly used to study the impact of drugs at the systems level. From the algorithmic standpoint, a drug can "attack" nodes or edges of a protein-protein interaction network In this work, we propose a new network strategy, "The Interface Attack", based on protein-protein interfaces. Similar interface architectures can occur between unrelated proteins. Consequently, in principle, a drug that binds to one has a certain probability of binding to others. The interface attack strategy simultaneously removes from the network all interactions that consist of similar interface motifs. This strategy is inspired by network pharmacology and allows inferring potential off-targets. We introduce a network model that we call "Protein Interface and Interaction Network (P2IN)", which is the integration of protein-protein interface structures and protein interaction networks. This interface based, network organization clarifies which protein pairs have structurally similar interfaces and which proteins may compete to bind the same surface region. We built the P2IN with the p53 signaling network and performed network robustness analysis. We show that (1) "hitting" frequent interfaces (a set of edges distributed around the network) might be as destructive as eleminating high degree proteins (hub nodes), (2) frequent interfaces are not always topologically critical elements in the network, and (3) interface attack may reveal functional changes in the system better than the attack of single proteins. In the off target detection case study, we found that drugs blocking the interface between CDK6 and CDKN2D may also affect the interaction between CDK4 and CDKN2D.Publication Metadata only A three-dimensional silver(I) framework assembled from 3,3′- thiodipropionate: synthesis, structure and molecular simulations for hydrogen gas adsorption(Pergamon-Elsevier Science Ltd, 2012) Arıcı, Mürsel; Yeşilel, Okan Zafer; Taş, Murat; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548A novel three dimensional Ag(I)-3,3'-thiodipropionate metal organic framework, [Ag-2(mu(8)-tdp)](n) (1) (tdpH(2) = 3,3'-thiodipropionic acid), was synthesized and structurally characterized by FT-IR and photoluminescence spectroscopy, single crystal X-ray diffraction techniques and thermal analysis (TG, DTG and DTA). The compound crystallized in the monoclinic crystal system with the space group C2/c. The X-ray crystallographic study of 1 shows a short Ag center dot center dot center dot Ag contact with a distance of 3.022 angstrom. The most striking feature of 1 is that it exhibits a 3D porous framework with 1D infinite channels, and complex 1 exhibits strong fluorescent emission bands in the solid state at room temperature. Moreover, atomically detailed simulations were used to assess the potential of the complex for H-2 storage applications.Publication Metadata only A two-dimensional photoluminescent cadmium(ii) coordination polymer containing a new coordination mode of pyridine-2,3-dicarboxylate: synthesis, structure and molecular simulations for gas storage and separation applications(Elsevier, 2013) Semerci, Fatih; Yesilel, Okan Zafer; Soylu, Mustafa Serkan; Buyukgungor, Orhan; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548A novel two-dimensional (2D) coordination polymer, [Cd(mu-pydc)(2-meim)](n) (1) (pydc = pyridine-2,3-dicarboxylate, 2-meim = 2-methylimidazole) was synthesized and characterized by spectral methods (FT-IR and photoluminescence), elemental analysis, thermal analysis (TG, DTG and DTA) and single crystal X-ray diffraction techniques. Complex 1 displays a 2D layer structure through the linkage of bridging carboxyl oxygen and pyridine nitrogen atoms of the pydc ligand. Each Cd(II) center exhibits a distorted octahedral coordination environment with four carboxylate oxygen atoms and two nitrogen atoms from the pydc and 2-meim ligands. In 1, the pydc ligand exhibits a new coordination mode. The distances of adjacent Cd(II) atoms are 3.679 and 7.742 angstrom. The 2D layers are further linked by C-H.. .pi and pi...pi stacking to construct a 3D supramolecular structure. In order to assess the potential of 1 in gas storage and gas separation applications, molecular simulations were performed. Furthermore, 1 exhibits blue photoluminescence in the solid state at room temperature.Publication Metadata only A zinc(II) metal organic framework based on flexible o-phenylenediacetate and rigid 4,4′-azobis(pyridine) ligands: synthesis, crystal structure and hydrogen gas adsorption property(Pergamon-Elsevier Science Ltd, 2015) Gunay, Gunes; Yesilel, Okan Zafer; Erer, Hakan; Tabak, Ahmet; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548A new three-dimensional (3D) metal organic framework, [Zn-2(mu(4)-o-pda)(2)(mu-abpy)](n) (1), has been synthesized by the hydrothermal reaction and characterized by FT-IR spectroscopy, elemental analysis, thermal analysis, X-ray powder diffraction, and single crystal X-ray diffraction techniques (o-H(2)pda = o-phenylenediacetic acid and abpy = 4,4'-azobis(pyridine)). Single crystal X-ray diffraction study reveals that complex 1 exhibits a binodal (3,7)-connected three-dimensional framework (3D) with the point symbol of (3.5(2))(3(2).4(4).5(7).6(7).7). Thermal analysis reveal that complex 1 is stable up to 300 degrees C. In order to investigate the potential of 1 in gas storage applications, we performed experiments and atomically detailed simulations to obtain H-2 adsorption isotherm at a pressure range of 0-1 atm at 77 K.Publication Metadata only Adsorption and transport of CH4, CO2, H-2 mixtures in a bio-MOF material from molecular simulations(Amer Chemical Soc, 2011) N/A; N/A; Department of Chemical and Biological Engineering; Atcı, Erhan; Eruçar, İlknur; Keskin, Seda; Master Student; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 260094; 40548Accurate description of gas adsorption and diffusion in nanoporous materials is crucial in envisioning new materials for adsorption-based and membrane-based gas separations. This study provides the first information about the equilibrium and transport properties of different gas mixtures in a bio-metal organic framework (bio-MOF). Adsorption isotherms and self-diffusivity coefficients of CH4, CO2, H-2, and their binary mixtures in bio-MOF-11 were computed using grand canonical Monte Carlo and equilibrium molecular dynamics simulations. Results showed that bio-MOF-11 exhibits significantly higher adsorption selectivity for CO2 over CH4 and H-2 than the widely studied MOFs. Bio-MOF-11 outperforms several isoreticular MOFs, traditional zeolites, and zeolite imidazolate frameworks in membrane-based separations of CH4/H-2, CO2/CH4, and CO2/H-2 mixtures due to its high gas permeability and permeation selectivity. The methods used in this work will assess the potential of bio-MOFs in gas separations and accelerate development of new bio-MOFs for targeted applications by providing molecular insights into adsorption transport of gas mixtures.Publication Metadata only Adsorption of Pt(cod)me(2) onto organic aerogels from supercritical solutions for the synthesis of supported platinum nanoparticles(Elsevier Science Bv, 2011) Yasar, N. S.; Zhang, L. C.; Aindow, M.; N/A; Department of Chemical and Biological Engineering; Bozbağ, Selmi Erim; Erkey, Can; Researcher; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; College of Engineering; N/A; 29633The thermodynamics and kinetics of adsorption of Pt(cod)me(2) onto resorcinol-formaldehyde aerogel (RFA) from supercritical carbon dioxide (scCO(2)) was investigated by using high performance liquid chromatography (HPLC) to measure Pt(cod)me(2) concentrations in the fluid phase. It was found that the adsorption isotherms of Pt(cod)me(2) at 35 degrees C for different CO2 pressures could be represented by modified Langmuir isotherms. The kinetics of adsorption was determined by following the Pt(cod)me(2) uptake of the RFA spheres; these data correspond closely to the behavior from a mass transfer model based on diffusion within the pore volume with the assumption of local equilibrium at the solid-fluid interface. The adsorbed Pt(cod)me(2) molecules were reduced at atmospheric pressure under flowing hydrogen at 200 degrees C. The resultant Pt nanoparticles were distributed uniformly on the surface and had narrow size distributions. The average particle size of the nanoparticles increased with platinum loading from 2.0 nm at 10 wt.% to 3.3 nm at 34 wt.%. The Pt nanoparticles in an RFA pellet had a uniform radial size distribution, even though the pellet was impregnated with Pt(cod)me(2) for too short a short period of time for the system to reach adsorption equilibrium. The high mobility of the atomic Pt evolved during the reduction process is believed to be responsible for this phenomenon. Performing the adsorption of Pt(cod)me(2) onto RFA at 80 degrees C led to concurrent reduction and Pt nanoparticle growth. (C) 2010 Elsevier B.V. All rights reserved.