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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Publication Metadata only Effects of ligand binding upon flexibility of proteins(Wiley-Blackwell, 2015) Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997Binding of a ligand on a protein changes the flexibility of certain parts of the protein, which directly affects its function. These changes are not the same at each point, some parts become more flexible and some others become stiffer. Here, an equation is derived that gives the stiffness map for proteins. The model is based on correlations of fluctuations of pairs of points in proteins, which may be evaluated at different levels of refinement, ranging from all atom molecular dynamics to general elastic network models, including the simplest case of isotropic Gaussian Network Model. The latter is used, as an example, to evaluate the changes of stiffness upon dimerization of ACK1. Proteins 2015; 83:805-808. (c) 2015 Wiley Periodicals, Inc.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 How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues(Cell Press, 2005) Haliloğlu, Türkan; Ma, Buyong; Nussinov, Ruth; Department of Chemical and Biological Engineering; Keskin, Özlem; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 26605The underlying physico-chemical principles of the interactions between domains in protein folding are similar to those between protein molecules in binding. Here we show that conserved residues and experimental hot spots at intermolecular binding interfaces overlap residues that vibrate with high frequencies. Similarly, conserved residues and hot spots are found in protein cores and are also observed to vibrate with high frequencies. In both cases, these residues contribute significantly to the stability. Hence, these observations validate the proposition that binding and folding are similar processes. In both packing plays a critical role, rationalizing the residue conservation and the experimental alanine scanning hot spots. We further show that high-frequency vibrating residues distinguish between protein binding sites and the remainder of the protein surface.Publication Metadata only Opportunities and challenges of MOF-based membranes in gas separations(Elsevier, 2015) Avci, Ahmet K.; N/A; Department of Chemical and Biological Engineering; Adatoz, Elda Beruhil; Keskin, Seda; PhD Student; Faculty Member; Department of Chemical and Biological Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 40548Gas separation using metal organic framework (MOF) membranes has become an increasingly important research field over the last years. Several recent studies have shown that thin-film MOF membranes and MOF/polymer composite membranes can outperform well known polymer and zeolite membranes in various gas separation applications. The continuously increasing number of experimental and computational studies emphasizes the superior membrane properties of MOFs. In this review, we present a summary of experimental and computational studies both for thin-film MOF membranes and MOF/polymer composite membranes. We aim to address opportunities and challenges related with use of MOF membranes for gas separations as well as give directions on the requirements for employing these membranes in practical applications. (C) 2015 Elsevier B.V. All rights reserved.Publication Metadata only The synthesis, characterization, and theoretical hydrogen gas adsorption properties of copper(II)-3,3′-thiodipropionate complexes with imidazole derivatives(Taylor and Francis Ltd, 2013) Arici, Mursel; Yesilel, Okan Zafer; Sahin, Onur; Buyukgungor, Orhan; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548Three new coordination polymers, [Cu((3)-tdp)(im)(2)](n) (1), {[Cu((3)-tdp)(1-mim)(2)]0.5H(2)O}(n) (2) and {[Cu-2((3)-tdp)(2)(4-mim)(4)]H2O}(n) (3) [tdpH(2)=3,3-thiodipropionic acid, im=imidazole, 1-mim=1-methylimidazole and 4-mim=4-methylimidazole], have been prepared and characterized by spectroscopic techniques (IR and UV-Vis), elemental analyzes, magnetic measurements, thermal analyzes, and single-crystal X-ray diffraction. Complexes 1-3 crystallize in the monoclinic system with space groups of C2/c and P2(1)/c, respectively. In 1-3, tdp is a bridging ligand to form 1-D chains, which are extended into a 2-D layer by hydrogen bonding and interactions. The 3,3-thiodipropionate exhibits an unexpected coordination mode in 1-3. Simulations were used to assess the potential of the complexes in H-2 storage applications.Publication Metadata only Control of optical anisotropy at large deformations in PMMA/chlorinated-PHB (PHB-Cl) blends: mechano-optical behavior(Elsevier Sci Ltd, 2006) Yalçın, Barış; Çakmak, Mükerrem; Arkın, Ali Hakan; Hazer, Baki; Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997There is a continuing need to produce polymer films with high optical clarity with ability to dial in the optical properties including refractive indices and optical anisotropies. In this research, we investigated the mechano-optical behavior of PMMA/PHB-Cl blend films during uniaxial deformation and mapped out the composition-birefringence-processing relationships. The results indicate the presence of a broad glass transition for the composition range investigated that indicates the development of micro-heterogeneities particularly at the higher concentration of PHB-Cl. However, this did not detrimentally influence the optical transparency of the solvent cast films as the size of these micro-heterogeneities remains well below the size range to affect the transparency. Optical retardation behavior of the films can be altered from negative to positive by increasing the PHB-Cl concentration from 0 to 20 wt%. The films with 18 wt% PHB-Cl are predicted to exhibit zero birefringence even when they are stretched to large deformations. This dialability of optical properties makes these materials suitable for optical device applications such as CD and DVDs as well as optical retarder films for liquid-crystal display applications. (c) 2006 Elsevier Ltd. All rights reserved.Publication Metadata only Gap metric concept and implications for multilinear model-based controller design(Amer Chemical Soc, 2003) Galan, O.; Romagnoli, J.A.; Palazoglu, A.; Department of Chemical and Biological Engineering; Arkun, Yaman; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 108526The gap metric concept is used within the context of multilinear model-based control. The concept of distance between dynamic systems is used as a criterion for selecting a set of models that can explain the nonlinear plant behavior in a given operating range. The case studies presented include a CSTR and a pH neutralization reactor. The gap metric is used to analyze the relationships among candidate models, resulting in a reduced model set that provides enough information to design multilinear controllers. The simulation and experimental results indicate good performance and stability features.Publication Metadata only MOF materials as therapeutic agents, drug carriers, imaging agents and biosensors in cancer biomedicine: recent advances and perspectives(Elsevier, 2021) Bieniek, Adam; Terzyk, Artur P.; Wisniewski, Marek; Roszek, Katarzyna; Kowalczyk, Piotr; Sarkisov, Lev; Kaneko, Katsumi; Department of Chemical and Biological Engineering; Keskin, Seda; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 40548We summarize recent advances in application of MOFs as therapeutic agents, drug carriers, imaging agents and biosensors in cancer biomedicine. A holistic perspective is adopted to produce a comprehensive, critical and readable document useful to a broad community in chemistry, material science, medical fields etc. None of the previous articles adopted a holistic approach focusing on a specific disease or area, such as cancer. MOFs have a tremendous potential in cancer diagnostics and treatment. Although a new field, the amount of literature and data accumulated in this area is vast, quickly growing and requires some systematization and processing. We propose a broad overview of MOF-related literature in the treatment and diagnosis of cancer. In our study, we set: (i) to consolidate the most important and up to date information from the field of MOFs applications in medicine, particularly in anticancer therapy; and to reflect these developments in one, comprehensive study, (ii) to highlight new and emerging topics in the field, (iii) to tabulate the large number of the application examples and case studies to make the information more accessible and easy to follow, (iv) and finally, to broadly reflect on the potential of MOFs in application to cancer treatment, including the existing challenges and emerging opportunities.Publication Metadata only Metal-organic framework-based materials for the abatement of air pollution and decontamination of wastewater(PERGAMON-ELSEVIER SCIENCE LTD, 2022) Erucar, Ilknur; Heidari, Golnaz; Zare, Ehsan Nazarzadeh; Moradi, Omid; Srivastava, Varsha; Iftekhar, Sidra; Sillanpaa, Mika; N/A; N/A; Department of Chemical and Biological Engineering; Harman, Hilal Dağlar; Altıntaş, Çiğdem; Keskin, Seda; PhD Student; Researcher; Faculty Member; Department of Chemical and Biological Engineering; N/A; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; N/A; 40548Developing new and efficient technologies for environmental remediation is becoming significant due to the increase in global concerns such as climate change, severe epidemics, and energy crises. Air pollution, primarily due to increased levels of H2S, SOx, NH3, NOx, CO, volatile organic compounds (VOC), and particulate matter (PM) in the atmosphere, has a significant impact on public health, and exhaust gases harm the natural sulfur, nitrogen, and carbon cycles. Similarly, wastewater discharged to the environment with metal ions, herbicides, pharmaceuticals, personal care products, dyes, and aromatics/organic compounds is a risk for health since it may lead to an outbreak of waterborne pathogens and increase the exposure to endocrine-disrupting agents. Therefore, developing new and efficient air and water quality management systems is critical. Metal-organic frameworks (MOFs) are novel materials for which the main application areas include gas storage and separation, water harvesting from the atmosphere, chemical sensing, power storage, drug delivery, and food preservation. Due to their versatile structural motifs that can be modified during synthesis, MOFs also have a great promise for green applications including air and water pollution remediation. The motivation to use MOFs for environmental applications prompted the modification of their structures via the addition of metal and functional groups, as well as the creation of heterostructures by mixing MOFs with other nanomaterials, to effectively remove haz-ardous contaminants from wastewater and the atmosphere. In this review, we focus on the state-of-the-art environmental applications of MOFs, particularly for water treatment and air pollution, by highlighting the groundbreaking studies in which MOFs have been used as adsorbents, membranes, and photocatalysts for the abatement of air and water pollution. We finally address the opportunities and challenges for the environmental applications of MOFs.Publication Metadata only ADCHEM 2009 special issue(Elsevier Sci Ltd, 2010) Engell, Sebastian; Department of Chemical and Biological Engineering; Arkun, Yaman; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 108526