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Publication Metadata only Conformational changes and small world association in proteins(Institute of Physics (IOP) Publishing, 2005) Cetinkaya, M.; Salway, L.; Demirel, M.; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Keskin, Özlem; Faculty Member; College of Engineering; 26605A set of proteins which exhibit domain motions, are analyzed by an elastic network model. We calculated the fluctuation and cooperativity of residues with low amplitude fluctuations across different domain motions. Slow modes that are associated with the function of proteins have common features among different protein structures. In addition, we have calculated network parameters such as connectivity and path length for the same set of proteins. Higher level of connectivity and lower level of path length are obtained as the protein moves from open to closed conformation. This paper focuses on the importance of large degree of conformational freedom in proteins while maintain their native state.Publication Metadata only Design of reverse logistics network for waste batteries with an application in Turkey(aidic Servizi Srl, 2013) N/A; Department of Industrial Engineering; Department of Industrial Engineering; Dönmez, İrem; Türkay, Metin; Master Student; Faculty Member; Graduate School of Sciences and Engineering; College of Engineering; N/A; 24956the demand for portable electronic devices grows everyday and the batteries that power them pose important environmental problems. Batteries contain heavy metals such as; lead, mercury, cadmium that can contaminate the environment when batteries are disposed of improperly. the question is "How to manage this large amount of waste batteries?" in order to minimize the negative impacts of batteries on the environment, legislations have been published in the last two decades. in Turkey, the Regulation on Control of Waste Batteries and accumulators aPaK is published in 2004 and the project 'Development of Waste Battery Disposal and Recycling Technologies' is in progress. Within the scope of the project we do research on logistics of waste batteries. a multi period mixed-integer linear programming (MILP) model is developed to design the reverse logistics network for waste batteries. We solved the model with the objective of minimizing the total present value of waste battery management system under a variety of scenarios in order to provide an effective decision support tool and offer useful outputs to decision-makers.Publication Metadata only Detection of interaction constants between biological clock proteins by Surface Plasmon Resonance(AIChE, 2012) Çakır, Bilal; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Kızılel, Seda; Kavaklı, İbrahim Halil; Gidon, Doğan; Asımgil, Hande; Kızılel, Rıza; Kepsütlü, Burcu; Demirer, Gözde Sultan; Faculty Member; Faculty Member; Undergraduated Student; PhD Student; Researcher; Master Student; Undergraduated Student; College of Engineering; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; 28376; 40319; N/A; N/A; 114475; N/A; N/AOrganisms adopt their behaviors and physiology to the appropriate time of the day to anticipate daily environmental changes and the circadian clock regulates their daily rhythms. In mammals, the clock is present in essentially every cell. A heterodimer of CLOCK and BMAL1 proteins binds to the E-box in Per and Cry promoters and activates their transcription. In this work, we have purified core clock proteins and characterized the affinity of previously identified clock-relevant transcription factors. We have investigated the mechanism of the clock complex and the interactions of clock proteins with and without DNA using Surface Plasmon Resonance (SPR). Kinetic parameters determined from real time data bring a solid insight into the interactions of the clock proteins with their cognate promoter.Publication Metadata only Gold nanoparticle-assisted AFM study of DNA damage and repair(2009) N/A; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; N/A; N/A; Department of Chemical and Biological Engineering; Kızılel, Seda; Kavaklı, İbrahim Halil; Demir, Enis; Asımgil, Hande; Faculty Member; Faculty Member; Master Student; PhD Student; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; 28376; 40319; N/A; N/AThe purpose of this research is to investigate gold nanoparticles as a potential scaffold for the characterization of DNA damage and repair using atomic force microscopy (AFM) techniques. The procedure consists of functionalizing the surface of gold nanoparticles with DNA which are then immobilized onto amine modified silicon or glass surfaces. Our objective is to examine various lesions in individual DNA molecules and follow in the AFM their direct reversal by DNA repair enzymes. In order to achieve this goal DNA repair proteins such as photolyase (repairs UV damaged thymine dimers in DNA using blue-light energy) is used as damage markers and imaged in complexes with DNA by AFM in order to locate and identify the damage sites. Force spectroscopy measurements will determine the mechanical Fingerprints of various types of DNA damage caused by UV and gamma radiation and directly follow damage reversal in the presence of the repair activities. AFM images will be further compared with in vitro photoreactivation assay results.Publication Metadata only Inhibitor peptide design for NF- KB: Markov model and genetic algorithm(IEEE, 2010) N/A; Department of Computer Engineering; Department of Chemical and Biological Engineering; Department of Computer Engineering; Department of Chemical and Biological Engineering; Ünal, Evrim Besray; Gürsoy, Attila; Erman, Burak; PhD Student; Faculty Member; Faculty Member; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; 8745; 179997Two peptide design approaches are proposed to block activities of disease related proteins. First approach employs a probabilistic method; the problem is set as Markov chain. The possible binding site of target protein and a path on this binding site are determined. 20 natural amino acids and 400 dipeptides are docked to the selected path using the AutoDock software. The statistical weight matrices for the binding energies are derived from AutoDock results; matrices are used to determine top 100 peptide sequences with affinity to target protein. Second approach utilizes a heuristic method for peptide sequence determination; genetic algorithm (GA) with tournament selection. The amino acids are the genes; the peptide sequences are the chromosomes of GA. Initial random population of 100 chromosomes leads to determination of 100 possible binding peptides, after 8-10 generations of GA. Thermodynamic properties of the peptides are analyzed by a method that we proposed previously. NF-κB protein is selected as case-study.Publication Metadata only Magnetic actuated moems resonant biosensor array(IEEE, 2010) Department of Electrical and Electronics Engineering; N/A; Department of Chemical and Biological Engineering; N/A; Department of Electrical and Electronics Engineering; Department of Chemical and Biological Engineering; Ürey, Hakan; Timurdoğan, Erman; Kavaklı, İbrahim Halil; Alaca, Burhanettin Erdem; Nargül, Sezin; Faculty Member; Undergraduate Student; Faculty Member; Faculty Member; PhD Student; College of Engineering; College of Engineering; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; 8579; N/A; 40319; 115108; N/AA biosensor platform is utilized in liquid for detection of His protein. T-shaped thin film nickel cantilevers are actuated magnetically using self-oscillation principle and the sensing is based on embedded diffraction gratings on the cantilevers with interferometric sensitivity. Experiments are performed in a custom 1ml liquid chamber and 5.7ng/ml detection sensitivity is demonstrated. Method is label-free, robust and allows mu ltip lexing. It also doesn't require any electrical connections to the MEMS sensor chip. Therefore, it is suitable for real-time multi analyte screening using a disposable chip in a portable device.Publication Metadata only Prediction of secondary structures of proteins using a two-stage method(Elsevier Science Bv, 2006) Department of Industrial Engineering; N/A; N/A; Department of Industrial Engineering; Türkay, Metin; Yılmaz, Özlem; Yüksektepe, Fadime Üney; Faculty Member; Master Student; PhD Student; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; 24956; N/A; N/AProtein structure determination and prediction has been a focal research subject in life sciences due to the importance of protein structure in understanding the biological and chemical activities in any organism. the experimental methods used to determine the structures of proteins demand sophisticated equipment and time. in order to overcome the shortcomings of the experimental methods, A host of algorithms aimed at predicting the location of secondary structure elements using statistical and computational methods are developed. However, prediction accuracies of these methods rarely exceeded 70%. in this paper a novel two-stage method to predict the location of secondary structure elements in a protein using the primary structure data only is presented. in the first stage of the proposed method, folding type of a protein is determined using a novel classification model for multi-class problems. the second stage of the method utilizes data available in the Protein Data Bank and determines the possible location of secondary structure elements in a probabilistic search algorithm. It is shown that the average accuracy of the predictions increased to 74.1%.Publication Open Access Uncertainty propagation based MINLP approach for artificial neural network structure reduction(Multidisciplinary Digital Publishing Institute (MDPI), 2022) Şıldır, Hasan; Sarrafi, Şahin; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Aydın, Erdal; Faculty Member; Koç University Tüpraş Energy Center (KUTEM) / Koç Üniversitesi Tüpraş Enerji Merkezi (KÜTEM); College of EngineeringThe performance of artificial neural networks (ANNs) is highly influenced by the selection of input variables and the architecture defined by hyper parameters such as the number of neurons in the hidden layer and connections between network variables. Although there are some black-box and trial and error based studies in the literature to deal with these issues, it is fair to state that a rigorous and systematic method providing global and unique solution is still missing. Accordingly, in this study, a mixed integer nonlinear programming (MINLP) formulation is proposed to detect the best features and connections among the neural network elements while propagating parameter and output uncertainties for regression problems. The objective of the formulation is to minimize the covariance of the estimated parameters while by (i) detecting the ideal number of neurons, (ii) synthesizing the connection configuration between those neurons, inputs and outputs, and (iii) selecting optimum input variables in a multi variable data set to design and ensure identifiable ANN architectures. As a result, suggested approach provides a robust and optimal ANN architecture with tighter prediction bounds obtained from propagation of parameter uncertainty, and higher prediction accuracy compared to the traditional fully connected approach and other benchmarks. Furthermore, such a performance is obtained after elimination of approximately 85% and 90% of the connections, for two case studies respectively, compared to traditional ANN in addition to significant reduction in the input subset.Publication Open Access Zr-MOFs for CF4/CH4, CH4/H-2, and CH4/N-2 separation: towards the goal of discovering stable and effective adsorbents(Royal Society of Chemistry (RSC), 2021) Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Demir, Hakan; Keskin, Seda; Faculty Member; College of Engineering; N/A; 40548Zirconium metal-organic frameworks (MOFs) can be promising adsorbents for various applications as they are highly stable in different chemical environments. In this work, a collection of Zr-MOFs comprised of more than 100 materials is screened for CF4/CH4, CH4/H-2, and CH4/N-2 separations using atomistic-level simulations. The top three MOFs for the CF4/CH4 separation are identified as PCN-700-BPDC-TPDC, LIFM-90, and BUT-67 exhibiting CF4/CH4 adsorption selectivities of 4.8, 4.6, and 4.7, CF4 working capacities of 2.0, 2.0, and 2.1 mol kg(-1), and regenerabilities of 85.1, 84.2, and 75.7%, respectively. For the CH4/H-2 separation, MOF-812, BUT-67, and BUT-66 are determined to be the top performing MOFs demonstrating CH4/H-2 selectivities of 61.6, 36.7, and 46.2, CH4 working capacities of 3.0, 4.1, and 3.4 mol kg(-1), and CH4 regenerabilities of 70.7, 82.7, and 74.7%, respectively. Regarding the CH4/N-2 separation, BUT-67, Zr-AbBA, and PCN-702 achieving CH4/N-2 selectivities of 4.5, 3.4, and 3.8, CH4 working capacities of 3.6, 3.9, and 3.5 mol kg(-1), and CH4 regenerabilities of 81.1, 84.0, and 84.5%, in successive order, show the best overall separation performances. To further elucidate the adsorption in top performing adsorbents, the adsorption sites in these materials are analyzed using radial distribution functions and adsorbate density profiles. Finally, the water affinities of Zr-MOFs are explored to comment on their practical use in real gas separation applications. Our findings may inspire future studies probing the adsorption/separation mechanisms and performances of Zr-MOFs for different gases.