Fen Bilimleri Enstitüsü: Recent submissions

  • Conformational transitions of proteins explored by Monte Carlo simulations integrated with collective modews 
    Çarşıbaşı, Nigar Kantarcı. (Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2009., 2009.)
    Elucidation of conformational transitions between open/closed or free/bound states of proteins sheds light on the mechanism of their action. In this thesis, a new technique (ANM-MC) is proposed, in which collective modes ...
  • Utilization of carbon dioxide and methane via catalytic reforming reactions 
    Aydınoğlu, Şeyma Özkara. (Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    The overall purpose of this research study was to investigate new catalysts to produce synthesis gas via CO2 reforming of methane under optimized reaction conditions. The thesis consists of four parts. In the first part ...
  • Development of a systems based modular approach to link complex diseases 
    Rende, Deniz. (Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2010., 2010.)
    A novel systems based modular approach was developed in this study to investigate the shared underlying mechanisms of three prevalent complex disorders: cardiovascular disease (CVD), Type 2 diabetes (T2D) and Alzheimer‘s ...
  • A theoretical study on catalytic steps of hydrogen production and purification 
    Sümer, Aslıhan. (Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2010., 2010.)
    The aim of this thesis is to obtain information on catalytic activity of transition metals used in different steps of hydrogen production and purification. Density functional theory calculations with periodic slabs have ...
  • Segmental orientation and conformational dynamics of polymer chains 
    Haliloğlu, Türkan. (Thesis (Ph.D)- Bogazici University. Institute for Graduate Studies in Science and Engineering, 1992., 1992.)
    Various remarkable features of polymers, as compared with metallic and inorganic materials, arise from the fact that macromolecules can take up various conformations. The study of macromolecular conformations and dynamics ...
  • System biology of yeast signal transduction 
    Arğa, Kazım Yalçın. (Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2007., 2007.)
    Reconstruction of protein interaction networks that represent groups of proteins contributing to the same cellular function is a key step towards quantitative studies of signal transduction pathways. In the present study, ...
  • Mixed-resolution elastic network models for biological supramolecules 
    Levitas, Ayşe Özge Kürkçüoğlu. (Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    Mixed coarse-graining approach has been recently introduced to the elastic network model to enable the modeling of a protein’s native conformation with regions of high- and low-resolution. In this model, each node of the ...
  • Stoichiometric models in metabolic systems biology of yeast 
    Çakır, Tunahan. (Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2006., 2006.)
    A system-level analysis of Saccharomyces cerevisiae metabolism was performed through integration of stoichiometric modeling and high-throughput ‘omics’ data. A bridge between metabolic networks and transcriptomics was built ...
  • Supercritical carbon dioxide immobilization of glucose oxidase on conducting polymers towards biosensor production 
    Talay, Defne Kayrak. (Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2007., 2007.)
    In this work, glucose oxidase (GOX) is immobilized on conducting polymer matrices (polypyrrole film, PPY; polyurethane/polpyrrole composite foam and film, PU/PPY) via Supercritical Fluid Immobilization (SFI) for further ...
  • Recognition and binding processes in HIV-1 protease 
    Özer, Asuman Nevra. (Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    HIV-1 protease is a drug target against AIDS and understanding its molecu- lar recognition processes is important in development of drugs. Here, the combined computational methodologies used put three different perspectives ...
  • pH and temperature dependence of the rate of dissolution of AgIO3 
    Uyanık, Ömer Lütfi. (Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1984., 1984.)
    In this thesis a theory based ona dissolution model was checked experimentally. The theory which is developed by B.V. Enüstün expresses the initial rate of dissolution for a 1:1 type ionic solid in terms of the model ...
  • Computational and experimental investigation of catalytic hydrocarbon fuel processing for autothermal hydrogen production 
    Avcı, Ahmet Kerim. (Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2003., 2003.)
    Catalytic conversion of hydrocarbon fuels within the context of the operation of a fuel processor for supplying hydrogen to vehicular and stationary fuel cells is investigated using computer-based modeling/simulation studies ...
  • Integrated analysis of metabolome profiles and gene expression in respiratory deficient deletion mutants of Saccharomyces Cerevisiae 
    Pir, Pınar. (Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2005., 2005.)
    A study on transcriptional and metabolic response of S. cerevisiae cells toenvironmental and genetic perturbations was made. Deletion mutants with BY4743backgound were used. Homozygous deletion mutants ho/ho (reference ...
  • Effect of temperature on collective dynamics of proteins: a time series analysis 
    Türe, Özlem. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    Molecular Dynamics (MD) simulations are used to analyze the internal motions of proteins. In this thesis, the molecular dynamics trajectories of the apo form of dihydrofolate reductase (DHFR), and both apo and holo forms ...
  • Au-based catalyst design for selective CO oxidation in hddrogen-rich streams 
    Tezcanlı, Sadi T. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    The objective of this study was to investigate the selective CO oxidation over Au/ -Al2O3 catalyst modified with various metal oxide promoters (such as Mg, Mn, Fe, Ni, Ce, and Co) in hydrogen-rich environment. All catalysts ...
  • Studies on the genes controlling glucose signaling in yeast 
    Şanoviç, Aylin. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    This project was aimed to study the phosphorylation or dephosphorylation of the proteins involved in glucose sensing, signal transduction and glucose repression pathways by transcription of genes encoding these proteins. ...
  • The dynamics underlying enhancement of E2 ligase activity by E3 ligases in sumoylation 
    Tozluoğlu, Melda. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    Covalent attachment of SUMO (Small Ubiquitin Like Modifier) to proteins, sumoylation, is a posttranslational modification that can alter intracellular localization, interactions with other proteins or lead to modifications ...
  • Preparation of catalytic cordierite monoliths for the selective oxidation of carbon monoxide 
    Döker, Yasemin Asiye. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    The objective of this study was to investigate the state-of-the-art preparation methods for environmentally friendly, engineered, multi-channeled catalysts called monoliths and to develop a preparation procedure for ...
  • Kinetic modeling of CO oxidation by genetic programming 
    Yarangüme, Verda. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    In this thesis, the kinetic modeling of CO oxidation was performed using genetic programming. A reaction rate equation was created from the experimental data, and then this equation was used to predict the mechanism of the ...
  • Molecular dynamics of substrate recognition and co-evolution in HIV-1 protease 
    Özen, Ayşegül. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)
    Human Immunodeficiency Virus Type 1 (HIV-1) protease recognizes at least ten cleavage sites as its natural substrates. There is little sequence homology between these substrates and they are asymmetric around the cleavage ...

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