• Molecular dynamics study of the interactions between thymoquinone and lipid bilayers 

  Ülgey, Esra. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022)

  Thymoquinone, a phytochemical with antitumor activity, and its derivative aminothymoquinone were investigated using Molecular Dynamics (MD) Simulations to understand their interactions with simple and complex bilayer models. ...
• A study on mathematical modeling of direct synthesis of dimethyl ether in structured membrane reactors 

  Köybaşı, Hayrettin Hasan. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022)

  Catalytic transformation of CO2 into dimethyl ether (DME) is modeled in a membrane microchannel reactor. The reactor geometry includes an α-Al2O3 supported SOD membrane layer, capable of in-situ H2O removal, residing between ...
• Subsets of slow dynamic modes reveal global information sources as allosteric sites 

  Altıntel, Bengi. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022)

  Allostery is a crucial biological regulation mechanism, and dynamic information flow offers a framework to characterize allosteric interactions in causal links. Here, using a novel application of the Transfer Entropy (TE) ...
• Structural dynamics of ABC transporters 

  Ersoy, Akarun Ayça. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022)

  The ATP-binding cassette transporters (ABC transporters) translocate sub strates across membranes by ATP binding and hydrolysis. To understand the com plex structural dynamics, transporters were investigated on three case ...
• A preliminary work on design and development of sour water gas shift catalysts for synthetic natural gas process 

  Özata, Hasretnur. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022)

  The main goal of this study is to design and develop a model sour water gas shift catalyst showing high performance in terms of activity, stability & selectivity and conducting performance screening by mimicking the ...
• Reconstruction of metabolic brain model with the aid of physiologically based pharmacokinetic modelling in the presence of autism spectrum disorder 

  Erimli, Sena. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022)

  Autism spectrum disorder (ASD) is a neurodevelopmental disorder with only symptomatic medical treatment with increasing prevalence. This study aims to reconstruct a genome-scale metabolic brain model that is expanded via ...
• Investigation of medulloblastoma metabolism by tissue-specific genome-scale brain metabolic model and identification of therapeutic targets 

  Özbek, İlkay İrem. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022)

  Medulloblastoma (MB) is the most prevalent pediatric brain tumor arising in the cerebellum. Since conventional therapies decrease life quality and cause deleterious effects on children, computer models are urgently ...
• Supercapacitors based on functionalized carbon materials 

  Korkut, Ayşe Saliha. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022)

  Electrical double layer capacitors store energy in the form of electrical charges at the interface between an electrolyte and a high surface area electrode. As their energy storage mechanism relies on physical interactions, ...
• Optimization of energy density in supercapacitors by utilizing a hybrid artificial neural networks-genetic algorithm based optimization algorithm 

  Kaya, Duygu. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022)

  Energy storage systems are required to meet the increased energy demand and re duce the need for fossil fuels. Energy storage devices are of interest to renewable energy systems and electric vehicles to provide a permanent ...
• Multi-scale modelling of supercapacitors : a combined simulation and machine learning approach 

  Sakallıoğlu, Sabri Hakan. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2022., 2022)

  Electrical double layer capacitors (EDLCs) store and release energy via re versible adsorption/desorption of ions at the electrode–electrolyte interface. Research on EDLCs mainly focus on improving their energy density ...
• 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 ...
• The use of different statistical tools in the identification of perturbation-responsive transcription factors in yeast 

  Çınar, Nil. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)

  S. cerevisiae transcription data, obtained under environmental perturbations, such as 16 different macronutrient (carbon, nitrogen, phosphorus and sulfur) limitation regimes in both aerobic and anaerobic conditions, and ...
• Determination of protein-protein binding sites using machine learning tools 

  Sümbül, Fidan. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)

  Protein-protein interactions are involved in almost all biological processes. Thus, the understanding of the principles underlying these interactions is of great significance. This is mainly to identify the functional sites ...
• Adaptive Clarke-Gawthrop self-tuning control of blood glucose concentration in patients with Type I diabetes 

  Çölmekçi, Ceylan. (Thesis (M.S.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2008., 2008.)

  Adaptive Clarke-Gawthrop type of self-tuning controller is used for regulating the blood glucose concentration in Type I diabetic patients. This control algorithm is proposed to be integrated into the automation pumps used ...

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