Browsing by Author "Bahar, Ivet."

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  • Analysis of folding kinetics for simplified model proteins 
    Özkan, Ş. Banu. (Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2001., 2001.)
    The conformational stochastics of simplified model chains that show an apparent two-state kinetics was explored.. A fundamental question addressed in the present analysis is to understand if the folding takes place through ...
  • Determination of protein structures using distance constraints 
    Samur, Başak. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1998., 1998.)
    Constraints of different types are applied to a protein chain of 30 residues by using a low resolution model adopted from the cooperative kinematics (CK) model of polymers. The aim was to investigate the importance of the ...
  • Efficient computational models and methods for investigating local polymer dynamics 
    Baysal, Canan. (Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1996., 1996.)
    Local Phenomena related to the isomerization of torsional angles in polymers are studied using computational tools with emphasis on the problem of efficiency. Molecular and Brownian Dynamics, Dynamic Rotational Isomeric ...
  • Identification of native conformations of proteins using a low resolution model 
    Özkan, Ş. Banu. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Sciences and Engineering, 1997., 1997.)
    Exhaustive enumeration is performed by using a low resolution model. The secondary structure elements of the proteins are kept as rigid blocks. Large ensembles of decoy structures are generated by rotating the virtual ...
  • Molecular Dynamics simulation of polymeric systems 
    Badur, Bertan Yılmaz. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1992., 1992.)
    In this thesis, the dynamic and static properties of a polymeric chain in a dilute solution was investigated with the method of molecular dynamics (MD) simulation. We investigated both the equilibrium properties of polymer ...
  • Molecular dynamics study of macromolecular motions and polypeptide helical stabilities in solution 
    Doruker, Pemra. (Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1995., 1995.)
    Molecular dynamics simulations have been performed to investigate the relative importance of solvent effect and intramolecular conformational potentials on the properties of polymers in dilute solition. Bead-spring, ...
  • Packing regularities in folded proteins 
    Bağcı, Elife Zerrin. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 2001., 2001.)
    Using lattice models of proteins is a common method to reduce conformational space. Despite the suitability of various lattice geometries, the optimal packing geometry of residues in folded structures, or the generic ...
  • 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 ...
  • Simulation of protein structure by a simplified model: |application to the rop dimer 
    Akten, E. Demet. (Thesis (M.S.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1996., 1996.)
    In this thesis, the estimation of the native three-dimensional structure of a dimeric protein, Rop, from its amino-acid sequence is performed. Rop is a small RNA-binding protein that is coded by certain plasmids and is ...

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