Browsing M.S. Theses by Subject "Molecular dynamics -- Computer simulation."

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Collective dynamics and conformational sampling of triosephosphate isomerase

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

Molecular dynamics simulations (30-60 ns runs) are performed on free/apo triosephosphate isomerase (TIM) to determine any correlation between collective motions and loop 6 dynamics. Native TIM is active only as a homo-dimer ...
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 ...
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 ...

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