Gungor Ozer

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The structure of chromatin, affected by many factors from DNA linker lengths to posttranslational modifications, is crucial to the regulation of eukaryotic cells. Combined experimental and computational methods have led to new insights into its structural and dynamical features, from interactions due to the flexible core histone tails or linker histones to(More)
Neuropeptide Y (NPY) has been found to adopt two stable conformations in vivo: (1) a monomeric form called the PP-fold in which a polyproline tail is folded onto an α-helix via a β-turn and (2) a dimeric form of the unfolded proteins in which the α-helices interact with each other via side chains. The transition pathway and rates between the two(More)
The chromatin fiber undergoes significant structural changes during the cell's life cycle to modulate DNA accessibility. Detailed mechanisms of such structural transformations of chromatin fibers as affected by various internal and external conditions such as the ionic conditions of the medium, the linker DNA length, and the presence of linker histones,(More)
The nonequilibrium stretching of decaalanine in vacuum using steered molecular dynamics and Jarzynski's relation led to the landmark determination of its potential of mean force by Park and Schulten (Chem. Phys. 2004). In so doing, the relative thermodynamics of the hydrogen-bond contacts and the entropy of the chain were quantified through the reversible(More)
Eukaryotic cells condense their genetic material in the nucleus in the form of chromatin, a macromolecular complex made of DNA and multiple proteins. The structure of chromatin is intimately connected to the regulation of all eukaryotic organisms, from amoebas to humans, but its organization remains largely unknown. The nucleosome repeat length (NRL) and(More)
Steered molecular dynamics, SMD, [S. Park and K. Schulten, J. Chem. Phys. 120, 5946 (2004)] combined with Jarzynski's equality has been used widely in generating free energy profiles for various biological problems, e.g., protein folding and ligand binding. However, the calculated averages are generally dominated by "rare events" from the ensemble of(More)
The potential of mean force (PMF) for stretching decaalanine in vacuum was determined earlier by Park and Schulten [J. Chem. Phys. 120, 5946 (2004)] in a landmark article demonstrating the efficacy of combining steered molecular dynamics and Jarzynski's nonequilibrium relation. In this study, the recently developed adaptive steered molecular dynamics (ASMD)(More)
POLIR (POLarizable for IR) (J. Chem. Phys. 2008, 129, 034504) is a polarizable, flexible, and transferable water potential which describes the IR spectrum in the O-H stretch region via the classical dipole correlation function with simple quantum corrections. POLIR also reproduces experimental spectral shifts in solutions of Ca(2+), Mg(2+), and Cu(2+) (J.(More)
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