Researcher:
Palazoğlu, Ahmet

Profile Picture
ORCID

OrgUnit Logo
Organizational Unit

Job Title

Other

First Name

Ahmet

Last Name

Palazoğlu

Name

Name Variants

Palazoğlu, Ahmet

Email Address

Birth Date

Filters

2003 - 20042

Advanced Search

Filter by

Settings

Researcher Of Publications: search.filters.isAuthorOfPublication.23646c2c-f12a-4819-bc9f-74433b815a69

Search Results

Now showing 1 - 2 of 2
  • Placeholder
    PublicationMetadata only
    Conformational similarities in isomerization dynamics of clusters
    (Amer Chemical Soc, 2003) Department of Chemistry; N/A; Department of Chemical and Biological Engineering; Department of Chemistry; Department of Chemical and Biological Engineering; Yurtsever, İsmail Ersin; Palazoğlu, Ahmet; Arkun, Yaman; Faculty Member; N/A; Faculty Member; College of Sciences; N/A; College of Engineering; 7129; N/A; 108526
    A method for characterization of the isomerization dynamics from classical trajectories is presented. A measure function describing the topological distance between two clusters of atoms is first developed. Next, this measure is used to identify the regions of the potential energy surface visited by the trajectories. Unlike the commonly used techniques such as simulated annealing or quenching, the proposed method does not require repeated treatment of the trajectory and can be safely used to study the isomerization dynamics of large systems, especially those of monatomic clusters.
  • Placeholder
    PublicationMetadata only
    Folding dynamics of proteins from denatured to native state: principal component analysis
    (Mary Ann Liebert, Inc, 2004) N/A; Department of Chemical and Biological Engineering; Department of Computer Engineering; Department of Chemical and Biological Engineering; Department of Chemical and Biological Engineering; Department of Computer Engineering; Department of Chemical and Biological Engineering; Palazoğlu, Ahmet; Gürsoy, Attila; Arkun, Yaman; Erman, Burak; Other; Faculty Member; Faculty Member; Faculty Member; College of Engineering; College of Engineering; College of Engineering; College of Engineering; N/A; 8745; 108526; N/A
    Several trajectories starting from random configurations and ending in the native state for chymotrypsin inhibitor 2, CI2, are generated using a Go-type model where the backbone torsional angles execute random jumps on which a drift towards their native values is superposed. Bond lengths and bond angles are kept fixed, and the size of the backbone atoms and side groups are recognized. The large datasets obtained are analyzed using a particular type of principal component analysis known as Karhunen - Loeve expansion (KLE). Trajectories are decomposed separately into modes in residue space and time space. General features of different folding trajectories are compared in the modal space and relationships between the structure of CI2 and its folding dynamics are obtained. Dynamic scaling and order reduction of the folding trajectories are discussed. A continuous wavelet transform is used to decompose the nonstationary folding trajectories into windows exhibiting different features of folding dynamics. Analysis of correlations confirms the known two-state nature of folding of CI2. All of the conserved residues of the protein are shown to be stationary in the small modes of the residue space. The sequential nature of folding is shown by examining the slow modes of the trajectories. The present model of protein folding dynamics is compared with the simple Rouse model of polymer dynamics. Principal component analysis is shown to be a very effective tool for the characterization of the general folding features of proteins.