Coarse grained models, bond orientational order, and the structural characterization of residue networks
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Authors
Okan, Osman Burak
Issue Date
2013-12
Type
Electronic thesis
Thesis
Thesis
Language
ENG
Keywords
Materials science and engineering
Alternative Title
Abstract
Proteins are polypeptide chains that fold into compact 3-dimensional shapes, which determine their molecular function. Due their unique chemistry, coarse graining with hard spheres at the amino acid level works well for proteins. Following this framework, the first goal of the current study is to portray protein structure as a sphere packing problem and decipher the universal characteristics of globular proteins at the residue level. One of the most direct ways of spotting structural features that are shared among proteins is to find proper analogues from simpler condensed matter systems. In this respect, sphere packing arguments provide the most direct route for structural comparisons as they successfully characterize a wide array of materials such as close packed crystals, dense liquids, and structural glasses.
Description
December 2013
School of Engineering
School of Engineering
Full Citation
Publisher
Rensselaer Polytechnic Institute, Troy, NY