Modeling of Protein Folding and Genetic Networks

Summary, in English

Models for potein folding are developed and applied to peptides and small proteins with both α-helix and β-sheet structure. The energy functions, in which effective hydrophobicity forces and hydrogen bonds are taken to be the two central terms, are sequence-based and deliberately kept simple.

The geometric representations of the protein chains are, by contrast, detailed and have torsion angles as the degrees of freedom. The thermodynamic properties of the models are studied using Monte Carlo methods and quantitative comparisons with experiments are carried out. To improve the sampling of compact states, a semi-local Monte Carlo update in the backbone torsion angles is developed. In addition, the thesis includes a study of a simple model for genetic networks, the Kauffman model.

• Author: Fredrik Sjunnesson
• Department/s: Computational Biology and Biological Physics - Undergoing reorganization
• Publishing year: 2003
• Language: English
• Document type: Dissertation
• Publisher: Department of Theoretical Physics, Lund University
• Topic: Biophysics
• Keywords: Matematisk och allmän teoretisk fysik; thermodynamics; two-state folding; Protein folding; all-atom model; Mathematical and general theoretical physics; Kauffman model.; local update; Monte Carlo; classical mechanics; quantum mechanics; relativity; statistical physics; gravitation; klassisk mekanik; kvantmekanik; relativitet; statistisk fysik; termodynamik; Fysicumarkivet A:2003:Sjunnesson
• Status: Published
• Supervisor: [unknown] [unknown]
• ISBN/ISSN/Other: ISBN: 91-628-5783-5
• Defence date: 3 October 2003
• Defence time: 13:15
• Defence place: Lecture Hall F, Dept. of Theoretical Physics
• Opponent: Ugo Bastolla