Modeling of Protein Folding and Genetic Networks

Fredrik Sjunnesson

Research output: ThesisDoctoral Thesis (compilation)

Abstract

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.
Original languageEnglish
QualificationDoctor
Awarding Institution
  • Computational Biology and Biological Physics
Supervisors/Advisors
  • [unknown], [unknown], Supervisor, External person
Award date2003 Oct 3
Publisher
ISBN (Print)91-628-5783-5
Publication statusPublished - 2003

Bibliographical note

Defence details

Date: 2003-10-03
Time: 13:15
Place: Lecture Hall F, Dept. of Theoretical Physics

External reviewer(s)

Name: Bastolla, Ugo
Title: [unknown]
Affiliation: [unknown]

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Subject classification (UKÄ)

  • 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

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