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Modeling of Protein Folding and Genetic Networks

Sjunnesson, Fredrik LU (2003)
Abstract (Swedish)
Popular Abstract in Swedish

Modeller för proteinveckning utvecklas och tillämpas på peptider och små proteiner som har både α-helix- och β-blad-struktur. Energifunktionerna, i vilka effektiva hydrofobicitetskrafter och vätebindningar är de två centrala termerna, är helt sekvensbaserade och har medvetet hållits enkla. Den geometriska representationen av proteinkedjorna är däremot detaljerad och har torsionsvinklar som frihetsgrader. Modellernas termodynamiska egenskaper studeras med hjälp av Monte Carlo-metoder och kvantitativa jämförelser med experiment görs. För att förbättra samplingen av kompakta tillstånd utvecklas en semilokal Monte Carlo-uppdatering som arbetar i torsionsvinklar längs proteinkedjans ryggrad. Dessutom... (More)
Popular Abstract in Swedish

Modeller för proteinveckning utvecklas och tillämpas på peptider och små proteiner som har både α-helix- och β-blad-struktur. Energifunktionerna, i vilka effektiva hydrofobicitetskrafter och vätebindningar är de två centrala termerna, är helt sekvensbaserade och har medvetet hållits enkla. Den geometriska representationen av proteinkedjorna är däremot detaljerad och har torsionsvinklar som frihetsgrader. Modellernas termodynamiska egenskaper studeras med hjälp av Monte Carlo-metoder och kvantitativa jämförelser med experiment görs. För att förbättra samplingen av kompakta tillstånd utvecklas en semilokal Monte Carlo-uppdatering som arbetar i torsionsvinklar längs proteinkedjans ryggrad. Dessutom studeras en enkel model för genetiska nätverk, Kauffman-modellen. (Less)
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... (More)
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. (Less)
Please use this url to cite or link to this publication:
author
opponent
  • Bastolla, Ugo
organization
publishing date
type
Thesis
publication status
published
subject
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
pages
114 pages
publisher
Department of Theoretical Physics, Lund University
defense location
Lecture Hall F, Dept. of Theoretical Physics
defense date
2003-10-03 13:15
ISBN
91-628-5783-5
language
English
LU publication?
yes
id
706759b2-aefd-49bb-90e4-37cfae45ea5f (old id 466179)
date added to LUP
2007-08-09 11:24:44
date last changed
2016-09-19 08:45:07
@misc{706759b2-aefd-49bb-90e4-37cfae45ea5f,
  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. <br/><br>
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       = {Sjunnesson, Fredrik},
  isbn         = {91-628-5783-5},
  keyword      = {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},
  language     = {eng},
  pages        = {114},
  publisher    = {ARRAY(0xab644e0)},
  title        = {Modeling of Protein Folding and Genetic Networks},
  year         = {2003},
}