Modeling of Protein Folding and Genetic Networks
(2003)- 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) - 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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/466179
- author
- Sjunnesson, Fredrik LU
- supervisor
- opponent
-
- Bastolla, Ugo
- organization
- publishing date
- 2003
- 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 13:15:00
- ISBN
- 91-628-5783-5
- language
- English
- LU publication?
- yes
- id
- 706759b2-aefd-49bb-90e4-37cfae45ea5f (old id 466179)
- date added to LUP
- 2016-04-04 10:58:24
- date last changed
- 2018-11-21 21:01:53
@phdthesis{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}},
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}},
language = {{eng}},
publisher = {{Department of Theoretical Physics, Lund University}},
school = {{Lund University}},
title = {{Modeling of Protein Folding and Genetic Networks}},
year = {{2003}},
}