Modeling of Protein Folding and Genetic Networks

Detta är en avhandling från Department of Theoretical Physics

Författare: Fredrik Sjunnesson; Lunds Universitet.; Lund University.; [2003]

Nyckelord: NATURVETENSKAP; NATURAL SCIENCES; gravitation statistical physics relativity quantum mechanics classical mechanics Monte Carlo local update Kauffman model. Mathematical and general theoretical physics all-atom model Protein folding two-state folding thermodynamics Matematisk och allmän teoretisk fysik klassisk mekanik kvantmekanik relativitet gravitation statistisk fysik termodynamik;

Sammanfattning: Models for potein folding are developed and applied to peptides and small proteins with both ?-helix and ?-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.

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