
Anders Irbäck
Professor

Studies of an off-lattice model for protein folding : Sequence dependence and improved sampling at finite temperature
Author
Summary, in English
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two dimensional and has two different "amino acids." Using numerical simulations of all chains containing eight or ten monomers, we examine the sequence dependence at a fixed temperature. It is shown that only a few of the chains exist in unique folded state at this temperature, and the energy level spectra of chains with different types of behavior are compared. Furthermore, we use this model as a testbed for two improved Monte Carlo algorithms. Both algorithms are based on letting some parameter of the model become a dynamical variable; one of the algorithms uses a fluctuating temperature and the other a fluctuating monomer sequence. We find that by these algorithms one gains large factors in efficiency in comparison with conventional methods.
Department/s
- Computational Biology and Biological Physics - Undergoing reorganization
- Department of Astronomy and Theoretical Physics - Undergoing reorganization
Publishing year
1995
Language
English
Pages
10298-10305
Publication/Series
Journal of Chemical Physics
Volume
103
Issue
23
Document type
Journal article
Publisher
American Institute of Physics (AIP)
Status
Published
ISBN/ISSN/Other
- ISSN: 0021-9606