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Contents
Contents
List of Tables
List of Figures
Introduction
Model and simulation algorithm
Monte Carlo methods and the Metropolis algorithm
The histogram technique
Simplified protein models
The cubic lattice model with engineered sequences
Implementation
Sequence selection and thermodynamic characterization
Folding trajectories
Thermal stability
Equilibrium distributions of Q
Heat capacities
Theory for the effect of potential inaccuracy on protein folding simulations
The importance of the potential in protein folding simulations
The Random Energy Model (REM) for the density of states of a heteropolymer
Effect of potential inaccuracy on the density of states
Monte Carlo simulations with inaccurate potentials
Introduction of potential inaccuracy
Effect of Potential Inaccuracies on MC simulations
Estimates for the potential accuracy required in realistic folding simulations
Theoretical analysis
The law of corresponding states
Estimates for the required potential accuracy
Implications
Effect of a compactness-dependent potential on folding thermodynamics and kinetics
Bibliography
Program details and source code
Antonio Francisco Pereira de Araujo
1999-02-23