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