Monte Carlo simulations of the HP model (the Ising model of protein folding)

Using Wang-Landau sampling with suitable Monte Carlo trial moves (pull moves and bond-rebridging moves combined) we have determined the density of states and thermodynamic properties for a short sequence of the HP protein model. For free chains these proteins are known to,first undergo a collapse transition to a globule state followed by a second transition into a native state. When placed in the proximity of an attractive surface, there is a competition between surface adsorption and folding that leads to an intriguing sequence of transitions. These transitions depend upon the relative interaction strengths and are largely inaccessible to standard Monte Carlo methods. (C) 2011 Elsevier B.V. All rights reserved.