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

TL;DR

This paper employs advanced Monte Carlo techniques to study the thermodynamic behavior of the HP protein model, revealing complex folding and adsorption transitions influenced by surface interactions.

Contribution

It introduces a combined Wang-Landau sampling approach with specialized trial moves to accurately determine density of states for the HP model.

Findings

Identification of collapse and folding transitions in the HP model.

Observation of competition between surface adsorption and folding.

Enhanced sampling method improves transition detection.

Abstract

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.