Density of States for HP Lattice Proteins

TL;DR

This paper investigates the density of states in a simplified HP lattice protein model, deriving exact results for short chains and employing advanced Monte Carlo methods for longer chains to understand their energetic properties.

Contribution

It introduces a multicanonical Monte Carlo method combined with chain growth techniques to efficiently compute the density of states for the HP lattice protein model.

Findings

Exact density of states for short chains via enumeration

Efficient simulation method for longer chains

Insights into energetic and thermodynamic properties

Abstract

The density of states contains all informations on energetic quantities of a statistical system, such as the mean energy, free energy, entropy, and specific heat. As a specific application, we consider in this work a simple lattice model for heteropolymers that is widely used for studying statistical properties of proteins. For short chains, we have derived exact results from conformational enumeration, while for longer ones we developed a multicanonical Monte Carlo variant of the nPERM-based chain growth method in order to directly simulate the density of states. For simplification, only two types of monomers with respective hydrophobic (H) and polar (P) residues are regarded and only the next-neighbour interaction between hydrophobic monomers, being nonadjacent along the chain, is taken into account. This is known as the HP model for the folding of lattice proteins.