Versatile approach to access the low temperature thermodynamics of lattice polymers and proteins

Abstract

We show that Wang-Landau sampling, combined with suitable Monte Carlo trial moves, provides a powerful method for both the ground state search and the determination of the density of states for the hydrophobic-polar (HP) protein model and the interacting self-avoiding walk (ISAW) model for homopolymers. We obtained accurate estimates of thermodynamic quantities for HP sequences with $>100$ monomers and for ISAWs up to $>500$ monomers. Our procedure possesses an intrinsic simplicity and overcomes the limitations inherent in more tailored approaches making it interesting for a broad range of protein and polymer models.

References in corpus (11)

• An efficient, multiple range random walk algorithm to calculate the density of states
• Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram
• Multicanonical Chain Growth Algorithm
• Thermodynamics of Lattice Heteropolymers
• Freezing and Collapse of Flexible Polymers on Regular Lattices in Three Dimensions
• Multi-Self-Overlap Ensemble for protein folding: ground state search and thermodynamics
• A New Monte Carlo Algorithm for Protein Folding
• Simulation of Lattice Polymers with Multi-Self-Overlap Ensemble
• A Growth-based Optimization Algorithm for Lattice Heteropolymers
• Long Range Moves for High Density Polymer Simulations
• Improving Wang-Landau sampling with adaptive windows

Cited by in corpus (29)

• A generic, hierarchical framework for massively parallel Wang-Landau sampling
• Scalable replica-exchange framework for Wang-Landau sampling
• First-order phase transition and tricritical scaling behavior of the Blume-Capel model: a Wang-Landau sampling approach
• Optimized Wang-Landau sampling of lattice polymers: Ground state search and folding thermodynamics of HP model proteins
• Sequence determines degree of knottedness in a coarse-grained protein model
• Generic folding and transition hierarchies for surface adsorption of hydrophobic-polar lattice model proteins
• Unraveling the beautiful complexity of simple lattice model polymers and proteins using Wang-Landau sampling
• Wang-Landau sampling: Improving accuracy
• Monte Carlo simulations of the HP model (the "Ising model" of protein folding)
• Implementation and performance analysis of bridging Monte Carlo moves for off-lattice single chain polymers in globular states
• Wang-Landau sampling: a criterion for halting the simulations
• A new paradigm for petascale Monte Carlo simulation: Replica exchange Wang-Landau sampling
• Control of accuracy in the Wang-Landau algorithm
• Phase transition of a single star polymer: a Wang-Landau sampling study
• Applying Deep Reinforcement Learning to the HP Model for Protein Structure Prediction
• Exploring new frontiers in statistical physics with a new, parallel Wang-Landau framework
• Topological effects in the thermal properties of knotted polymer rings
• A portable and flexible implementation of the Wang--Landau algorithm in order to determine the Density of States
• Exploring Replica-Exchange Wang-Landau sampling in higher-dimensional parameter space
• A study of polymer knots using a simple knot invariant written consisting of multiple contour integrals
• Convergence of Stochastic Approximation Monte Carlo and modified Wang-Landau algorithms: Tests for the Ising model
• "Pull moves" for rectangular lattice polymer models are not fully reversible
• The Rubber Band Revisited: Wang-Landau Simulation
• The Wang-Landau Algorithm as Stochastic Optimization and Its Acceleration
• Surface adsorption of lattice HP proteins: Thermodynamics and structural transitions using Wang-Landau sampling
• Phase diagram of the Wako-Saito-Munoz-Eaton beta-hairpin Model obtained with partition function zeros
• Performance of Wang-Landau algorithm in lattice model of liquid crystals
• Spectral properties of unimodular lattice triangulations
• A Parallel Trajectory Swapping Wang - Landau Study Of The HP Protein Model