Unraveling the beautiful complexity of simple lattice model polymers and proteins using Wang-Landau sampling

Abstract

We describe a class of "bare bones" models of homopolymers which undergo coil-globule collapse and proteins which fold into their native states in free space or into denatured states when captured by an attractive substrate as the temperature is lowered. We then show how, with the use of a properly chosen trial move set, Wang-Landau Monte Carlo sampling can be used to study the rough free energy landscape and ground (native) states of these intriguingly simple systems and thus elucidate their thermodynamic complexity.

arXiv comment22 pages, 6 figures

References in corpus (19)

• An efficient, multiple range random walk algorithm to calculate the density of states
• Multicanonical Ensemble: A New Approach to Simulate First-order Phase Transitions
• Determining the density of states for classical statistical models: A random walk algorithm to produce a flat histogram
• Understanding and Improving the Wang-Landau Algorithm
• Multicanonical Chain Growth Algorithm
• Growth Algorithms for Lattice Heteropolymers at Low Temperatures
• Thermodynamics of Lattice Heteropolymers
• Transitions of tethered polymer chains: A simulation study with the bond fluctuation lattice model
• Versatile approach to access the low temperature thermodynamics of lattice polymers and proteins
• Freezing and Collapse of Flexible Polymers on Regular Lattices in Three Dimensions
• Conformational Transitions of Non-Grafted Polymers Near an Adsorbing Substrate
• 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
• Substrate Specificity of Peptide Adsorption: A Model Study
• Substrate Adhesion of a Nongrafted Flexible Polymer in a Cavity
• Monte Carlo simulations of the HP model (the "Ising model" of protein folding)

Cited by in corpus (8)

• Scalable replica-exchange framework for Wang-Landau sampling
• Generic folding and transition hierarchies for surface adsorption of hydrophobic-polar lattice model proteins
• "Pull moves" for rectangular lattice polymer models are not fully reversible
• Transitions of tethered chain molecules under tension
• Computational Statistical Mechanics of a confined, three-dimensional Coulomb gas
• Surface adsorption of lattice HP proteins: Thermodynamics and structural transitions using Wang-Landau sampling
• A Parallel Trajectory Swapping Wang - Landau Study Of The HP Protein Model
• Efficient implementation of the Wang-Landau algorithm for systems with length-scalable potential energy functions