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

DOI10.1007/S10955-011-0266-ZzbMATH Open1227.82102arXiv1301.3466OpenAlexW2019757781MaRDI QIDQ644934FDOQ644934

Authors: Juan-Miguel Gracia 

Publication date: 7 November 2011

Published in: Journal of Statistical Physics (Search for Journal in Brave)

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.

Full work available at URL: https://arxiv.org/abs/1301.3466

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zbMATH Keywords

protein adsorptionWang-Landau samplinglattice homopolymerslattice proteins

Mathematics Subject Classification ID

Lattice systems (Ising, dimer, Potts, etc.) and systems on graphs arising in equilibrium statistical mechanics (82B20) Statistical mechanics of polymers (82D60)

Cites Work

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• A Generalized Wang–Landau Algorithm for Monte Carlo Computation
• The HP model of protein folding: a challenging testing ground for Wang-Landau sampling
• Exact Results for Supersymmetric<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>σ</mml:mi></mml:math>Models
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Cited In (12)

• Monte Carlo simulations of systems with complex energy landscapes
• The Rubik's cube problem revisited: a statistical thermodynamic approach
• Title not available (Why is that?)
• Phase transitions in a single polymer chain: a micro-canonical analysis of Wang-Landau simulations
• The rubber band revisited: Wang-Landau simulation
• Entropic sampling of simple polymer models within Wang–Landau algorithm
• Multi-objectivization, fitness landscape transformation and search performance: a case of study on the HP model for protein structure prediction
• The HP model of protein folding: a challenging testing ground for Wang-Landau sampling
• Application of Wang-Landau sampling to a protein model using SMMP
• Efficient algorithm for computing exact partition functions of lattice polymer models
• Conformational gap and heat capacity peaks of short lattice polymers
• Constraint-handling through multi-objective optimization: the hydrophobic-polar model for protein structure prediction

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