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

DOI10.1007/S10955-011-0266-ZMaRDI QIDQ644934zbMATH OpenOpenAlexFDO

Authors Juan-Miguel Gracia

Publication date 7 November 2011

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

Full work available at URL https://arxiv.org/abs/1301.3466, https://www.dora.lib4ri.ch/wsl/islandora/object/wsl%3A5873

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)

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.

Recommendations

• The HP model of protein folding: a challenging testing ground for Wang-Landau sampling
• Entropic sampling of simple polymer models within Wang–Landau algorithm
• Application of Wang-Landau sampling to a protein model using SMMP
• Monte Carlo simulations of systems with complex energy landscapes
• The rubber band revisited: Wang-Landau simulation

Cites work

• scientific article; zbMATH DE number 1528424 (Why is no real title available?)
• scientific article; zbMATH DE number 1775449 (Why is no real title available?)
• A Generalized Wang–Landau Algorithm for Monte Carlo Computation
• A constraint-based approach to fast and exact structure prediction in three-dimensional protein models
• 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
• Modeling traffic flow at a single-lane urban roundabout
• The HP model of protein folding: a challenging testing ground for Wang-Landau sampling

Cited in

(13)

• Monte Carlo simulations of systems with complex energy landscapes
• The Rubik's cube problem revisited: a statistical thermodynamic approach
• Phase transitions in a single polymer chain: a micro-canonical analysis of Wang-Landau simulations
• scientific article; zbMATH DE number 5504052 (Why is no real title available?)
• 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
• Phase transitions of single semistiff polymer chains

This page was built for publication: Unraveling the beautiful complexity of simple lattice model polymers and proteins using Wang-Landau sampling

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q644934)