Wang-Landau simulation of Gō model molecules
1Institut für Physik, Martin-Luther-Universität, D-06099, Halle (Saale), Germany.
The European Physical Journal. E, Soft Matter
|January 27, 2016
Summary
Gō models, used for protein structure prediction, were studied by varying the cut-off distance. This research clarifies the impact of this parameter on homopolymer chain thermodynamics and structure.
Area of Science:
- Computational physics
- Biophysics
- Polymer physics
Background:
- Gō-like models are foundational in computational physics for protein structure prediction.
- These models utilize a native contact matrix to represent low-energy polymer configurations.
- Previous studies have explored various potentials and cut-off distances for defining these contacts.
Purpose of the Study:
- To investigate the physical consequences of varying the cut-off distance in Gō models.
- To analyze thermodynamic and structural properties of homopolymer chains using different cut-off distances.
- To compare findings with existing Gō models for proteins and peptides.
Main Methods:
- Development of Gō models for a square-well tangent sphere homopolymer chain.
- Application of flat-histogram Monte Carlo simulations, specifically Wang-Landau type.
- Comprehensive analysis of thermodynamic and structural properties across the full temperature range.
Main Results:
- The choice of cut-off distance significantly influences the thermodynamic and structural behavior of the homopolymer Gō model.
- Distinct phase transitions and structural characteristics were observed correlating with different cut-off values.
- Quantitative differences and qualitative similarities to protein/peptide Gō models were identified.
Conclusions:
- The cut-off distance is a critical parameter in Gō model construction, affecting physical outcomes.
- This study provides a detailed understanding of parameter sensitivity in simplified polymer models.
- Findings contribute to refining Gō models for broader applications in biophysics and materials science.
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