"Pull Moves" for Rectangular Lattice Polymer Models Are Not Fully Reversible

@article{Gyrffy2012PullMF,
  title={"Pull Moves" for Rectangular Lattice Polymer Models Are Not Fully Reversible},
  author={D{\'a}niel Gy{\"o}rffy and P{\'e}ter Z{\'a}vodszky and Andr{\'a}s Szil{\'a}gyi},
  journal={IEEE/ACM Transactions on Computational Biology and Bioinformatics},
  year={2012},
  volume={9},
  pages={1847-1849}
}
"Pull moves” is a popular move set for lattice polymer model simulations. We show that the proof given for its reversibility earlier is flawed, and some moves are irreversible, which leads to biases in the parameters estimated from the simulations. We show how to make the move set fully reversible. 
View on ACM
arxiv.org
6 Citations
Background Citations
2
Methods Citations
1

Figures from this paper

6 Citations

Advances in Monte Carlo techniques with application to lattice protein aggregation

It is shown that the MBAR-enhanced Monte Carlo improves simulation efficiency of the lattice-protein aggregation model and, since it can also be applied to continuous models, provides a promising alternative to the study of more realistic systems.

Efficient conformational space exploration in ab initio protein folding simulation

The non-uniform scaling helps tackle the difficulty faced by a real energy function, whereas the integration of 20×20 pairwise information overcomes the limitations faced by the HP energy function.

A Firefly-Inspired Method for Protein Structure Prediction in Lattice Models

A Firefly-inspired algorithmic approach for protein structure prediction over two different lattice models in three-dimensional space, with the aim of justifying future research on larger instances within lattice model settings, eventually leading to the ultimate goal of implementations for off-lattice models.

Effect of protein structure on evolution of cotranslational folding

A biologically intuitive evolutionary model is developed to show that avoiding premature protein degradation can be a sufficient evolutionary force to drive evolution of cotranslational folding.

MBAR-enhanced lattice Monte Carlo simulation of the effect of helices on membrane protein aggregation

A local landscape mapping method for protein structure prediction in the HP model

Results show that the recently proposed Hybrid Monte Carlo Ant Colony Optimization heuristic in the HP model performs better than the other heuristics in all benchmark instances when the fragment assembly-like strategy is used while in the case of pull moves-based neighborhood its performance is comparable to that of simulated annealing.

References

SHOWING 1-10 OF 24 REFERENCES

Long range moves for high density polymer simulations

A set of long range moves that work well even when all sites in a lattice simulation are filled are devised and test and it is demonstrated that for a 27-mer cube, the ground state of random heteropolymers can quickly be reached.

Improved simulations of lattice peptide adsorption.

This work examines the implementation of "pull" moves and discusses the most efficient way of selecting them, and explicitly shows how Wang-Landau sampling may be used to calculate the appropriate density of states for a peptide chain in contact with a single surface.

Monte Carlo Calculations on the Dynamics of Polymers in Dilute Solution

A method is described for simulating the dynamical behavior of a linear polymer in dilute solution, subject to random collision with solvent molecules. Equilibrium distributions of various chain…

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

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…

Unraveling the Beautiful Complexity of Simple Lattice Model Polymers and Proteins Using Wang-Landau Sampling

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.

Exact and Monte Carlo computations on a lattice model for change of conformation of a polymer

Conformational changes of linear polymers are studied by means of dynamic lattice models. The relaxation rates for the following four parameters describing the conformation of the polymer are studied…

Improving the Wang–Landau algorithm for polymers and proteins

The 1/t Wang–Landau algorithm is tested on simple models of polymers and proteins and it is found that this method resolves the problem of the saturation of the error present in the original algorithm, but for lattice proteins, which have a rough energy landscape with an unknown energy minimum, the density of states does not converge in all runs.

A lattice statistical mechanics model of the conformational and sequence spaces of proteins

Exhaustive exploration of the full conformational space is computationally possible because molecules are modeled as short chains on a 2D square lattice.

Protein Folding on the Hexagonal Lattice in the Hp Model

The hexagonal lattice is introduced as a biologically meaningful alternative to the standard square lattice for the study of protein folding in the HP model and alleviates the "sharp turn" problem and models certain aspects of the protein secondary structure more realistically.

A Local Move Set for Protein Folding in Triangular Lattice Models

This paper considers an HP-like model which uses a more appropriate grid structure, namely the 2D triangular grid and the face-centered cubic lattice in 3D, and considers a local-search approach for finding an optimal embedding.