Method for sampling compact configurations for semistiff polymers

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Jul;84(1 Pt 2):016702. doi: 10.1103/PhysRevE.84.016702. Epub 2011 Jul 7.

Abstract

The sampling of compact configurations is crucial when investigating structural properties of semistiff polymers, like proteins and DNA, using Monte Carlo methods. A sampling scheme for a continuous model based on configuration biasing is introduced, tested, and compared with conventional methods. The proposed configuration biased Monte Carlo method, used together with the Wang-Landau sampling scheme, enables us to obtain any thermodynamic property within the statistical ensemble in use. Using the proposed method, it is possible to collect statistical data of interest for a wide range of compactions (from stretched up to several toroid loops) in a single computer experiment. A second-order-like stretched-toroid phase transition is observed for a semistiff polymer, and the critical temperature is estimated.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation*
  • Elasticity*
  • Models, Molecular
  • Molecular Conformation
  • Monte Carlo Method
  • Polymers / chemistry*

Substances

  • Polymers