Method for sampling compact configurations for semistiff polymers

Alexey Siretskiy, Christer Elvingson, Pavel Vorontsov-Velyaminov, and Malek O. Khan
Phys. Rev. E 84, 016702 – Published 7 July 2011

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.

  • Figure
  • Figure
  • Figure
  • Figure
  • Figure
  • Figure
  • Figure
3 More
  • Received 7 March 2011

DOI:https://doi.org/10.1103/PhysRevE.84.016702

©2011 American Physical Society

Authors & Affiliations

Alexey Siretskiy* and Christer Elvingson

  • Department of Physical and Analytical Chemistry, Uppsala University, SE-751 23 Uppsala, Sweden

Pavel Vorontsov-Velyaminov

  • Faculty of Physics, St. Petersburg State University, St. Petersburg 198504, Russia

Malek O. Khan§

  • Department of Physical and Analytical Chemistry, Uppsala University, SE-751 23 Uppsala, Sweden and FOI, Swedish Defense Research Agency, SE-164 90 Stockholm, Sweden

  • *alexey.siretskiy@fki.uu.se
  • christer.elvingson@fki.uu.se
  • voron.wgroup@gmail.com
  • §malek.khan@fki.uu.se

Article Text (Subscription Required)

Click to Expand

References (Subscription Required)

Click to Expand
Issue

Vol. 84, Iss. 1 — July 2011

Reuse & Permissions
Access Options
Author publication services for translation and copyediting assistance advertisement

Authorization Required


×
×

Images

×

Sign up to receive regular email alerts from Physical Review E

Log In

Cancel
×

Search


Article Lookup

Paste a citation or DOI

Enter a citation
×