Computational Mechanics

, Volume 35, Issue 2, pp 146–152

Three-dimensional director-field predictions of viral DNA packing arrangements

Authors

  • W. S. Klug
    • Division of Engineering and Applied ScienceCalifornia Institute of Technology
    • Mechanical and Aerospace Engineering DepartmentUniversity of California
  • M. T. Feldmann
    • Center for Advanced Computing ResearchCalifornia Institute of Technology
    • Division of Engineering and Applied ScienceCalifornia Institute of Technology
Article

DOI: 10.1007/s00466-004-0613-x

Cite this article as:
Klug, W., Feldmann, M. & Ortiz, M. Computational Mechanics (2005) 35: 146. doi:10.1007/s00466-004-0613-x

Abstract

In this work we develop a discrete director-field model for coarse-grained description of packing arrangements of DNA within bacteriophage virus heads. This computational lattice model allows us to explore the complex energy landscape of fully three-dimensional configurations of packaged DNA. By minimizing the system’s free energy by means of the simulated annealing and the conjugate gradient methods, we make predictions about favorable packing conformations. In particular we show that the planar-wrapped inverse spool conformation is stable everywhere inside a virus except in a central core region, where the DNA tends to buckle out of the spooling plane.

Keywords

Viral DNAPackagingEnergy minimizationNumerical optimization

Copyright information

© Springer-Verlag Berlin Heidelberg 2004