Packaging stiff polymers in small containers: A molecular dynamics study

Abstract

The question of how stiff polymers are able to pack into small containers is particularly relevant to the study of DNA packaging in viruses. A reduced version of the problem based on coarse-grained representations of the main components of the system -- the DNA polymer and the spherical viral capsid -- has been studied by molecular dynamics simulation. The results, involving longer polymers than in earlier work, show that as polymers become more rigid there is an increasing tendency to self-organize as spools that wrap from the inside out, rather than the inverse direction seen previously. In the final state, a substantial part of the polymer is packed into one or more coaxial spools, concentrically layered with different orientations, a form of packaging achievable without twisting the polymer.

4 pages, 4 figures (minor changes in revised version)

References in corpus (3)

• Polymer packaging and ejection in viral capsids: shape matters
• Packing of elastic wires in spherical cavities
• Molecular dynamics simulation: a tool for exploration and discovery using simple models

Cited by in corpus (5)

• Spontaneous Domain Formation in Spherically-Confined Elastic Filaments
• Nonmonotonic dependence of polymer glass mechanical response on chain bending stiffness
• Rigidity-induced scale invariance in polymer ejection from capsid
• GPU molecular dynamics: Algorithms and performance
• Spool-nematic ordering of dsDNA and dsRNA under confinement