Packaging stiff polymers in small containers: A molecular dynamics study

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.

Figure 1

Fraction of spheres inside shell (dashed lines, increasing $f_a$ from left) and fraction of fully inserted chains vs time (reduced units).

Figure 2

Radial density distributions (reduced units) for several $f_a$ values.

Figure 3

Mean distance of chain spheres from the shell center as a function of (normalized) location along chain contour.

Figure 4

Orientational correlation plots and pictures of selected chains; details and color schemes are explained in the text (in the grayscale print version, dark gray = blue/violet, medium gray = red, light gray = yellow/green); cases (a)–(e) are for $f_a=5000$, (f) and (g) are for $f_a=3000$ and 1000.