Dynamics of Polymer Decompression: Expansion, Unfolding, and Ejection

Abstract

The dynamics of polymer decompression from a compact state to swollen conformation can be formally described as nonlinear diffusion. We discuss two basic examples: (i) the expansion, or unfolding from a compact state, and (ii) the ejection of a compressed polymer through a pore. The problem can be solved exactly for case (i), but not for case (ii). Even in such situations, a scheme called uniform approximation is shown to be useful to get a physical insight involved. Its application to the case (ii) is able to account for conflicting numerical data in a consistent way.

Dynamics of polymer ejection from capsid

“…Also, the predictions for the scaling τ ∼ N α in these references were seen not to hold for our simulations. This we ascribe to nonequilibrium effects, which are well described in [8]. Qualitatively, capsid ejection results from a drift component due to high monomer density inside the capsid and diffusion.…”

“…In capsid ejection, where the polymer is initially in a packed conformation, tension spreading inside the capsid can hardly explain the obtained scaling, at least for higher monomer densities. As pointed out in [8], in capsid ejection the time-dependent radially transmitted pressure drop has a role analogous to tension spreading in polymer translocation.…”

“…Using this scaling relation and the lower bound for the translocation time, derived in [21], the authors obtained the scaling relation τ ∼ N 1+ν φ 1/(1−3ν) (1) for the ejection time. Sakaue and Yoshinaga presented an analytical formulation for the capsid ejection process [8]. They noted that the origin of the scaling in Eq.…”

“…Viral packaging in and ejection from a bacteriophage are extensively studied processes [2][3][4][5][6][7][8]. It is well established that, e.g., a double-stranded (ds) DNA assumes a spooled conformation inside a capsid [6,[9][10][11].…”

Polymer Detachment Kinetics from Adsorbing Surface: Theory, Simulation and Similarity to Infiltration into Porous Medium

“…An equation similar to PME has been discussed recently by Sakaue et al [21] in the context of polymer expansion and unfolding from a compact state. In this case the consideration has been based on the dynamics of concentration blobs [20] rather than tensile blobs like here.…”