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We consider the dynamics of pore-driven polymer translocation through a nanopore to a two-dimensional semi-infinite space when the chain is initially confined and equilibrated in a narrow channel. To this end, we use Langevin dynamics (LD) simulations and iso-flux tension propagation (IFTP) theory to characterize local and global dynamics of the translocating chain. The dynamics of the process can be described by the IFTP theory in very good agreement with the LD simulations for all values of confinement in the channel. The theory reveals that for channels with a size comparable to or less than the end-to-end distance of the unconfined chain, in which the blob theory works, the scaling form of the translocation time depends on both the chain contour length and the channel width. Conversely, for a very narrow channel, the translocation time only depends on the chain contour length and is similar to that of a rod due to the absence of spatial chain fluctuations.
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Scaling regimes for wormlike chains confined to cylindrical surfaces under tension
We compute the free energy of confinement F for a wormlike chain (WLC), with persistence length lp, that is confined to the surface of a cylinder of radius R under an external tension f using a mean field variational approach. For long chains, we analytically determine the behavior of the chain in a variety of regimes, which are demarcated by the interplay of lp, the Odijk deflection length (ld = (R2lp)1/3), and the Pincus length (lf = kBT/f, with kBT being the thermal energy). The theory accurately reproduces the Odijk scaling for strongly confined chains at f = 0, with F ∼ Ll−1/3p R−2/3. For moderate values of f, the Odijk scaling is discernible only when lp R for strongly confined chains. Confinement does not significantly alter the scaling of the mean extension for sufficiently high tension. The theory is used to estimate unwrapping forces for DNA from nucleosomes.
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- PAR ID:
- 10512510
- Publisher / Repository:
- The European Physical Journal E
- Date Published:
- Journal Name:
- The European Physical Journal E
- Volume:
- 47
- Issue:
- 1
- ISSN:
- 1292-8941
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript
- Journal Article:
- https://doi.org/10.1140/epje/s10189-023-00384-6
