Scaling regimes of a semiflexible polymer in a rectangular channel

Werner, Erik; Mehlig, B.

doi:10.1103/physreve.91.050601

Cited by 29 publications

(48 citation statements)

References 35 publications

(102 reference statements)

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“…Although there are challenges in using DNA beyond those discussed here, for example the inability to tune the system so that different confinement regimes span multiple decades in channel size [39,74], DNA remains the most convenient model system for studying confined polymers. While it may ultimately prove challenging to use DNA to test the existing models down to the prefactors for the scaling laws [23,25,[41][42][43], there is no better experimental system to directly visualize the effects of confinement at the single molecule level and investigate the universal properties of confined polymers at the scaling level.…”

Section: Discussionmentioning

confidence: 99%

Wall depletion length of a channel-confined polymer

Cheong

Dorfman

2017

Phys. Rev. E

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Numerous experiments have taken advantage of DNA as a model system to test theories for a channel-confined polymer. A tacit assumption in analyzing these data is the existence of a well defined depletion length characterizing DNA-wall interactions such that the experimental system (a polyelectrolyte in a channel with charged walls) can be mapped to the theoretical model (a neutral polymer with hard walls). We test this assumption using pruned-enriched Rosenbluth method (PERM) simulations of a DNA-like semiflexible polymer confined in a tube. The polymer-wall interactions are modeled by augmenting a hard wall interaction with an exponentially decaying, repulsive soft potential. The free energy, mean span, and variance in the mean span obtained in the presence of a soft wall potential are compared to equivalent simulations in the absence of the soft wall potential to determine the depletion length. We find that the mean span and variance about the mean span have the same depletion length for all soft potentials we tested. In contrast, the depletion length for the confinement free energy approaches that for the mean span only when depletion length no longer depends on channel size. The results have implications for the interpretation of DNA confinement experiments under low ionic strengths. * dorfman@umn.edu

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Section: Discussionmentioning

confidence: 99%

Wall depletion length of a channel-confined polymer

Cheong

Dorfman

2017

Phys. Rev. E

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“…Note however that the conditions defining the extended de Gennes regime for rectangular channels differ from Eq. (1) [16]. …”

Section: Discussionmentioning

confidence: 99%

“…In this regime the universal scaling relation (3) does not hold. The observables are expected to scale differently for different ranges of L [16], and it remains to be determined how the finite-size effects depend on the parameters of the confined polymer system.…”

Section: Discussionmentioning

confidence: 99%

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Finite-size corrections for confined polymers in the extended de Gennes regime

et al. 2015

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Theoretical results for the extension of a polymer confined to a channel are usually derived in the limit of infinite contour length. But experimental studies and simulations of DNA molecules confined to nanochannels are not necessarily in this asymptotic limit. We calculate the statistics of the span and the end-to-end distance of a semiflexible polymer of finite length in the extended de Gennes regime, exploiting the fact that the problem can be mapped to a one-dimensional weakly self-avoiding random walk. The results thus obtained compare favourably with pruned-enriched Rosenbluth method (PERM) simulations of a three-dimensional discrete wormlike chain model of DNA confined in a nanochannel. We discuss the implications for experimental studies of linear λ-DNA confined to nanochannels at the high ionic strengths used in many experiments.

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“…This parameter determines the ratio of the coefficients P 1 and P 2 in Eq. (5). We show in Appendix A that…”

Section: Model Calculationmentioning

confidence: 91%

Hairpins in the conformations of a confined polymer

et al. 2018

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If a semiflexible polymer confined to a narrow channel bends around by 180°, the polymer is said to exhibit a hairpin. The equilibrium extension statistics of the confined polymer are well understood when hairpins are vanishingly rare or when they are plentiful. Here, we analyze the extension statistics in the intermediate situation via experiments with DNA coated by the protein RecA, which enhances the stiffness of the DNA molecule by approximately one order of magnitude. We find that the extension distribution is highly non-Gaussian, in good agreement with Monte-Carlo simulations of confined discrete wormlike chains. We develop a simple model that qualitatively explains the form of the extension distribution. The model shows that the tail of the distribution at short extensions is determined by conformations with one hairpin.

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Scaling regimes of a semiflexible polymer in a rectangular channel

Cited by 29 publications

References 35 publications

Wall depletion length of a channel-confined polymer

Wall depletion length of a channel-confined polymer

Finite-size corrections for confined polymers in the extended de Gennes regime

Hairpins in the conformations of a confined polymer

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