Confined polymers in the extended de Gennes regime

Werner, Erik; Mehlig, B.

doi:10.1103/physreve.90.062602

Cited by 44 publications

(108 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…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%

“…The models developed for channel-confined polymers make scaling law predictions for the confinement free energy, F , the average size of the confined chain, X , and the variance about that size, δX 2 , for a neutral polymer confined by hard walls [29][30][31][39][40][41]. In some cases, the prefactors for the scaling laws are known exactly [41][42][43].…”

Section: Introductionmentioning

confidence: 99%

“…In some cases, the prefactors for the scaling laws are known exactly [41][42][43]. These thermodynamic quantities depend on the contour length L of the polymer, its persistence length l p , the effective width w of the polymer backbone, and the channel size D. The persistence length and effective width of DNA, which are affected by the relative amount of screening of electrostatics by the ionic environment, can be obtained from polyelectrolyte theory [44][45][46][47], albeit with some uncertainty arising from the effect of the intercalating dye [48][49][50][51][52][53][54].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Wall depletion length of a channel-confined polymer

Cheong

Dorfman

2017

Phys. Rev. E

View full text Add to dashboard Cite

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

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Wall depletion length of a channel-confined polymer

Cheong

Dorfman

2017

Phys. Rev. E

View full text Add to dashboard Cite

show abstract

“…We expect that the method described in Ref. [30] may be applied to circular DNA, but this has not yet been shown. An alternative way to derive the scalings (though not the prefactors) of Eqs.…”

Section: Theory For the Extended De Gennes Regimementioning

confidence: 99%

“…[28][29][30] In this regime, an asymptotically exact theory for the equilibrium statistics of a linear polymer predicts that the mean and variance of the extension are given by [31] ! "# = 1.18…”

Section: Theory For the Extended De Gennes Regimementioning

confidence: 99%

Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics

Alizadehheidari¹,

Werner

Noble³

et al. 2015

Macromolecules

View full text Add to dashboard Cite

Studies of circular DNA confined to nanofluidic channels are relevant both from a fundamental polymer-physics perspective and due to the importance of circular DNA molecules in vivo. We here observe the unfolding of DNA from the circular to linear configuration as a light-induced double strand break occurs, characterize the dynamics, and compare the equilibrium conformational statistics of linear and circular configurations. This is important because it allows us to determine to which extent existing statistical theories describe the extension of confined circular DNA. We find that the ratio of the extensions of confined linear and circular DNA configurations increases as the buffer concentration decreases. The experimental results fall between theoretical predictions for the extended de Gennes regime at weaker confinement and the Odijk regime at stronger confinement. We show that it is possible to directly distinguish between circular and linear DNA molecules by measuring the emission intensity from the DNA. Finally, we determine the rate of unfolding and show that this rate is larger for more confined DNA, possibly reflecting the corresponding larger difference in entropy between the circular and linear configurations.

show abstract

Equilibrium Distribution of Semiflexible Polymer Chains between a Macroscopic Dilute Solution Phase and Small Voids of Cylindrical Shape

Wang

Tang

Wang

2015

Macro Theory & Simulations

View full text Add to dashboard Cite

The equilibrium partition coefficients (K) are calculated for self-avoiding, semiflexible chains with the same finite contour length (L) and a variety of persistence length (l p ) values, partitioning between a macroscopic dilute solution phase and confined solution phases in cylindrical voids in the steric exclusion limit. It is found that, for the range of K -values most relevant to polymer separation in size exclusion chromatograph (0:19K90:9), the geometric mean of the radius of gyration (R g ) and the mean span (X) performs better than R g or X alone in collapsing the partition curves of the various linear semiflexible chains onto a single curve. The dependence of the confinement free energy (DA) on the persistence length is also examined. For those chains having the same L, the pore diameter D < min l p ; 2L=3 À Á is found to be the necessary and sufficient condition for DA to decrease with the increase of l p .

show abstract

Confined polymers in the extended de Gennes regime

Cited by 44 publications

References 34 publications

Wall depletion length of a channel-confined polymer

Wall depletion length of a channel-confined polymer

Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics

Equilibrium Distribution of Semiflexible Polymer Chains between a Macroscopic Dilute Solution Phase and Small Voids of Cylindrical Shape

Contact Info

Product

Resources

About