Free Energy and Extension of a Wormlike Chain in Tube Confinement

Chen, Jeff Z. Y.

doi:10.1021/ma4020824

Cited by 50 publications

(65 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…18 The scaling of static properties in this ‘classic Odijk regime’ has been extensively studied, so much so that the prefactors in these scaling relations are known to multiple decimal places. 19,20 Our recent work confirmed the existence of a universal backfolded Odijk regime, wherein the deflection segments can form hairpins inside the channel. 10,13 Indeed, our calculations of the static properties in the backfolded Odijk regime 13 showed excellent agreement with Odijk’s theory.…”

Section: Introductionsupporting

confidence: 61%

Kirkwood Diffusivity of Long Semiflexible Chains in Nanochannel Confinement

Muralidhar

Dorfman

2015

Macromolecules

View full text Add to dashboard Cite

We compute the axial diffusivity of asymptotically long semiflexible polymers confined in square channels. Our calculations employ the Kirkwood approximation of the mobility tensor by combining computational fluid dynamics (CFD) calculations of the hydrodynamic tensor in channel confinement with pruned-enriched Rosenbluth method (PERM) simulations of a discrete wormlike chain model. Three key results emerge from our study. First, for the classic de Gennes regime, we confirm that Brochard and de Gennes’ blob theory correctly predicts the scaling of the axial diffusivity, contrary to the conclusions of previous analyses. Second, for the extended de Gennes regime, we show that a modified blob theory, which has been used to incorporate the effect of local stiffness on DNA diffusion in nanoslits, explains the deviation from the prediction of classic blob theory for diffusion in nanochannels. Third, we provide a calculation similar to the modified blob theory to explain the relative insensitivity of the diffusivity to channel size for channels between the extended de Gennes regime and the Odijk regime, which is the most relevant regime for experiments and technological applications of DNA confinement in nanochannels. Our results are not only relevant to the dynamics of confined semiflexible polymers such as DNA, but also reveal interesting analogies between confinement in channels and slits.

show abstract

Section: Introductionsupporting

confidence: 61%

Kirkwood Diffusivity of Long Semiflexible Chains in Nanochannel Confinement

Muralidhar

Dorfman

2015

Macromolecules

View full text Add to dashboard Cite

show abstract

“…Since the average projection of each bond along the cylinder axis is ℓ b cos θ ≈ ℓ b (1 − θ 2 /2), the reduction of the mean-squared end-to-end distance becomes 1 − R 2 e 1/2 /L ≈ θ 2 /2 = r ef f ℓp 2/3 /2. These scaling arguments can be made more precise to yield, [25][26][27] for L/ℓ p ≫ 1, [12] and typical experiments [43,44]. The shaded stripe indicates the I-N coexistence region, ρi < ρ < ρn, as predicted by Chen [12].…”

mentioning

confidence: 99%

“…It would be very interesting to study the corresponding static and dynamic collective structure factors, but this is beyond our scope here. It remains a challenge to extend the analytic theories [8][9][10][11][12]26] to self-consistently predict the length scales λ and r ef f from the molecular parameters ℓ p , d and L and the polymer density.…”

mentioning

confidence: 99%

Anomalous Fluctuations of Nematic Order in Solutions of Semiflexible Polymers

2016

View full text Add to dashboard Cite

The nematic ordering in semiflexible polymers with contour length L exceeding their persistence length ℓ_{p} is described by a confinement of the polymers in a cylinder of radius r_{eff} much larger than the radius r_{ρ} expected from the respective concentration of the solution. Large-scale molecular dynamics simulations combined with density functional theory are used to locate the isotropic-nematic (I-N) transition and to validate this cylindrical confinement. Anomalous fluctuations due to chain deflections from neighboring chains in the nematic phase are proposed. Considering deflections as collective excitations in the nematically ordered phase of semiflexible polymers elucidates the origins of shortcomings in the description of the I-N transition by existing theories.

show abstract

“…1). Little is known about this phase diagram for rectangular channels, except in the limit of very strong confinement [11,24,25]. To interpret a given experiment it is necessary to determine which regime in the phase diagram it corresponds to, and what the resulting scaling relations for the extension statistics are.…”

mentioning

confidence: 99%

Scaling regimes of a semiflexible polymer in a rectangular channel

Werner

Mehlig

2015

Phys. Rev. E

View full text Add to dashboard Cite

We derive scaling relations for the extension statistics and the confinement free energy for a semiflexible polymer confined to a channel with a rectangular cross section. Our motivation is recent numerical results [Gupta et al., J. Chem. Phys. 140, 214901 (2014)] indicating that extensional fluctuations are quite different in rectangular channels compared to square channels. Our results are of direct relevance for interpreting current experiments on DNA molecules confined to nanochannels, as many experiments are performed for rectangular channels with large aspect ratios, while theoretical and simulation results are usually obtained for square channels.

show abstract

Free Energy and Extension of a Wormlike Chain in Tube Confinement

Cited by 50 publications

References 26 publications

Kirkwood Diffusivity of Long Semiflexible Chains in Nanochannel Confinement

Kirkwood Diffusivity of Long Semiflexible Chains in Nanochannel Confinement

Anomalous Fluctuations of Nematic Order in Solutions of Semiflexible Polymers

Scaling regimes of a semiflexible polymer in a rectangular channel

Contact Info

Product

Resources

About