Polymer segregation under confinement: Free energy calculations and segregation dynamics simulations

Polson, James M.; Montgomery, Logan

doi:10.1063/1.4898714

Cited by 24 publications

(56 citation statements)

References 36 publications

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“…In the case of linear polymers, there is a slight decrease in ∆F with increasing density. As we noted previously, 31 these trends are consistent with the observation by Jung et al 22 that polymer miscibility decreases with increasing L/(D + σ ) and decreasing φ . In the case of ring polymers, there is no clear trend with varying φ .…”

Section: Resultssupporting

confidence: 93%

“…Results for linear polymers with other φ values were presented in our earlier study. 31 For both systems, the overlap free energy barrier increases monotonically with increasing confinement aspect ratio L/(D + σ ) for fixed monomer density.…”

Section: Resultsmentioning

confidence: 89%

“…tions in our previous study of polymer segregation, 31 as well as in simulation studies of polymer translocation [36][37][38][39] and backfolding of confined polymers. 40 To implement the SCH method, we carry out many independent simulations, each of which employs a unique "window potential" of the form:…”

Section: Modelmentioning

confidence: 99%

“…2 In addition, such theoretical insight will be of value for interpreting results of in vitro experiments of DNA separation in nanochannels. 16 Polymer segregation under confinement in channels has been the subject of numerous simulation studies 3,[17][18][19][20][21][22][23][24][25][26][27][28][29][30][31] These studies have mostly employed simple bead-spring polymer models com-Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island, C1A 4P3, Canada. E-mail: jpolson@upei.ca ‡ Present address: Department of Physics and Atmospheric Science, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.…”

Section: Introductionmentioning

confidence: 99%

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Segregation of polymers under cylindrical confinement: effects of polymer topology and crowding

Polson

Kerry

2018

Soft Matter

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Monte Carlo computer simulations are used to study the segregation behaviour of two polymers under cylindrical confinement. Using a multiple-histogram method, the conformational free energy, F, of the polymers was measured as a function of the centre-of-mass separation distance, λ. We examined the scaling of the free energy functions with the polymer length, the length and diameter of the confining cylinder, the polymer topology (i.e. linear vs. ring polymers), and the packing fraction and size of mobile crowding agents. In the absence of crowders, the observed scaling of F(λ) is similar to that predicted using a simple model employing the de Gennes blob model and the approximation that the free energy of overlapping chains in a tube is equal to that of two isolated chains each in a tube of half the cross-sectional area. Simulations were used to test the latter approximation and reveal that it yields poor quantitative predictions. This, along with generic finite-size effects, likely gives rise to the discrepancies between the predicted and measured values of scaling exponents for F(λ). For segregation in the presence of crowding agents, the free energy barrier generally decreases with increasing crowder packing fraction, thus reducing the entropic forces driving segregation. However, for fixed packing fraction, the barrier increases as the crowder/monomer size ratio decreases.

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Section: Resultssupporting

confidence: 93%

Section: Resultsmentioning

confidence: 89%

Section: Modelmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Segregation of polymers under cylindrical confinement: effects of polymer topology and crowding

Polson

Kerry

2018

Soft Matter

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“…Recently, we employed Monte Carlo methods to measure the free energy functions for segregating polymers in nanotubes and examined the scaling of the functions with respect to polymer contour length, persistence length, and channel dimensions for both infinite-length and finite-length tubes. 33 In the present study, we carry out similar calculations for a single folded polymer confined to a cylindrical channel. We consider several different variations of the system.…”

Section: Introductionmentioning

confidence: 99%

Free Energy of a Folded Polymer under Cylindrical Confinement

2017

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Monte Carlo computer simulations are used to study the conformational free energy of a folded polymer confined to a long cylindrical tube. The polymer is modeled as a hard-sphere chain. Its conformational free energy F is measured as a function of λ, the end-to-end distance of the polymer. In the case of a flexible linear polymer, F (λ) is a linear function in the folded regime with a gradient that scales as f ≡ |dF/dλ| ∼ N 0 D −1.20±0.01 for a tube of diameter D and a polymer of length N. This is close to the prediction f ∼ N 0 D −1 obtained from simple scaling arguments. The discrepancy is due in part to finite-size effects associated with the de-Gennes blob model. A similar discrepancy was observed for the folding of a single arm of a three-arm star polymer. We also examine backfolding of a semiflexible polymer of persistence length P in the classic Odijk regime. In the overlap regime, the derivative scales f ∼ N 0 D −1.72±0.02 P −0.35±0.01 , which is close to the prediction f ∼ N 0 D −5/3 P −1/3 obtained from a scaling argument that treats interactions between deflection segments at the second virial level. In addition, the measured free energy cost of forming a hairpin turn is quantitatively consistent with a recent theoretical calculation. Finally, we examine the scaling of F (λ) for a confined semiflexible chain in the presence of an S-loop composed of two hairpins. While the predicted scaling of the free energy gradient is the same as that for a single hairpin, we observe a scaling of f ∼ D −1.91±0.03 P −0.36±0.01 . Thus, the quantitative discrepancy between this measurement and the predicted scaling is somewhat greater for Sloops than for single hairpins.

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Arm retraction and escape transition in semi-flexible star polymer under cylindrical confinement

Račko

Cifra

2015

J Mol Model

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We studied the structure and dynamics of star-shaped polymers by means of coarse-grained molecular dynamics simulations and analysis of structural transitions of semi-flexible macromolecules confined in nano-channels. The conformation of star arms in narrow channels is given by the channel width, arm flexibility and number of arms aligned together in the given region along the channel. We focused on the conformation transition, where all arms are initially stretched in one direction of the narrow channel and were interested in the process of how individual arms escape into a free volume region of channel. We found that the escape transition does not proceed from arm ends but progresses by extension of a loop starting from the branch point; the arms escape in individual steps and the extension of arms depends on how many arms align in parallel in the channel.

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Polymer segregation under confinement: Free energy calculations and segregation dynamics simulations

Cited by 24 publications

References 36 publications

Segregation of polymers under cylindrical confinement: effects of polymer topology and crowding

Segregation of polymers under cylindrical confinement: effects of polymer topology and crowding

Free Energy of a Folded Polymer under Cylindrical Confinement

Arm retraction and escape transition in semi-flexible star polymer under cylindrical confinement

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