Segregation of polymers in confined spaces

Liu, Ya; Chakraborty, Bulbul

doi:10.1088/1478-3975/9/6/066005

Cited by 19 publications

(21 citation statements)

References 35 publications

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“…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%

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: Introductionmentioning

confidence: 99%

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

Polson

Kerry

2018

Soft Matter

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“…Polymer miscibility under confinement has also been studied using analytic forms of the free energy function estimated using a de Gennes blob scaling analysis. 15,16,21 Assuming that the polymer chain remains in conformational quasi-equilibrium, the free energy functions can be used to predict the dynamics of polymer segregation. Arnold and Jun used such a simple model to study segregation in infinitely long cylinders and interpret results from Langevin simulations.…”

Section: Introductionmentioning

confidence: 99%

“…12,13 Computer simulation studies have provided insight into the segregation of polymers under confinement. 4,[14][15][16][17][18][19][20][21][22][23][24][25] Most studies have considered systems comprised of flexible linear polymers, 4,[14][15][16][17][18]20,21,23,25 though some have have examined segregation of ring polymers, 19,22,24 as well as the effects of bending rigidity 23 and molecular crowding. 24 In the case of linear polymers, the role of cylindrical confinement in modulating the entropic repulsion has been investigated by examining the dependence of the polymer miscibility and intrachain ordering statistics on the confinement dimensions and chain density.…”

Section: Introductionmentioning

confidence: 99%

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

Polson

Montgomery

2014

The Journal of Chemical Physics

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Monte Carlo simulations are used to study the behavior of two polymers under confinement in a cylindrical tube. Each polymer is modeled as a chain of hard spheres. We measure the free energy of the system, F, as a function of the distance between the centers of mass of the polymers, λ, and examine the effects on the free energy functions of varying the channel diameter D and length L, as well as the polymer length N and bending rigidity κ. For infinitely long cylinders, F is a maximum at λ = 0, and decreases with λ until the polymers are no longer in contact. For flexible chains (κ = 0), the polymers overlap along the cylinder for low λ, while above some critical value of λ they are longitudinally compressed and non-overlapping while still in contact. We find that the free energy barrier height, ΔF ≡ F(0) - F(∞), scales as ΔF/k(B)T ∼ ND(-1.93 ± 0.01), for N ⩽ 200 and D ⩽ 9σ, where σ is the monomer diameter. In addition, the overlap free energy appears to scale as F/k(B)T = Nf(λ/N; D) for sufficiently large N, where f is a function parameterized by the cylinder diameter D. For channels of finite length, the free energy barrier height increases with increasing confinement aspect ratio L/D at fixed volume fraction ϕ, and it decreases with increasing ϕ at fixed L/D. Increasing the polymer bending rigidity κ monotonically reduces the overlap free energy. For strongly confined systems, where the chain persistence length P satisfies D ≪ P, F varies linearly with λ with a slope that scales as F'(λ) ∼ -k(B)TD(-β)P(-α), where β ≈ 2 and α ≈ 0.37 for N = 200 chains. These exponent values deviate slightly from those predicted using a simple model, possibly due to insufficiently satisfying the conditions defining the Odijk regime. Finally, we use Monte Carlo dynamics simulations to examine polymer segregation dynamics for fully flexible chains and observe segregation rates that decrease with decreasing entropic force magnitude, f ≡ |dF/dλ|. For both infinite-length and finite-length channels, the polymers are not conformationally relaxed at later times during segregation.

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“…This process has been the subject of numerous theoretical and computer simulation studies in recent years. [4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23] Most of these studies have examined the segregation behavior of flexible linear polymers, [4][5][6][7][8][9]11,12,14,16,19,20 though some have also investigated the behavior of ring polymers. 10,13,15,17,18,21 In addition, the effects of of bending rigidity, 14,19 macromolecular crowding, 15,18,21 and electrostatics 22,23 on the segregation dynamics and thermodynamics have been examined in detail.…”

Section: Introductionmentioning

confidence: 99%

Free energy and segregation dynamics of two channel-confined polymers of different length

Polson,

Zhu

2021

Preprint

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Polymers confined to a narrow channel are subject to strong entropic forces that tend to drive the molecules apart. In this study, we use Monte Carlo computer simulations to study the segregation behavior of two flexible hard-sphere polymers under confinement in a cylindrical channel. We focus on the effects of using polymers of different lengths. We measure the variation of the conformational free energy, F , with the centerof-mass separation distance, λ. The simulations reveal four different separation regimes, characterized by different scaling properties of the free energy with respect to the polymer lengths and the channel diameter, D. We propose a regime map in which the state of the system is determined by the values of the quantities N 2 /N 1 and λ/(N 1 + N 2 )D −β , where N 1 and N 2 are the polymer lengths, and where β ≈ 0.64. The observed scaling behavior of F (λ) in each regime is in reasonable agreement with predictions using a simple theoretical model. In addition, we use MC dynamics simulations to study the segregation dynamics of initially overlapping polymers by measurement of the incremental mean first-passage time with respect to λ. For systems characterized by a wide range of λ in which a short polymer is nested within a longer one, the segregation dynamics are close to that expected for two noninteracting 1D random walkers undergoing unbiased diffusion. When the free energy gradient is large segregation is rapid and characterized by out-of-equilibrium effects.

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Segregation of polymers in confined spaces

Cited by 19 publications

References 35 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

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

Free energy and segregation dynamics of two channel-confined polymers of different length

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