Equilibrium organization, conformation, and dynamics of two polymers under box-like confinement

Polson, James M.; Rehel, Desiree A.

doi:10.1039/d1sm00308a

Cited by 2 publications

(7 citation statements)

References 56 publications

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“…As noted in our previous study 47 the simulations employed to study polymer dynamics are much less efficient than the MC simulations used to examine the configurational statistics. Consequently, systems using much shorter polymers are required in the former case for computational feasibility.…”

Section: Anisometry In Box Geometrymentioning

confidence: 97%

“…In a recent study, we examined the organization and dynamics of two identical polymers confined to a box with a square cross section using freely-jointed chains of O( 102 ) monomers. 47 Such short chains were used because of the time consuming nature of the BD simulations. The disadvantage of such a model is its inability to tune the ratios of the relevant polymer length scales, i.e.…”

Section: Long Chains In Cavities With Symmetric Cross Sectionsmentioning

confidence: 99%

“…Since c c /c k is fixed, these distributions in effect correspond to polymers of larger polymer width w. The distributions in row (c) were calculated using freely-jointed chains, as in our previous study. 47 The distributions in each column correspond to three different values of L/R g . The graphs in row (d) are cross sections of the distributions for y = 0.…”

Section: Long Chains In Cavities With Symmetric Cross Sectionsmentioning

confidence: 99%

“…Recently, we used Brownian dynamics and Monte Carlo simulation methods to study the organization and dynamics of two flexible Lennard-Jones chains trapped in cavities resembling those with square cross sections used in ref. 45 and 47. We calculated the position probability distributions in the lateral plane and the centre-of-mass dynamics and measured their variation with lateral box size and polymer length.…”

Section: Introductionmentioning

confidence: 99%

“…In this study, we build on our previous work in ref. 47 and use Monte Carlo (MC) and Brownian dynamics (BD) simulations to study systems of two polymers entrapped in cavities of comparable shape and size as those used in the experiments. We address issues arising from the previous study by incorporating features that improve the semblance of the molecular model to the DNA systems studied in ref.…”

Section: Introductionmentioning

confidence: 99%

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Equilibrium behaviour of two cavity-confined polymers: effects of polymer width and system asymmetries

Rehel

Polson

2023

Soft Matter

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Section: Anisometry In Box Geometrymentioning

confidence: 97%

Section: Long Chains In Cavities With Symmetric Cross Sectionsmentioning

confidence: 99%

Section: Long Chains In Cavities With Symmetric Cross Sectionsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Equilibrium behaviour of two cavity-confined polymers: effects of polymer width and system asymmetries

Rehel

Polson

2023

Soft Matter

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Confinement anisotropy drives polar organization of two DNA molecules interacting in a nanoscale cavity

et al. 2022

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There is growing appreciation for the role phase transition based phenomena play in biological systems. In particular, self-avoiding polymer chains are predicted to undergo a unique confinement dependent demixing transition as the anisotropy of the confined space is increased. This phenomenon may be relevant for understanding how interactions between multiple dsDNA molecules can induce self-organized structure in prokaryotes. While recent in vivo experiments and Monte Carlo simulations have delivered essential insights into this phenomenon and its relation to bacteria, there are fundamental questions remaining concerning how segregated polymer states arise, the role of confinement anisotropy and the nature of the dynamics in the segregated states. To address these questions, we introduce an artificial nanofluidic model to quantify the interactions of multiple dsDNA molecules in cavities with controlled anisotropy. We find that two dsDNA molecules of equal size confined in an elliptical cavity will spontaneously demix and orient along the cavity poles as cavity eccentricity is increased; the two chains will then swap pole positions with a frequency that decreases with increasing cavity eccentricity. In addition, we explore a system consisting of a large dsDNA molecule and a plasmid molecule. We find that the plasmid is excluded from the larger molecule and will exhibit a preference for the ellipse poles, giving rise to a non-uniform spatial distribution in the cavity that may help explain the non-uniform plasmid distribution observed during in vivo imaging of high-copy number plasmids in bacteria.

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Equilibrium organization, conformation, and dynamics of two polymers under box-like confinement

Abstract: Motivated by recent nanofluidics experiments, we use Brownian dynamics and Monte Carlo simulations to study the conformation, organization and dynamics of two polymer chains confined to a single box-like cavity....

Cited by 2 publications

References 56 publications

Equilibrium behaviour of two cavity-confined polymers: effects of polymer width and system asymmetries

Equilibrium behaviour of two cavity-confined polymers: effects of polymer width and system asymmetries

Confinement anisotropy drives polar organization of two DNA molecules interacting in a nanoscale cavity

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