Conformations and orientational ordering of semiflexible polymers in spherical confinement

Milchev, A.; Егоров, С. А.; Nikoubashman, Arash; Binder, Kurt

doi:10.1063/1.4983131

Cited by 20 publications

(17 citation statements)

References 82 publications

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“…Therefore, the orientation entropy of long SLPs favours that many chains are close to the sphere centre. On the other hand, the density curve with a small shoulder near the wall attributes to the density oscillations "layering" induced by confinement, well known for dense fluids near hard walls [31,67,68]. Further, the average distance <r> from the sphere centre to the monomers of long SLPs is shown in Figure 8b.…”

Section: Comparison With Mixtures Of Semiflexible Linear and Ring Polmentioning

confidence: 73%

“…We also systematically examine the dependence of the separation structure for long SRPs in the binary mixtures on Kb,long and ρ. The average distance <r> from the sphere centre to the monomers of To visualize the conformation characteristic of long SRPs confined in a hard sphere, we define the average orientation order parameter P 2 (cosθ') of long SRPs as follows [31][32][33]:…”

Section: Segregated Structure In Binary Srps Mixturementioning

confidence: 99%

“…Moreover, the shapes of ring chains change from prolate, crumpled structures to planar, rigid rings with the increase of the stiffness [25]. Semiflexible linear polymers (SLPs) in the spherical confinement has been extensively studied [26][27][28][29][30][31][32][33], whether a single (long) or many (short) semiflexible linear polymers [31][32][33]. Milchev et al [31,32] investigated the competition between the nematic order and confinement of semiflexible linear polymers in a spherical cavity at relatively large densities by using molecular dynamics (MD) simulation.…”

Section: Introductionmentioning

confidence: 99%

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Entropy-Induced Separation of Binary Semiflexible Ring Polymer Mixtures in Spherical Confinement

Zhou¹,

Guo²,

Li³

et al. 2019

Polymers

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Coarse-grained molecular dynamics simulations are used to investigate the conformations of binary semiflexible ring polymers (SRPs) of two different lengths confined in a hard sphere. Segregated structures of SRPs in binary mixtures are strongly dependent upon the number density of system (ρ), the bending energy of long SRPs (Kb, long), and the chain length ratio of long to short SRPs (α). With a low ρ or a weak Kb, long at a small ratio α, long SRPs are immersed randomly in the matrix of short SRPs. As ρ and bending energy of long SRPs (Kb, long) are increased up to a certain value for a large ratio α, a nearly complete segregation between long and short SRPs is observed, which can be further characterized by the ratio of tangential and radial components of long SRPs velocity. These explicit segregated structures of the two components in spherical confinement are induced by a delicate competition between the entropic excluded volume (depletion) effects and bending contributions.

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Section: Comparison With Mixtures Of Semiflexible Linear and Ring Polmentioning

confidence: 73%

Section: Segregated Structure In Binary Srps Mixturementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Entropy-Induced Separation of Binary Semiflexible Ring Polymer Mixtures in Spherical Confinement

Zhou¹,

Guo²,

Li³

et al. 2019

Polymers

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“…As described in previous work for confined single-component systems of semiflexible polymers, ,, we carry out standard MD simulations using two choices for the radius R of the rigid spheres confining the polymers, R = 35 and 70, and the repulsive potential acting from the sphere surfaces is chosen to have the same form as the monomer–monomer repulsion, also with the same range σ = 1 and strength ϵ = 1. We use graphics processing units (GPUs) and apply HOOMD Blue software. , Figure presents typical snapshot pictures of equilibrated configurations that will be analyzed in the next sections.…”

Section: Model and Methodsmentioning

confidence: 99%

Phase Separation in a Binary Mixture of Semiflexible Polymers Confined in a Repulsive Sphere

2021

Self Cite

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Lyotropic solutions containing two types of semiflexible macromolecules in spherical confinement are studied by molecular dynamics simulations and density functional theory, using a coarse-grained model. The case of strong stiffness disparity between both types of polymers is treated, and for simplicity, we take the contour lengths of both types of polymers to be equal. Only sphere radii larger than this contour length are considered, so that many chains can be packed inside the sphere, even when the chains are stretched out in a nematic state. For the chosen polymer solution, in the bulk one finds with increasing monomer concentration a transition from an isotropic phase through an isotropic–nematic two-phase region to a homogeneous nematic phase to which both constituents contribute. In the corresponding confined systems, there is an interplay between these phase transitions and surface enrichment of one component (typically, but not always, the stiffer one). In rather dilute confined solutions, the main effect of the surfaces is that the random orientation of the end-to-end vectors of the stiff chains is perturbed in a surface shell whose thickness is roughly the contour length. In more concentrated systems, a thin layer of wall-attached stiff chains is observed in addition, while (for equal mole fractions of both constituents) the stiffer component can also form an almost cylindrical domain with a bipolar orientational order, surrounded in the remainder of the sphere by the less stiff component. Topological defects in the nematic order can be identified, similar to the case where a single type of semiflexible polymer is confined in a sphere. The radial profiles of monomer concentrations and of various order parameters are compared to analogous data near planar and cylindrical repulsive walls, to provide a comprehensive picture of confinement effects on such polymer solutions.

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“…1A). This coarse-grained approach allows us to simulate realistic confining diameters of a few µm and actin filament concentration in the µM range though not reaching concentrations where excluded volume interactions would cause nematic ordering (dense confined semi-flexible polymers were examined by Milchev et al [Milchev et al, 2017]). We also consider cases where the confining size is smaller or comparable to the filament persistence length, as is the case in many cellular systems as well as prior experiments in vitro.…”

Section: Introductionmentioning

confidence: 99%

Organization of Associating or Crosslinked Actin Filaments in Confinement

Koudehi

Rutkowski

Vavylonis

2019

Preprint

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AbstractA key factor of actin cytoskeleton organization in cells is the interplay between the dynamical properties of actin filaments and cell geometry, which restricts, confines and directs their orientation. Crosslinking interactions among actin filaments, together with geometrical cues and regulatory proteins can give rise to contractile rings in dividing cells and actin rings in neurons. Motivated by recent in vitro experiments, in this work we performed computer simulations to study basic aspects of the interplay between confinement and attractive interactions between actin filaments. We used a spring-bead model and Brownian dynamics to simulate semiflexible actin filaments that polymerize in a confining sphere with a rate proportional to the monomer concentration. We model crosslinking, or attraction through the depletion interaction, implicitly as an attractive short-range potential between filament beads. In confining geometries smaller than the persistence length of actin filaments, we show rings can form by curving of filaments of length comparable to, or longer than the confinement diameter. Rings form for optimal ranges of attractive interactions that exist in between open bundles, irregular loops, aggregated and unbundled morphologies. The probability of ring formation is promoted by attraction to the confining sphere boundary and decreases for large radii and initial monomer concentrations, in agreement with prior experimental data. The model reproduces ring formation along the flat axis of oblate ellipsoids.

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Conformations and orientational ordering of semiflexible polymers in spherical confinement

Cited by 20 publications

References 82 publications

Entropy-Induced Separation of Binary Semiflexible Ring Polymer Mixtures in Spherical Confinement

Entropy-Induced Separation of Binary Semiflexible Ring Polymer Mixtures in Spherical Confinement

Phase Separation in a Binary Mixture of Semiflexible Polymers Confined in a Repulsive Sphere

Organization of Associating or Crosslinked Actin Filaments in Confinement

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