Unexpected relaxation dynamics of a self-avoiding polymer in cylindrical confinement

Arnold, Axel; Bozorgui, Behnaz; Frenkel, Daan; Ha, Bae‐Yeun; Jun, Suckjoon

doi:10.1063/1.2799513

Cited by 48 publications

(104 citation statements)

References 21 publications

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“…It is a dynamic variable for the polymer and is a measure of elasticity of the polymer. Our results for the effective spring constant are in good agreement with the blob model, unlike the case of the polymer inside the nanochannel [12][13][14].…”

Section: Introductionsupporting

confidence: 87%

Accuracy of the blob model for single flexible polymers inside nanoslits that are a few monomer sizes wide

2014

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The de Gennes' blob model is extensively used in different problems of polymer physics. This model is theoretically applicable when the number of monomers inside each blob is large enough. For confined flexible polymers, this requires the confining geometry to be much larger than the monomer size. In this paper, the opposite limit of polymer in nanoslits with one to several monomers width is studied, using molecular dynamics simulations. Extension of the polymer inside nanoslits, confinement force on the plates, and the effective spring constant of the confined polymer are investigated. Despite the theoretical limitations of the blob model, the simulation results are explained with the blob model very well. The agreement is observed for the static properties and the dynamic spring constant of the polymer. A theoretical description of the conditions under which the dynamic spring constant of the polymer is independent of the small number of monomers inside blobs is given. Our results on the limit of applicability of the blob model can be useful in the design of nanotechnology devices.

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Section: Introductionsupporting

confidence: 87%

Accuracy of the blob model for single flexible polymers inside nanoslits that are a few monomer sizes wide

2014

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“…25 Often, bead-spring models have been used to simulate the dynamics of such polymers in confinement via Brownian Dynamics (BD) simulations, both with 7,26,27 and without hydrodynamic interactions (HI). 28 The coarse-grained nature of these models allows simulation of experimentally relevant molecular weights with a small number of beads for a sufficiently long time. 29 Because such bead-spring models do not have the necessary resolution when the confinement size is of the order of the persistence length of the polymer, finer models have been used recently for Metropolis Monte Carlo 6,22 and lattice Boltzmann-based simulations 30 of semiflexible chains in confinement.…”

Section: Introductionmentioning

confidence: 99%

Kirkwood Diffusivity of Long Semiflexible Chains in Nanochannel Confinement

Muralidhar

Dorfman

2015

Macromolecules

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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.

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“…For strong compaction, φ c has to be as large as φ c = 0.5-0.6. In this high volume fraction, (cylindrical) confinement can induce wall-layering of hard spheres (e.g., monomers and crowders) 39,54 . Accordingly, simulation details can enter into the picture of crowding, even though their consequences may not be biologically meaningful.…”

Section: Chain Compaction For the Case A C > Amentioning

confidence: 99%

Effects of molecular crowding and confinement on the spatial organization of a biopolymer

Jeon

Jung

2016

Soft Matter

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A chain molecule can be entropically collapsed in a crowded medium in a free or confined space. Here, we present a unified view of how molecular crowding collapses a flexible polymer in three distinct spaces: free, cylindrical, and (two-dimensional) slit-like. Despite their seeming disparities, a few general features characterize all these cases, even though the φ c -dependence of chain compaction differs between the two cases: a > a c and a < a c , where φ c is the volume fraction of crowders, a the monomer size, and a c the crowder size. For a > a c (applicable to a coarse-grained model of bacterial chromosomes), chain size depends on the ratio aφ c /a c , and "full" compaction occurs universally at aφ c /a c ≈ 1; for a c > a (relevant for protein folding), it is controlled by φ c alone and crowding has a modest effect on chain size in a cellular environment (φ c ≈ 0.3). Also for a typical parameter range of biological relevance, molecular crowding can be viewed as effectively reducing the solvent quality, independently of confinement.

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Unexpected relaxation dynamics of a self-avoiding polymer in cylindrical confinement

Cited by 48 publications

References 21 publications

Accuracy of the blob model for single flexible polymers inside nanoslits that are a few monomer sizes wide

Accuracy of the blob model for single flexible polymers inside nanoslits that are a few monomer sizes wide

Kirkwood Diffusivity of Long Semiflexible Chains in Nanochannel Confinement

Effects of molecular crowding and confinement on the spatial organization of a biopolymer

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