Scaling, crumpled wires, and genome packing in virions

Holanda, V. H. de; Gomes, M. A. F.

doi:10.1103/physreve.94.062406

Cited by 6 publications

(4 citation statements)

References 53 publications

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“…In the mechanical model presented here, the packing fraction is easily estimated from the geometric parameters in section 3, f ≈ 0.002−0.015, much smaller than the actual values encountered in phages. The behavior at high packing fractions has been explored recently using macroscopic mechanical models to represent the phage-DNA system [28,29,30].…”

Section: Discussionmentioning

confidence: 99%

A mechanical model of bacteriophage DNA ejection

Arun¹,

Ghosal

2017

Physics Letters A

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Single molecule experiments on bacteriophages show an exponential scaling for the dependence of mobility on the length of DNA within the capsid. It has been suggested that this could be due to the "capstan mechanism" -- the exponential amplification of friction forces that result when a rope is wound around a cylinder as in a ship's capstan. Here we describe a desktop experiment that illustrates the effect. Though our model phage is a million times larger, it exhibits the same scaling observed in single molecule experiments.Comment: 17 pages, 2 figures, 1 table + Supplementary Informatio

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Section: Discussionmentioning

confidence: 99%

A mechanical model of bacteriophage DNA ejection

Arun¹,

Ghosal

2017

Physics Letters A

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“…The injection of filaments into cavities is a basic problem involving elasticity and self-exclusion. These are two aspects of great importance in nature, with a wide range of influence from polymeric packing [1,2] to DNA packaging in viral capsids [3][4][5][6]. The structures formed by the confinement of wires packaged [3,7] and crumpled surfaces [8] present anomalous characteristics [3] that are of interest to soft matter physics and statistical physics.…”

Section: Introductionmentioning

confidence: 99%

Deformation of loops in 2D packing of flexible rods

Sobral¹,

Holanda²,

Leal³

et al. 2021

J. Phys. D: Appl. Phys.

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The injection of a long flexible rod into a two-dimensional domain yields a complex pattern commonly studied through the elasticity theory, packing analysis, and fractal geometries. ‘Loop’ is a one-vertex entity that naturally formed in this system. The role of the elastic features of each loop in 2D packing has not yet been discussed. In this work, we point out how the shape of a given loop in the complex structure allows estimating local deformations and forces. First, we build sets of symmetric free loops and perform compression experiments. Then, tight packing configurations are analyzed using image processing. We find that the dimensions of the loops, confined or not, obey the same dependence on the deformation. The results are consistent with a simple model based on 2D elastic theory for filaments, where the rod adopts the shape of Euler’s elasticas between its contact points. The force and the stored energy are obtained from numerical integration of the analytic expressions. In an additional experiment, we obtain that the compression force for deformed loops corroborates the theoretical findings. The importance of the shape of the loop is discussed and we hope that the theoretical curves may allow statistical considerations in future investigations.

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“…Crumpled structures are often considered a model complex system in soft matter. Crumpling is found both in nature, from geological deformations [1] to the packing of genetic material [2,3], and in scientific applications: Crumpled graphene, for instance, has been used to develop high-performance biosensors [4] and electrodes for batteries and supercapacitors [5,6,7] by leveraging the increased functional surface area of these porous structures. However, crumpling often proceeds in an unpredictable manner: As a thin sheet is confined, stresses spontaneously localize to produce a complex network of creases in the sheet [8,9].…”

Section: Introductionmentioning

confidence: 99%

Simulation of crumpled sheets via alternating quasistatic and dynamic representations

Andrejevic¹,

Rycroft²

2021

Preprint

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In this work, we present a method for simulating the large-scale deformation and crumpling of thin, elastoplastic sheets. Motivated by the physical behavior of thin sheets during crumpling, we adopt two different formulations of the governing equations of motion: a quasistatic formulation that effectively describes smooth deformations, and a fully dynamic formulation that captures large changes in the sheet's velocity. The former is a differential-algebraic system solved implicitly, while the latter is a purely differential system solved explicitly, using a hybrid integration scheme that adaptively alternates between the two representations. We demonstrate the capacity of this method to effectively simulate a variety of crumpling phenomena. Finally, we show that statistical properties, notably the accumulation of creases under repeated loading, as well as the area distribution of facets, are consistent with experimental observations.

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Scaling, crumpled wires, and genome packing in virions

Cited by 6 publications

References 53 publications

A mechanical model of bacteriophage DNA ejection

A mechanical model of bacteriophage DNA ejection

Deformation of loops in 2D packing of flexible rods

Simulation of crumpled sheets via alternating quasistatic and dynamic representations

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