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      Compaction of quasi-one-dimensional elastoplastic materials

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          Abstract

          Insight into crumpling or compaction of one-dimensional objects is important for understanding biopolymer packaging and designing innovative technological devices. By compacting various types of wires in rigid confinements and characterizing the morphology of the resulting crumpled structures, here, we report how friction, plasticity and torsion enhance disorder, leading to a transition from coiled to folded morphologies. In the latter case, where folding dominates the crumpling process, we find that reducing the relative wire thickness counter-intuitively causes the maximum packing density to decrease. The segment size distribution gradually becomes more asymmetric during compaction, reflecting an increase of spatial correlations. We introduce a self-avoiding random walk model and verify that the cumulative injected wire length follows a universal dependence on segment size, allowing for the prediction of the efficiency of compaction as a function of material properties, container size and injection force.

          Abstract

          Principles underlying crumpling of one-dimensional objects may be relevant to both biomolecular processes and to design of mechanical devices. By compacting various wires under rigid confinement and modelling observed geometric features, the authors show how friction, plasticity and torsion enhance disorder and lead to a transition from coiled to folded geometries.

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          Most cited references36

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          Mechanics of DNA packaging in viruses.

          A new generation of single-molecule experiments has opened up the possibility of reexamining many of the fundamental processes of biochemistry and molecular biology from a unique and quantitative perspective. One technique producing a host of intriguing results is the use of optical tweezers to measure the mechanical forces exerted by molecular motors during key processes such as the transcription of DNA or the packing of a viral genome into its capsid. The objective of the current article is to respond to such measurements on viruses and to use the theory of elasticity and a simple model of charge and hydration forces to derive the force required to pack DNA into a viral capsid as a function of the fraction of the viral genome that has been packed. The results are found to be in excellent accord with recent measurements and complement previous theoretical work. Because the packing of DNA in viral capsids occurs under circumstances of high internal pressure, we also compute how much pressure a capsid can sustain without rupture.
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            Forced crumpling of self-avoiding elastic sheets.

            Thin elastic sheets are important materials across length scales ranging from mesoscopic (polymerized membranes, clay platelets, virus capsids) to macroscopic (paper, metal foils). The crumpling of such sheets by external forces is characterized by the formation of a complex pattern of folds. We have investigated the role of self-avoidance, the fact that the sheets cannot self-intersect, for the crumpling process by large-scale computer simulations. At moderate compression, the force-compression relations of crumpled sheets for both self-avoiding and phantom sheets are found to obey universal power-law behaviours. However, self-avoiding sheets are much stiffer than phantom sheets and, for a given compression, develop many more folds. Moreover, self-avoidance is relevant already at very small volume fractions. The fold-length distribution for crumpled sheets is determined, and is found to be well-described by a log-normal distribution. The stiffening owing to self-avoidance is reflected in the changing nature of the sheet-to-sheet contacts from line-like to two-dimensionally extended with increasing compression.
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              Forces during bacteriophage DNA packaging and ejection.

              The conjunction of insights from structural biology, solution biochemistry, genetics, and single-molecule biophysics has provided a renewed impetus for the construction of quantitative models of biological processes. One area that has been a beneficiary of these experimental techniques is the study of viruses. In this article we describe how the insights obtained from such experiments can be utilized to construct physical models of processes in the viral life cycle. We focus on dsDNA bacteriophages and show that the bending elasticity of DNA and its electrostatics in solution can be combined to determine the forces experienced during packaging and ejection of the viral genome. Furthermore, we quantitatively analyze the effect of fluid viscosity and capsid expansion on the forces experienced during packaging. Finally, we present a model for DNA ejection from bacteriophages based on the hypothesis that the energy stored in the tightly packed genome within the capsid leads to its forceful ejection. The predictions of our model can be tested through experiments in vitro where DNA ejection is inhibited by the application of external osmotic pressure.
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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group
                2041-1723
                06 June 2017
                2017
                : 8
                : 15568
                Affiliations
                [1 ]Department of Theoretical Physics, Saarland University , 66041 Saarbrücken, Germany
                [2 ]Department of Experimental Physics, Saarland University , 66041 Saarbrücken, Germany
                [3 ]Department of Physics, Institute for Advanced Studies in Basic Sciences , Zanjan 45195, Iran
                [4 ]Van der Waals-Zeeman Institute, University of Amsterdam , 1098 XH Amsterdam, The Netherlands
                [5 ]Present address: Laboratory of Physics and Physical Chemistry of Foods, Wageningen University, Wageningen, The Netherlands
                Author notes
                Article
                ncomms15568
                10.1038/ncomms15568
                5467171
                28585550
                b9fae274-160f-4b12-82f7-88ad132870bb
                Copyright © 2017, The Author(s)

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

                History
                : 07 July 2016
                : 07 April 2017
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