1
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Miranda JP, Locatelli E, Valeriani C. Self-Organized States from Solutions of Active Ring Polymers in Bulk and under Confinement. J Chem Theory Comput 2024; 20:1636-1645. [PMID: 38153343 DOI: 10.1021/acs.jctc.3c00818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
In the present work, we study, by means of numerical simulations, the structural and dynamical behavior of a suspension of active ring polymers in bulk and under lateral confinement. At high activity, when changing the distance between the confining planes and the polymers' density, we identify the emergence of a self-organized dynamical state, characterized by the coexistence of slowly diffusing clusters of rotating disks and faster rings moving in between them. We further assess that self-organization is robust in a range of polymer sizes, and we identify a critical value of the activity, necessary to trigger cluster formation. This system has distinctive features resembling at the same time polymers, liquid crystals, and active systems, where the interplay between activity, topology, and confinement leads to a spontaneous segregation in an initially one-component solution.
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Affiliation(s)
- Juan Pablo Miranda
- Dep. Est. de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, 28040 Madrid, Spain
- GISC - Grupo Interdisciplinar de Sistemas Complejos, 28040 Madrid, Spain
| | - Emanuele Locatelli
- Department of Physics and Astronomy, University of Padova, 35131 Padova, Italy
- INFN, Sezione di Padova, via Marzolo 8, I-35131 Padova, Italy
| | - Chantal Valeriani
- Dep. Est. de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, 28040 Madrid, Spain
- GISC - Grupo Interdisciplinar de Sistemas Complejos, 28040 Madrid, Spain
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2
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Zeng L, Reisner WW. Mixing and demixing arising from compression of two semiflexible polymer chains in nanochannels. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023; 46:88. [PMID: 37755600 DOI: 10.1140/epje/s10189-023-00346-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 09/03/2023] [Indexed: 09/28/2023]
Abstract
We use molecular dynamics simulation to probe the non-equilibrium physics of two nanochannel-confined semiflexible polymers in a homogeneous flow field. We find that for sufficiently stiff chains the internal organization of the two chains takes the form of interwoven folds and circular coils. This organization can lead to mixing or demixing depending on chain stiffness and flow speed. At low and intermediate flow, the two chains adopt a folded configuration, which favours mixing. At high flow, the two chains adopt a predominantly coiled configuration. The coiled configuration results in demixing when the chains are compressed from an initially demixed condition and mixing when the chains are compressed from an initially mixed condition. We find that the mixing/demixing behaviour is governed by the ratio of the number of folded segments of one chain relative to the other at low flow and by the degree of coiling in both chains at high flow. For decreasing stiffness, the chains start to aggregate locally instead of mixing smoothly at low and intermediate flow. In the limit of completely flexible chains, the two chains either completely segregate at low flow, or adopt a locally demixed configuration consisting of large aggregates of one chain relative to the other that undergo complex stochastic dynamics, diffusing, disintegrating, and reforming at intermediate flow. The transition from complete segregation to the aggregate-dominated configuration occurs when the linear intra-chain ordering breaks down.
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Affiliation(s)
- Lili Zeng
- Department of Physics, McGill University, 3600 University Street, Montreal, QC, H3A 2T8, Canada.
| | - Walter W Reisner
- Department of Physics, McGill University, 3600 University Street, Montreal, QC, H3A 2T8, Canada
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3
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Tortora MMC, Jost D. Orientational Wetting and Topological Transitions in Confined Solutions of Semiflexible Polymers. Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c02350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Affiliation(s)
- Maxime M. C. Tortora
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS, Laboratoire de Biologie et Modélisation de la Cellule, 69364 Lyon CEDEX 07, France
| | - Daniel Jost
- Université de Lyon, ENS de Lyon, Université Claude Bernard, CNRS, Laboratoire de Biologie et Modélisation de la Cellule, 69364 Lyon CEDEX 07, France
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4
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Adherent Moving of Polymers in Spherical Confined Binary Semiflexible Ring Polymer Mixtures. BIOPHYSICA 2022. [DOI: 10.3390/biophysica2040044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Based on the coarse-grained model, we used molecular dynamics methods to calculate and simulate a semiflexible long ring–semiflexible short ring blended polymer system confined in a hard sphere. We systematically studied the distribution and motion characteristics of the long ring chain. The results show that when the short ring is short enough (Lshort < 20), the long ring (Llong = 50) is separated from the blend system and then distributed against the inner wall. As the length of the short ring increases (Lshort ≥ 20), the long ring can no longer be separated from the blending system. Moreover, we found that the long ring demonstrates a random direction of adherent walking behavior on the inner surface of the hard sphere. The velocity of the long ring decreases with the increase in the short ring length Lshort. Specifically for Lshort ≥ 20, the system does not undergo phase separation and the speed of the long ring decreases sharply along with the long ring distributed inside the confined bulk. This is related to the inner wall layer moving faster than the inside bulk of the restricted system. Our simulation results can help us to understand the distribution of macromolecules in biological systems in confined systems, including the restricted chromosome partitioning distribution and packing structure of circular DNA molecules.
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5
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Knot Factories with Helical Geometry Enhance Knotting and Induce Handedness to Knots. Polymers (Basel) 2022; 14:polym14194201. [PMID: 36236148 PMCID: PMC9572405 DOI: 10.3390/polym14194201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/25/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022] Open
Abstract
We performed molecular dynamics simulations of DNA polymer chains confined in helical nano-channels under compression in order to explore the potential of knot-factories with helical geometry to produce knots with a preferred handedness. In our simulations, we explore mutual effect of the confinement strength and compressive forces in a range covering weak, intermediate and strong confinement together with weak and strong compressive forces. The results find that while the common metrics of polymer chain in cylindrical and helical channels are very similar, the DNA in helical channels exhibits greatly different topology in terms of chain knottedness, writhe and handedness of knots. The results show that knots with a preferred chirality in terms of average writhe can be produced by using channels with a chosen handedness.
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6
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Sleiman JL, Burton RH, Caraglio M, Gutierrez Fosado YA, Michieletto D. Geometric Predictors of Knotted and Linked Arcs. ACS POLYMERS AU 2022; 2:341-350. [PMID: 36254317 PMCID: PMC9562465 DOI: 10.1021/acspolymersau.2c00021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Inspired by how certain proteins “sense”
knots and
entanglements in DNA molecules, here, we ask if local geometric features
that may be used as a readout of the underlying topology of generic
polymers exist. We perform molecular simulations of knotted and linked
semiflexible polymers and study four geometric measures to predict
topological entanglements: local curvature, local density, local 1D
writhe, and nonlocal 3D writhe. We discover that local curvature is
a poor predictor of entanglements. In contrast, segments with maximum
local density or writhe correlate as much as 90% of the time with
the shortest knotted and linked arcs. We find that this accuracy is
preserved across different knot types and also under significant spherical
confinement, which is known to delocalize essential crossings in knotted
polymers. We further discover that nonlocal 3D writhe is the best
geometric readout of the knot location. Finally, we discuss how these
geometric features may be used to computationally analyze entanglements
in generic polymer melts and gels.
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Affiliation(s)
- Joseph L. Sleiman
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Robin H. Burton
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Michele Caraglio
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Yair Augusto Gutierrez Fosado
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
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7
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Zeng L, Reisner WW. Organized states arising from compression of single semiflexible polymer chains in nanochannels. Phys Rev E 2022; 105:064501. [PMID: 35854522 DOI: 10.1103/physreve.105.064501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
We use molecular dynamics simulation to probe the nonequilibrium physics of single nanochannel-confined semiflexible polymers in a homogeneous flow field. The flow field compresses the polymer against the end of the nanochannel, simulating an experiment of a nanochannel confined chain compressed against a slit barrier. The flow-based compression gives rise to a packing of the chain against the channel end that possesses a striking organization, consisting of interweaving of folds and circular coils. For stiff chains at low flow, we find that the organization is dominated by repeated hairpin folds. For stiff chains at higher flow, we observe that circular coils arise along with the folds, with folding and coiling domains becoming interwoven at the highest flow speeds. Chain organization is retained even when the chain persistence length is on order of the channel width. We show that the global polymer organization, consisting of a number of defined folds and coiled loops, arises from the minimization of the total chain free energy.
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Affiliation(s)
- Lili Zeng
- Department of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 2T8, Canada
| | - Walter W Reisner
- Department of Physics, McGill University, 3600 University Street, Montreal, Quebec H3A 2T8, Canada
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8
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Celoria D, Mahler BI. A statistical approach to knot confinement via persistent homology. Proc Math Phys Eng Sci 2022; 478:20210709. [PMID: 35645602 PMCID: PMC9116441 DOI: 10.1098/rspa.2021.0709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 04/08/2022] [Indexed: 11/12/2022] Open
Abstract
In this paper, we study how randomly generated knots occupy a volume of space using topological methods. To this end, we consider the evolution of the first homology of an immersed metric neighbourhood of a knot's embedding for growing radii. Specifically, we extract features from the persistent homology (PH) of the Vietoris-Rips complexes built from point clouds associated with knots. Statistical analysis of our data shows the existence of increasing correlations between geometric quantities associated with the embedding and PH-based features, as a function of the knots' lengths. We further study the variation of these correlations for different knot types. Finally, this framework also allows us to define a simple notion of deviation from ideal configurations of knots.
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Affiliation(s)
- Daniele Celoria
- Mathematical Institute, University of Oxford, Radcliffe Observatory, Andrew Wiles Building, Woodstock Rd, Oxford OX2 6GG, UK
| | - Barbara I Mahler
- Mathematical Institute, University of Oxford, Radcliffe Observatory, Andrew Wiles Building, Woodstock Rd, Oxford OX2 6GG, UK
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9
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Rothörl J, Wettermann S, Virnau P, Bhattacharya A. Knot formation of dsDNA pushed inside a nanochannel. Sci Rep 2022; 12:5342. [PMID: 35351953 PMCID: PMC8964721 DOI: 10.1038/s41598-022-09242-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/17/2022] [Indexed: 12/23/2022] Open
Abstract
Recent experiments demonstrated that knots in single molecule dsDNA can be formed by compression in a nanochannel. In this manuscript, we further elucidate the underlying molecular mechanisms by carrying out a compression experiment in silico, where an equilibrated coarse-grained double-stranded DNA confined in a square channel is pushed by a piston. The probability of forming knots is a non-monotonic function of the persistence length and can be enhanced significantly by increasing the piston speed. Under compression knots are abundant and delocalized due to a backfolding mechanism from which chain-spanning loops emerge, while knots are less frequent and only weakly localized in equilibrium. Our in silico study thus provides insights into the formation, origin and control of DNA knots in nanopores.
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10
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Park CB, Sung BJ. Effects of Packaging History on the Ejection of a Polymer Chain from a Small Confinement. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Chung Bin Park
- Department of Chemistry and Research Institute for Basic Science, Sogang University, Seoul 04107, Republic of Korea
| | - Bong June Sung
- Department of Chemistry and Research Institute for Basic Science, Sogang University, Seoul 04107, Republic of Korea
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11
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Soh BW, Doyle PS. Equilibrium Conformation of Catenated DNA Networks in Slitlike Confinement. ACS Macro Lett 2021; 10:880-885. [PMID: 35549205 DOI: 10.1021/acsmacrolett.1c00299] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A kinetoplast is a planar network of catenated DNA rings with topology that resembles that of chain mail armor. In this work, we use single-molecule experiments to probe the conformation of kinetoplasts confined to slits. We find that the in-plane size of kinetoplasts increases with degree of confinement, akin to the slitlike confinement of linear DNA. The change in kinetoplast size with channel height is consistent with the scaling prediction from a Flory-type approach for a 2D polymer. With an increase in extent of confinement, the kinetoplasts appear to unfold and take on more uniform circular shapes, in contrast to the broad range of conformations observed for kinetoplasts in bulk.
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Affiliation(s)
- Beatrice W. Soh
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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12
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Mesoscale Simulation of Bacterial Chromosome and Cytoplasmic Nanoparticles in Confinement. ENTROPY 2021; 23:e23050542. [PMID: 33924872 PMCID: PMC8146307 DOI: 10.3390/e23050542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/22/2021] [Accepted: 04/26/2021] [Indexed: 11/18/2022]
Abstract
In this study we investigated, using a simple polymer model of bacterial chromosome, the subdiffusive behaviors of both cytoplasmic particles and various loci in different cell wall confinements. Non-Gaussian subdiffusion of cytoplasmic particles as well as loci were obtained in our Langevin dynamic simulations, which agrees with fluorescence microscope observations. The effects of cytoplasmic particle size, locus position, confinement geometry, and density on motions of particles and loci were examined systematically. It is demonstrated that the cytoplasmic subdiffusion can largely be attributed to the mechanical properties of bacterial chromosomes rather than the viscoelasticity of cytoplasm. Due to the randomly positioned bacterial chromosome segments, the surrounding environment for both particle and loci is heterogeneous. Therefore, the exponent characterizing the subdiffusion of cytoplasmic particle/loci as well as Laplace displacement distributions of particle/loci can be reproduced by this simple model. Nevertheless, this bacterial chromosome model cannot explain the different responses of cytoplasmic particles and loci to external compression exerted on the bacterial cell wall, which suggests that the nonequilibrium activity, e.g., metabolic reactions, play an important role in cytoplasmic subdiffusion.
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13
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Nikoubashman A. Ordering, phase behavior, and correlations of semiflexible polymers in confinement. J Chem Phys 2021; 154:090901. [DOI: 10.1063/5.0038052] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Arash Nikoubashman
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
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14
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Grossman D, Katzav E, Sharon E. Packing of stiff rods on ellipsoids: Geometry. Phys Rev E 2021; 103:013001. [PMID: 33601586 DOI: 10.1103/physreve.103.013001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
We suggest a geometrical mechanism for the ordering of slender filaments inside nonisotropic containers, using cortical microtubules in plant cells and the packing of viral genetic material inside capsids as concrete examples. We show analytically how the shape of the cell affects the ordering of phantom elastic rods that are not self-avoiding (i.e., self-crossing is allowed). We find that for oblate cells, the preferred orientation is along the equator, while for prolate spheroids with an aspect ratio close to 1, the orientation is along the principal (long axis). Surprisingly, at a high enough aspect ratio, a configurational phase transition occurs and the rods no longer point along the principal axis, but at an angle to it, due to high curvature at the poles. We discuss some of the possible effects of self-avoidance using energy considerations. These results are relevant to other packing problems as well, such as the spooling of filament in the industry or spider silk inside water droplets.
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Affiliation(s)
- Doron Grossman
- Racah Institute of Physics, Hebrew University, Jerusalem 9190401, Israel
| | - Eytan Katzav
- Racah Institute of Physics, Hebrew University, Jerusalem 9190401, Israel
| | - Eran Sharon
- Racah Institute of Physics, Hebrew University, Jerusalem 9190401, Israel
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15
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Guo F, Li K, Wu J, He L, Zhang L. Effects of Topological Constraints on Penetration Structures of Semi-Flexible Ring Polymers. Polymers (Basel) 2020; 12:E2659. [PMID: 33187232 PMCID: PMC7696204 DOI: 10.3390/polym12112659] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/03/2020] [Accepted: 11/08/2020] [Indexed: 11/24/2022] Open
Abstract
The effects of topological constraints on penetration structures of semi-flexible ring polymers in a melt are investigated using molecular dynamics simulations, considering simultaneously the effects of the chain stiffness. Three topology types of rings are considered: 01-knot (the unknotted), 31-knot and 61-knot ring polymers, respectively. With the improved algorithm to detect and quantify the inter-ring penetration (or inter-ring threading), the degree of ring threading does not increase monotonously with the chain stiffness, existing a peak value at the intermediate stiffness. It indicates that rings interpenetrate most at intermediate stiffness where there is a balance between coil expansion (favoring penetrations) and stiffness (inhibiting penetrations). Meanwhile, the inter-ring penetration would be suppressed with the knot complexity of the rings. The analysis of effective potential between the rings provides a better understanding for this non-monotonous behavior in inter-ring penetration.
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Affiliation(s)
- Fuchen Guo
- Department of Physics, Zhejiang University, Hangzhou 310027, China; (F.G.); (K.L.); (J.W.)
| | - Ke Li
- Department of Physics, Zhejiang University, Hangzhou 310027, China; (F.G.); (K.L.); (J.W.)
| | - Jiaxin Wu
- Department of Physics, Zhejiang University, Hangzhou 310027, China; (F.G.); (K.L.); (J.W.)
| | - Linli He
- Department of Physics, Wenzhou University, Wenzhou 325035, China
| | - Linxi Zhang
- Department of Physics, Zhejiang University, Hangzhou 310027, China; (F.G.); (K.L.); (J.W.)
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16
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Kumar S, Chauhan K, Singh S, Foster D. Polymer in wedge-shaped confinement: Effect on the θ temperature. Phys Rev E 2020; 101:030502. [PMID: 32290024 DOI: 10.1103/physreve.101.030502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/29/2020] [Indexed: 11/07/2022]
Abstract
The equilibrium properties of a finite-length linear polymer chain confined in an infinite wedge composed of two perfectly reflecting hard walls meeting at a variable apex angle (α) are presented. One end of the polymer is anchored a distance y from the apex on the conical axis of symmetry, while the other end is free. We report here, the nonmonotonic behavior of θ temperature as a function of y for a finite-length chain. Data collapse for different chain lengths indicates that such behavior will exist for all finite lengths. We delineate the origin of such nonmonotonic behavior, which may have potential applications in understanding the cellular process occurring in nanoconfined geometries.
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Affiliation(s)
- Sanjay Kumar
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - Sadhana Singh
- Department of Physics, Banaras Hindu University, Varanasi 221005, India
| | - Damien Foster
- Centre for Data Science, Coventry University, Coventry CV1 5FB, United Kingdom
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17
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Abstract
Unraveling the packing structure of dense assemblies of semiflexible rings is not only fundamental for the dynamical description of polymer rings, but also key to understand biopackaging, such as observed in circular DNA of viruses or genome folding. Here we use X-ray tomography to study the geometrical and topological features of disordered packings of rubber bands in a cylindrical container. Assemblies of short bands assume a liquid-like disordered structure, with short-range orientational order, and reveal only minor influence of the container. In the case of longer bands, the confinement causes folded configurations and the bands interpenetrate and entangle. Most of the systems are found to display a threading network which percolates the system. Surprisingly, for long bands whose diameter is more than twice the diameter of the container, we found that all bands interpenetrate each other, in a complex fully entangled structure.
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Affiliation(s)
- Leopoldo R Gómez
- Department of Physics, Universidad Nacional del Sur-IFISUR-CONICET, 8000 Bahía Blanca, Argentina;
| | | | - Thorsten Pöschel
- Institut für Multiscale Simulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91052 Erlangen, Germany
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18
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Valdés A, Coronel L, Martínez-García B, Segura J, Dyson S, Díaz-Ingelmo O, Micheletti C, Roca J. Transcriptional supercoiling boosts topoisomerase II-mediated knotting of intracellular DNA. Nucleic Acids Res 2020; 47:6946-6955. [PMID: 31165864 PMCID: PMC6649788 DOI: 10.1093/nar/gkz491] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/09/2019] [Accepted: 05/22/2019] [Indexed: 12/04/2022] Open
Abstract
Recent studies have revealed that the DNA cross-inversion mechanism of topoisomerase II (topo II) not only removes DNA supercoils and DNA replication intertwines, but also produces small amounts of DNA knots within the clusters of nucleosomes that conform to eukaryotic chromatin. Here, we examine how transcriptional supercoiling of intracellular DNA affects the occurrence of these knots. We show that although (−) supercoiling does not change the basal DNA knotting probability, (+) supercoiling of DNA generated in front of the transcribing complexes increases DNA knot formation over 25-fold. The increase of topo II-mediated DNA knotting occurs both upon accumulation of (+) supercoiling in topoisomerase-deficient cells and during normal transcriptional supercoiling of DNA in TOP1 TOP2 cells. We also show that the high knotting probability (Pkn ≥ 0.5) of (+) supercoiled DNA reflects a 5-fold volume compaction of the nucleosomal fibers in vivo. Our findings indicate that topo II-mediated DNA knotting could be inherent to transcriptional supercoiling of DNA and other chromatin condensation processes and establish, therefore, a new crucial role of topoisomerase II in resetting the knotting–unknotting homeostasis of DNA during chromatin dynamics.
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Affiliation(s)
- Antonio Valdés
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Lucia Coronel
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
| | - Belén Martínez-García
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Joana Segura
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Sílvia Dyson
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Ofelia Díaz-Ingelmo
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Cristian Micheletti
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
| | - Joaquim Roca
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
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19
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Fonseca ER, Mendoza CI. Self-assembly of core-corona particles confined in a circular box. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:015101. [PMID: 31505470 DOI: 10.1088/1361-648x/ab42fc] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Using Monte Carlo simulations, we study the assembly of colloidal particles interacting via isotropic core-corona potentials in two dimensions and confined in a circular box. We explore the structural variety at low temperatures as function of the number of particles (N) and the size of the confining box and find a rich variety of patterns that are not observed in unconfined flat space. For a small number of particles [Formula: see text], we identify the zero-temperature minimal energy configurations at a given box size. When the number of particles is large ([Formula: see text]), we distinguish different regimes that appear in route towards close packing configurations as the box size decreases. These regimes are characterized by the increase in the number of branching points and their coordination number. Interestingly, we obtain anisotropic open structures with unexpected variety of rotational symmetries that can be controlled by changing the model parameters, and some of the structures have chirality, in spite of the isotropy of the interactions and of the confining box. For arbitrary temperatures, we employ Monte Carlo integration to obtain the average energy and the configurational entropy of the system, which are then used to construct a phase diagram as function of temperature and box radius. Our findings show that confined core-corona particles can be a suitable system to engineer particles with highly complex internal structure that may serve as building blocks in hierarchical assembly.
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Affiliation(s)
- Erik R Fonseca
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Apdo. Postal 70-360, 04510 CdMx, Mexico
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20
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Rosa A, Di Stefano M, Micheletti C. Topological Constraints in Eukaryotic Genomes and How They Can Be Exploited to Improve Spatial Models of Chromosomes. Front Mol Biosci 2019; 6:127. [PMID: 31803755 PMCID: PMC6873889 DOI: 10.3389/fmolb.2019.00127] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/28/2019] [Indexed: 11/13/2022] Open
Affiliation(s)
- Angelo Rosa
- Scuola Internazionale Superiore di Studi Avanzati, Trieste, Italy
| | - Marco Di Stefano
- Centre Nacional d'Anàlisi Genòmica-Centre de Regulació Genòmica, Barcelona, Spain
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21
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Soik SM, Sharp TA. Effects of spherical confinement and backbone stiffness on flexible polymer jamming. Phys Rev E 2019; 99:052505. [PMID: 31212486 DOI: 10.1103/physreve.99.052505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Indexed: 11/07/2022]
Abstract
We use molecular simulations to study jamming of a crumpled bead-spring model polymer in a finite container and compare to jamming of repulsive spheres. After proper constraint counting, the onset of rigidity is seen to occur isostatically as in the case of repulsive spheres. Despite this commonality, the presence of the curved container wall and polymer backbone bonds introduce new mechanical properties. Notably, these include additional bands in the vibrational density of states that reflect the material structure as well as oscillations in local contact number and density near the wall but with lower amplitude for polymers. Polymers have fewer boundary contacts, and this low-density surface layer strongly reduces the global bulk modulus. We further show that bulk-modulus dependence on backbone stiffness can be described by a model of stiffnesses in series and discuss potential experimental and biological applications.
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Affiliation(s)
- Samuel M Soik
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Tristan A Sharp
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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22
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Fanalista F, Birnie A, Maan R, Burla F, Charles K, Pawlik G, Deshpande S, Koenderink GH, Dogterom M, Dekker C. Shape and Size Control of Artificial Cells for Bottom-Up Biology. ACS NANO 2019; 13:5439-5450. [PMID: 31074603 PMCID: PMC6543616 DOI: 10.1021/acsnano.9b00220] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/10/2019] [Indexed: 05/27/2023]
Abstract
Bottom-up biology is an expanding research field that aims to understand the mechanisms underlying biological processes via in vitro assembly of their essential components in synthetic cells. As encapsulation and controlled manipulation of these elements is a crucial step in the recreation of such cell-like objects, microfluidics is increasingly used for the production of minimal artificial containers such as single-emulsion droplets, double-emulsion droplets, and liposomes. Despite the importance of cell morphology on cellular dynamics, current synthetic-cell studies mainly use spherical containers, and methods to actively shape manipulate these have been lacking. In this paper, we describe a microfluidic platform to deform the shape of artificial cells into a variety of shapes (rods and discs) with adjustable cell-like dimensions below 5 μm, thereby mimicking realistic cell morphologies. To illustrate the potential of our method, we reconstitute three biologically relevant protein systems (FtsZ, microtubules, collagen) inside rod-shaped containers and study the arrangement of the protein networks inside these synthetic containers with physiologically relevant morphologies resembling those found in living cells.
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Affiliation(s)
- Federico Fanalista
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Anthony Birnie
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Renu Maan
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Federica Burla
- Department
of Living Matter, Biological Soft Matter Group, AMOLF, Science Park
104, 1098 XG Amsterdam, The Netherlands
| | - Kevin Charles
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Grzegorz Pawlik
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Siddharth Deshpande
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Gijsje H. Koenderink
- Department
of Living Matter, Biological Soft Matter Group, AMOLF, Science Park
104, 1098 XG Amsterdam, The Netherlands
| | - Marileen Dogterom
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
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23
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Abstract
We examine how channel confinement affects the equilibrium properties of topologically linked ring polymers and, by contrast, of equivalent unlinked rings, too. By performing extensive simulations of semiflexible rings of different chain length, N, and channel diameter, D, we discover three notable properties purely due to linking. First, upon entering the weak confinement regime, the length of the physically linked portion, lLKThe, becomes independent of chain length. Next, even when confinement is strong enough to pull apart and segregate unlinked rings, lLK stays much larger than in the highly stretched limit. Finally, at fixed N, lLK varies approximately as D0.5, and we provide a simple scaling argument for this power-law behavior. These properties, which may hold for different link topologies, can be tested by current experimental setups on DNA rings confined in microchannels. Moreover, they could be relevant for the efficient in vivo unlinking of newly replicated bacterial chromosomes.
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24
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Bimodality in the knotting probability of semiflexible rings suggested by mapping with self-avoiding polygons. REACT FUNCT POLYM 2019. [DOI: 10.1016/j.reactfunctpolym.2018.11.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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25
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Affiliation(s)
- Iurii Chubak
- Faculty of Physics, University of Vienna, Vienna, Austria
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26
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Pereira MCF, Brackley CA, Lintuvuori JS, Marenduzzo D, Orlandini E. Entropic elasticity and dynamics of the bacterial chromosome: A simulation study. J Chem Phys 2018; 147:044908. [PMID: 28764377 DOI: 10.1063/1.4995992] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the compressional elasticity of the bacterial nucleoid (DNA plus associated proteins), where DNA is confined into a cylindrical container and subjected to the action of a "piston"-a spherical bead to which an external force is applied. We quantify the effect of steric interactions (excluded volume) on the force-extension curves as the polymer is compressed. We find that non-DNA-binding proteins, even at low densities, exert an osmotic force which can be a lot larger than the entropic force exerted by the compressed DNA. The trends we observe are qualitatively robust with respect to changes in protein sizes and are similar for neutral and charged proteins (and DNA). We also quantify the dynamics of DNA expansion following removal of the "piston": while the expansion is well fitted by power laws, the apparent exponent depends on protein concentration and protein-DNA interaction in a significant way. We further highlight an interesting kinetic process which we observe during the expansion of DNA interacting with DNA-binding proteins when the interaction strength is intermediate: the proteins bind while the DNA is packaged by the compression force, but they "pop-off" one-by-one as the force is removed, leading to a slow unzipping kinetics. Finally, we quantify the importance of supercoiling, which is an important feature of bacterial DNA in vivo.
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Affiliation(s)
- M C F Pereira
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - C A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - J S Lintuvuori
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Universite Paris-Saclay, 91405 Orsay Cedex, France
| | - D Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - E Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Università di Padova, Via Marzolo 8, Padova, 35131 PD, Italy
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27
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Bernier S, Huang A, Reisner W, Bhattacharya A. Evolution of Nested Folding States in Compression of a Strongly Confined Semiflexible Chain. Macromolecules 2018. [DOI: 10.1021/acs.macromol.7b02748] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Simon Bernier
- Department of Physics, McGill University, 3600 rue university, Montreal, Quebec H3A 2T8, Canada
| | - Aiqun Huang
- Department of Physics, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
| | - Walter Reisner
- Department of Physics, McGill University, 3600 rue university, Montreal, Quebec H3A 2T8, Canada
| | - Aniket Bhattacharya
- Department of Physics, University of Central Florida, 4111 Libra Drive, Orlando, Florida 32816, United States
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28
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Abstract
Since the 1920s, packing arguments have been used to rationalize crystal structures in systems ranging from atomic mixtures to colloidal crystals. Packing arguments have recently been applied to complex nanoparticle structures, where they often, but not always, work. We examine when, if ever, packing is a causal mechanism in hard particle approximations of colloidal crystals. We investigate three crystal structures composed of their ideal packing shapes. We show that, contrary to expectations, the ordering mechanism cannot be packing, even when the thermodynamically self-assembled structure is the same as that of the densest packing. We also show that the best particle shapes for hard particle colloidal crystals at any finite pressure are imperfect versions of the ideal packing shape.
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29
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Ruggiero F, Aruta R, Netti PA, Torino E. Confinement of a polymer chain: An entropic study by Monte Carlo method. AIChE J 2017. [DOI: 10.1002/aic.15951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Flavia Ruggiero
- Center for Advanced Biomaterials for HealthCare; IIT@CRIB, Istituto Italiano di Tecnologia; Naples Italy
- Dept. of Chemical, Materials and Industrial Production Engineering; University of Naples Federico II; Naples Italy
| | - Rosaria Aruta
- Center for Advanced Biomaterials for HealthCare; IIT@CRIB, Istituto Italiano di Tecnologia; Naples Italy
- Dept. of Chemical, Materials and Industrial Production Engineering; University of Naples Federico II; Naples Italy
| | - Paolo Antonio Netti
- Center for Advanced Biomaterials for HealthCare; IIT@CRIB, Istituto Italiano di Tecnologia; Naples Italy
- Dept. of Chemical, Materials and Industrial Production Engineering; University of Naples Federico II; Naples Italy
- Interdisciplinary Research Center of Biomaterials, University of Naples Federico II; Naples Italy
| | - Enza Torino
- Center for Advanced Biomaterials for HealthCare; IIT@CRIB, Istituto Italiano di Tecnologia; Naples Italy
- Interdisciplinary Research Center of Biomaterials, University of Naples Federico II; Naples Italy
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30
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Milchev A, Egorov SA, Nikoubashman A, Binder K. Conformations and orientational ordering of semiflexible polymers in spherical confinement. J Chem Phys 2017; 146:194907. [PMID: 28527445 PMCID: PMC5438305 DOI: 10.1063/1.4983131] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 04/25/2017] [Indexed: 12/28/2022] Open
Abstract
Semiflexible polymers in lyotropic solution confined inside spherical nanoscopic "containers" with repulsive walls are studied by molecular dynamics simulations and density functional theory, as a first step to model confinement effects on stiff polymers inside of miniemulsions, vesicles, and cells. It is shown that the depletion effects caused by the monomer-wall repulsion depend distinctly on the radius R of the sphere. Further, nontrivial orientational effects occur when R, the persistence length ℓp, and the contour length L of the polymers are of similar magnitude. At intermediate densities, a "shell" of wall-attached chains is forming, such that the monomers belonging to those chains are in a layer at about the distance of one monomer from the container wall. At the same time, the density of the centers of mass of these chains is peaked somewhat further inside, but still near the wall. However, the arrangement of chains is such that the total monomer density is almost uniform in the sphere, apart from a small layering peak at the wall. It is shown that excluded volume effects among the monomers are crucial to account for this behavior, although they are negligible for comparable isolated single semiflexible chains of the same length.
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Affiliation(s)
- Andrey Milchev
- Institute for Physical Chemistry, Bulgarian Academia of Sciences, 1113 Sofia, Bulgaria
| | - Sergei A Egorov
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
| | - Arash Nikoubashman
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
| | - Kurt Binder
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
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31
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Jain A, Dorfman KD. Simulations of knotting of DNA during genome mapping. BIOMICROFLUIDICS 2017; 11:024117. [PMID: 28798853 PMCID: PMC5533507 DOI: 10.1063/1.4979605] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/21/2017] [Indexed: 05/28/2023]
Abstract
Genome mapping involves the confinement of long DNA molecules, in excess of 150 kilobase pairs, in nanochannels near the circa 50 nm persistence length of DNA. The fidelity of the map relies on the assumption that the DNA is linearized by channel confinement, which assumes the absence of knots. We have computed the probability of forming different knot types and the size of these knots for long chains (approximately 164 kilobase pairs) via pruned-enriched Rosenbluth method simulations of a discrete wormlike chain model of DNA in channel sizes ranging from 35 nm to 60 nm. Compared to prior simulations of short DNA in similar confinement, these long molecules exhibit both complex knots, with up to seven crossings, and multiple knots per chain. The knotting probability is a very strong function of channel size, ranging from 0.3% to 60%, and rationalized in the context of Odijk's theory for confined semiflexible chains. Overall, the knotting probability and knot size obtained from these equilibrium measurements are not consistent with experimental measurements of the properties of anomalously bright regions along the DNA backbone during genome mapping experiments. This result suggests that these events in experiments are either knots formed during the processing of the DNA prior to injection into the nanochannel or regions of locally high DNA concentration without a topological constraint. If so, knots during genome mapping are not an intrinsic problem for genome mapping technology.
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Affiliation(s)
- Aashish Jain
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
| | - Kevin D Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota-Twin Cities, 421 Washington Ave. SE, Minneapolis, Minnesota 55455, USA
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32
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Affiliation(s)
- G. D’Adamo
- SISSA, International School for Advanced Studies, via Bonomea 265, I-34136 Trieste, Italy
| | - E. Orlandini
- Dipartimento
di Fisica e Astronomia, Università di Padova and Sezione INFN, Via Marzolo 8, I-35100 Padova, Italy
| | - C. Micheletti
- SISSA, International School for Advanced Studies, via Bonomea 265, I-34136 Trieste, Italy
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33
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Mortazavi F, Habibi M, Nedaaee Oskoee E. Translocation of a granular chain in a horizontally vibrated saw-tooth channel. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2016; 39:93. [PMID: 27761780 DOI: 10.1140/epje/i2016-16093-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 09/27/2016] [Indexed: 06/06/2023]
Abstract
We study the translocation mechanism of a granular chain in a horizontally vibrated saw-tooth channel using MD simulations and macro-scale experiments and show that the translocation speed is independent of the chain length as long as the chain length is larger than the spatial period of the saw-tooth. With the help of simulation, we explore the effect of geometry of the container and frequency and amplitude of vibration as well as chain flexibility on the chain drift speed. We observe that the most efficient transport is achieved when one of the channel walls is shifted with respect to the other wall by an amount equal to half the spatial period of the saw-tooth. We define a persistence length for the chain and show that the translocation speed depends on the ratio of persistence length over the spatial period of the saw-tooth. The optimum translocation occurs when this ratio is about 0.4. We also determine the optimum saw-tooth angle for the translocation of the chain as well as the optimum distance between the two walls. Some properties of this system are similar to those of polymer systems.
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Affiliation(s)
- Fariba Mortazavi
- Institute for Advanced Studies in Basic Sciences, Gava Zang, 45195-159, Zanjan, Iran
| | - Mehdi Habibi
- Institute for Advanced Studies in Basic Sciences, Gava Zang, 45195-159, Zanjan, Iran.
- Van der Waals-Zeeman Institute, University of Amsterdam, 1098 XH, Amsterdam, The Netherlands.
| | - Ehsan Nedaaee Oskoee
- Institute for Advanced Studies in Basic Sciences, Gava Zang, 45195-159, Zanjan, Iran
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34
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Torino E, Aruta R, Sibillano T, Giannini C, Netti PA. Synthesis of semicrystalline nanocapsular structures obtained by Thermally Induced Phase Separation in nanoconfinement. Sci Rep 2016; 6:32727. [PMID: 27604818 PMCID: PMC5015022 DOI: 10.1038/srep32727] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 08/08/2016] [Indexed: 12/18/2022] Open
Abstract
Phase separation of a polymer solution exhibits a peculiar behavior when induced in a nanoconfinement. The energetic constraints introduce additional interactions between the polymer segments that reduce the number of available configurations. In our work, this effect is exploited in a one-step strategy called nanoconfined-Thermally Induced Phase Separation (nc-TIPS) to promote the crystallization of polymer chains into nanocapsular structures of controlled size and shell thickness. This is accomplished by performing a quench step of a low-concentrated PLLA-dioxane-water solution included in emulsions of mean droplet size <500 nm acting as nanodomains. The control of nanoconfinement conditions enables not only the production of nanocapsules with a minimum mean particle diameter of 70 nm but also the tunability of shell thickness and its crystallinity degree. The specific properties of the developed nanocapsular architectures have important implications on release mechanism and loading capability of hydrophilic and lipophilic payload compounds.
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Affiliation(s)
- Enza Torino
- Center for Advanced Biomaterials for Health Care @CRIB - Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci n. 53, 80125, Napoli, Italy
- University of Naples Federico II, Interdisciplinary Research Center of Biomaterials, CRIB P.le Tecchio 80, 80125, Naples, Italy
| | - Rosaria Aruta
- Center for Advanced Biomaterials for Health Care @CRIB - Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci n. 53, 80125, Napoli, Italy
- University of Naples Federico II, Department of Chemical, Materials and Industrial Production Engineering, P.le Tecchio 80, 80125, Naples, Italy
| | - Teresa Sibillano
- CNR - IC Istituto di Cristallografia, via Amendola 122/O, 70126 Bari-Italia
| | - Cinzia Giannini
- CNR - IC Istituto di Cristallografia, via Amendola 122/O, 70126 Bari-Italia
| | - Paolo A. Netti
- Center for Advanced Biomaterials for Health Care @CRIB - Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci n. 53, 80125, Napoli, Italy
- University of Naples Federico II, Interdisciplinary Research Center of Biomaterials, CRIB P.le Tecchio 80, 80125, Naples, Italy
- University of Naples Federico II, Department of Chemical, Materials and Industrial Production Engineering, P.le Tecchio 80, 80125, Naples, Italy
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35
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Rapaport DC. Packaging stiff polymers in small containers: A molecular dynamics study. Phys Rev E 2016; 94:030401. [PMID: 27739828 DOI: 10.1103/physreve.94.030401] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Indexed: 06/06/2023]
Abstract
The question of how stiff polymers are able to pack into small containers is particularly relevant to the study of DNA packaging in viruses. A reduced version of the problem based on coarse-grained representations of the main components of the system-the DNA polymer and the spherical viral capsid-has been studied by molecular dynamics simulation. The results, involving longer polymers than in earlier work, show that as polymers become more rigid there is an increasing tendency to self-organize as spools that wrap from the inside out, rather than the inverse direction seen previously. In the final state, a substantial part of the polymer is packed into one or more coaxial spools, concentrically layered with different orientations, a form of packaging achievable without twisting the polymer.
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Affiliation(s)
- D C Rapaport
- Department of Physics, Bar-Ilan University, Ramat-Gan 52900, Israel
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36
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Teich EG, van Anders G, Klotsa D, Dshemuchadse J, Glotzer SC. Clusters of polyhedra in spherical confinement. Proc Natl Acad Sci U S A 2016; 113:E669-78. [PMID: 26811458 PMCID: PMC4760782 DOI: 10.1073/pnas.1524875113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Dense particle packing in a confining volume remains a rich, largely unexplored problem, despite applications in blood clotting, plasmonics, industrial packaging and transport, colloidal molecule design, and information storage. Here, we report densest found clusters of the Platonic solids in spherical confinement, for up to [Formula: see text] constituent polyhedral particles. We examine the interplay between anisotropic particle shape and isotropic 3D confinement. Densest clusters exhibit a wide variety of symmetry point groups and form in up to three layers at higher N. For many N values, icosahedra and dodecahedra form clusters that resemble sphere clusters. These common structures are layers of optimal spherical codes in most cases, a surprising fact given the significant faceting of the icosahedron and dodecahedron. We also investigate cluster density as a function of N for each particle shape. We find that, in contrast to what happens in bulk, polyhedra often pack less densely than spheres. We also find especially dense clusters at so-called magic numbers of constituent particles. Our results showcase the structural diversity and experimental utility of families of solutions to the packing in confinement problem.
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Affiliation(s)
- Erin G Teich
- Applied Physics Program, University of Michigan, Ann Arbor, MI 48109
| | - Greg van Anders
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Daphne Klotsa
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Julia Dshemuchadse
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Sharon C Glotzer
- Applied Physics Program, University of Michigan, Ann Arbor, MI 48109; Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109; Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109; Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109
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37
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Suma A, Rosa A, Micheletti C. Pore Translocation of Knotted Polymer Chains: How Friction Depends on Knot Complexity. ACS Macro Lett 2015; 4:1420-1424. [PMID: 35614794 DOI: 10.1021/acsmacrolett.5b00747] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Knots can affect the capability of polymers to translocate through narrow pores in complex and counterintuitive ways that are still relatively unexplored. We report here on a systematic theoretical and computational investigation of the driven translocation of flexible chains accommodating a large repertoire of knots trapped at the pore entrance. These include composite knots, which are the most common form of spontaneous entanglement in long polymers. Two unexpected results emerge from this study. First, the high force translocation compliance does not decrease systematically with knot complexity. Second, the response of composite knots is so dependent on the order of their factor knots, that their hindrance can even be lower than some of their prime components. We show that the resulting rich and seemingly disparate phenomenology can be captured in a seamless framework based on the mechanism by which the tractive force is propagated along and past the knots. The quantitative scheme can be viably used for predictive purposes and, hence, ought to be useful in applicative contexts, too.
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Affiliation(s)
- Antonio Suma
- SISSA, International School for Advanced
Studies, via Bonomea 265, I-34136 Trieste, Italy
| | - Angelo Rosa
- SISSA, International School for Advanced
Studies, via Bonomea 265, I-34136 Trieste, Italy
| | - Cristian Micheletti
- SISSA, International School for Advanced
Studies, via Bonomea 265, I-34136 Trieste, Italy
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38
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Trefz B, Virnau P. Scaling behavior of topologically constrained polymer rings in a melt. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:354110. [PMID: 26291467 DOI: 10.1088/0953-8984/27/35/354110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Large scale molecular dynamics simulations on graphic processing units (GPUs) are employed to study the scaling behavior of ring polymers with various topological constraints in melts. Typical sizes of rings containing 3(1), 5(1) knots and catenanes made up of two unknotted rings scale like N(1/3) in the limit of large ring sizes N. This is consistent with the crumpled globule model and similar findings for unknotted rings. For small ring lengths knots occupy a significant fraction of the ring. The scaling of typical ring sizes for small N thus depends on the particular knot type and the exponent is generally larger than 0.4.
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Affiliation(s)
- Benjamin Trefz
- Graduate School Material Science in Mainz, Staudinger Weg 9, 55128 Mainz, Germany. Johannes Gutenberg University Mainz, Department of Physics, Staudingerweg 7, 55128 Mainz, Germany
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39
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Suma A, Orlandini E, Micheletti C. Knotting dynamics of DNA chains of different length confined in nanochannels. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:354102. [PMID: 26291786 DOI: 10.1088/0953-8984/27/35/354102] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Langevin dynamics simulations are used to characterize the typical mechanisms governing the spontaneous tying, untying and the dynamical evolution of knots in coarse-grained models of DNA chains confined in nanochannels. In particular we focus on how these mechanisms depend on the chain contour length, Lc, at a fixed channel width D = 56 nm corresponding to the onset of the Odijk scaling regime where chain backfoldings and hence knots are disfavoured but not suppressed altogether. We find that the lifetime of knots grows significantly with Lc, while that of unknots varies to a lesser extent. The underlying kinetic mechanisms are clarified by analysing the evolution of the knot position along the chain. At the considered confinement, in fact, knots are typically tied by local backfoldings of the chain termini where they are eventually untied after a stochastic motion along the chain. Consequently, the lifetime of unknots is mostly controlled by backfoldings events at the chain ends, which is largely independent of Lc. The lifetime of knots, instead, increases significantly with Lc because knots can, on average, travel farther along the chain before being untied. The observed interplay of knots and unknots lifetimes underpins the growth of the equilibrium knotting probability of longer and longer chains at fixed channel confinement.
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Affiliation(s)
- Antonio Suma
- SISSA, International School for Advanced Studies, via Bonomea 265, I-34136 Trieste, Italy
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Poier P, Likos CN, Moreno A, Blaak R. An Anisotropic Effective Model for the Simulation of Semiflexible Ring Polymers. Macromolecules 2015; 48:4983-4997. [PMID: 26240439 PMCID: PMC4519991 DOI: 10.1021/acs.macromol.5b00603] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/29/2015] [Indexed: 01/27/2023]
Abstract
We derive and introduce anisotropic effective pair potentials to coarse-grain solutions of semiflexible ring polymers of various lengths. The system has been recently investigated by means of full monomer-resolved computer simulations, revealing a host of unusual features and structure formation, which, however, cannot be captured by a rotationally averaged effective pair potential between the rings' centers of mass [Bernabei M.; Soft Matter2013, 9, 1287]. Our new coarse-graining strategy is to picture each ring as a soft, penetrable disk. We demonstrate that for the short- and intermediate-length rings the new model is quite capable of capturing the physics in a quantitative fashion, whereas for the largest rings, which resemble flexible ones, it fails at high densities. Our work opens the way for the physical justification of general, anisotropic penetrable interaction potentials.
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Affiliation(s)
- Peter Poier
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Christos N. Likos
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Angel
J. Moreno
- Centro de Física
de Materiales (CSIC-UPV/EHU) and Materials Physics Center (MPC), Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
- Donostia International
Physics Center, Paseo Manuel de Lardizabal
4, E-20018 San Sebastián, Spain
| | - Ronald Blaak
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
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Self-assembling knots of controlled topology by designing the geometry of patchy templates. Nat Commun 2015; 6:6423. [DOI: 10.1038/ncomms7423] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 01/27/2015] [Indexed: 01/04/2023] Open
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Slimani MZ, Bacova P, Bernabei M, Narros A, Likos CN, Moreno AJ. Cluster Glasses of Semiflexible Ring Polymers. ACS Macro Lett 2014; 3:611-616. [PMID: 25083314 PMCID: PMC4111402 DOI: 10.1021/mz500117v] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 06/10/2014] [Indexed: 12/19/2022]
Abstract
We present computer simulations of concentrated solutions of unknotted nonconcatenated semiflexible ring polymers. Unlike in their flexible counterparts, shrinking involves a strong energetic penalty, favoring interpenetration and clustering of the rings. We investigate the slow dynamics of the centers-of-mass of the rings in the amorphous cluster phase, consisting of disordered columns of oblate rings penetrated by bundles of prolate ones. Scattering functions reveal a striking decoupling of self- and collective motions. Correlations between centers-of-mass exhibit slow relaxation, as expected for an incipient glass transition, indicating the dynamic arrest of the cluster positions. However, self-correlations decay at much shorter time scales. This feature is a manifestation of the fast, continuous exchange and diffusion of the individual rings over the matrix of clusters. Our results reveal a novel scenario of glass formation in a simple monodisperse system, characterized by self-collective decoupling, soft caging, and mild dynamic heterogeneity.
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Affiliation(s)
- Mohammed Zakaria Slimani
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, E-20018 San Sebastián, Spain
| | - Petra Bacova
- Departamento
de Física de Materiales, Universidad del País Vasco (UPV/EHU), Apartado 1072, E-20080 San Sebastián, Spain
- Materials Physics Center MPC, Paseo
Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
| | - Marco Bernabei
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, E-20018 San Sebastián, Spain
- Departament
de Fisica Fonamental, Universitat de Barcelona, Martí i Franquès 1, E-08028 Barcelona, Spain
| | - Arturo Narros
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Christos N. Likos
- Faculty
of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Angel J. Moreno
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, E-20018 San Sebastián, Spain
- Materials Physics Center MPC, Paseo
Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
- Centro de Física de Materiales (CSIC, UPV/EHU), Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
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Abstract
We propose a mechanism in which two molecular knots pass through each other and swap positions along a polymer strand. Associated free energy barriers in our simulations only amount to a few kBT, which may enable the interchange of knots on a single DNA strand.
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Kolli HB, Frezza E, Cinacchi G, Ferrarini A, Giacometti A, Hudson TS. Communication: From rods to helices: Evidence of a screw-like nematic phase. J Chem Phys 2014; 140:081101. [DOI: 10.1063/1.4866808] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Fathizadeh A, Heidari M, Eslami-Mossallam B, Ejtehadi MR. Confinement dynamics of a semiflexible chain inside nano-spheres. J Chem Phys 2013; 139:044912. [PMID: 23902024 DOI: 10.1063/1.4816626] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is performed by gradually decreasing the diameter of a spherical shell which envelopes a confined chain. The latter procedure is carried out by injecting the chain inside a spherical shell through a hole on the shell surface. The chain is modeled with a rigid body molecular dynamics simulation and its parameters are adjusted to DNA base-pair elasticity. Directional order parameter is employed to analyze and compare the confined chain and the conformations of the chain for two different sizes of the spheres are studied in both procedures. It is shown that for the confined chains in the sphere sizes of our study, they appear in spiral or tennis-ball structures, and the tennis-ball structure is more likely to be observed in more compact confinements. Our results also show that the dynamical procedure of confinement and the rate of the confinement are influential parameters of the structure of the chain inside spherical cavities.
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Affiliation(s)
- A Fathizadeh
- Sharif University of Technology, Institute for Nanoscience and Nanotechnology, P.O. Box 14588-89694, Tehran, Iran
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Tubiana L, Rosa A, Fragiacomo F, Micheletti C. Spontaneous Knotting and Unknotting of Flexible Linear Polymers: Equilibrium and Kinetic Aspects. Macromolecules 2013. [DOI: 10.1021/ma4002963] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- L. Tubiana
- Department of Theoretical Physics, Jožef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - A. Rosa
- SISSA—Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea
265, 34136 Trieste, Italy
| | - F. Fragiacomo
- Dipartimento di Fisica, Università degli Studi di Milano, Via Celoria 16, 20133 Milano, Italy
| | - C. Micheletti
- SISSA—Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea
265, 34136 Trieste, Italy
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Di Stefano M, Rosa A, Belcastro V, di Bernardo D, Micheletti C. Colocalization of coregulated genes: a steered molecular dynamics study of human chromosome 19. PLoS Comput Biol 2013; 9:e1003019. [PMID: 23555238 PMCID: PMC3610629 DOI: 10.1371/journal.pcbi.1003019] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 02/19/2013] [Indexed: 01/12/2023] Open
Abstract
The connection between chromatin nuclear organization and gene activity is vividly illustrated by the observation that transcriptional coregulation of certain genes appears to be directly influenced by their spatial proximity. This fact poses the more general question of whether it is at all feasible that the numerous genes that are coregulated on a given chromosome, especially those at large genomic distances, might become proximate inside the nucleus. This problem is studied here using steered molecular dynamics simulations in order to enforce the colocalization of thousands of knowledge-based gene sequences on a model for the gene-rich human chromosome 19. Remarkably, it is found that most (≈ 88%) gene pairs can be brought simultaneously into contact. This is made possible by the low degree of intra-chromosome entanglement and the large number of cliques in the gene coregulatory network. A clique is a set of genes coregulated all together as a group. The constrained conformations for the model chromosome 19 are further shown to be organized in spatial macrodomains that are similar to those inferred from recent HiC measurements. The findings indicate that gene coregulation and colocalization are largely compatible and that this relationship can be exploited to draft the overall spatial organization of the chromosome in vivo. The more general validity and implications of these findings could be investigated by applying to other eukaryotic chromosomes the general and transferable computational strategy introduced here.
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Affiliation(s)
- Marco Di Stefano
- International School for Advanced Studies (SISSA), Trieste, Italy
| | - Angelo Rosa
- International School for Advanced Studies (SISSA), Trieste, Italy
- * E-mail: (AR); (CM)
| | - Vincenzo Belcastro
- Philip Morris International R&D, Philip Morris Products S.A., Neuchâtel, Switzerland
| | - Diego di Bernardo
- Telethon Institute of Genetics and Medicine (TIGEM), Napoli, Italy
- Department of Informatics and Systems Engineering, University “Federico II”, Napoli, Italy
| | - Cristian Micheletti
- International School for Advanced Studies (SISSA), Trieste, Italy
- * E-mail: (AR); (CM)
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Abstract
Filopodia are long, thin protrusions formed when bundles of fibers grow outwardly from a cell surface while remaining closed in a membrane tube. We study the subtle issue of the mechanical stability of such filopodia and how this depends on the deformation of the membrane that arises when the fiber bundle adopts a helical configuration. We calculate the ground state conformation of such filopodia, taking into account the steric interaction between the membrane and the enclosed semiflexible fiber bundle. For typical filopodia we find that a minimum number of fibers is required for filopodium stability. Our calculation elucidates how experimentally observed filopodia can obviate the classical Euler buckling condition and remain stable up to several tens of . We briefly discuss how experimental observation of the results obtained in this work for the helical-like deformations of enclosing membrane tubes in filopodia could possibly be observed in the acrosomal reactions of the sea cucumber Thyone, and the horseshoe crab Limulus. Any realistic future theories for filopodium stability are likely to rely on an accurate treatment of such steric effects, as analysed in this work.
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Petrov AS, Douglas SS, Harvey SC. Effects of pulling forces, osmotic pressure, condensing agents and viscosity on the thermodynamics and kinetics of DNA ejection from bacteriophages to bacterial cells: a computational study. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:115101. [PMID: 23399864 PMCID: PMC3705564 DOI: 10.1088/0953-8984/25/11/115101] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this work, we report on simulations of double-stranded DNA (dsDNA) ejection from bacteriophage φ29 into a bacterial cell. The ejection was studied with a coarse-grained model, in which viral dsDNA was represented by beads on a torsion-less string. The bacteriophage's capsid and the bacterial cell were defined by sets of spherical constraints. To account for the effects of the viscous medium inside the bacterial cell, the simulations were carried out using a Langevin dynamics protocol. Our simplest simulations (involving constant viscosity and no external biasing forces) produced results compatible with the push-pull model of DNA ejection, with an ejection rate significantly higher in the first part of ejection than in the latter parts. Additionally, we performed more complicated simulations, in which we included additional factors such as external forces, osmotic pressure, condensing agents and ejection-dependent viscosity. The effects of these factors (independently and in combination) on the thermodynamics and kinetics of DNA ejection were studied. We found that, in general, the dependence of ejection forces and ejection rates on the amount of DNA ejected becomes more complex if the ejection is modeled with a broader, more realistic set of parameters and influences (such as variation in the solvent's viscosity and the application of an external force). However, certain combinations of factors and numerical parameters led to the opposition of some ejection-driving and ejection-inhibiting influences, ultimately causing an apparent simplification of the ejection profiles.
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Affiliation(s)
- Anton S Petrov
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
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Orlandini E, Micheletti C. Knotting of linear DNA in nano-slits and nano-channels: a numerical study. J Biol Phys 2013; 39:267-75. [PMID: 23860873 PMCID: PMC3662413 DOI: 10.1007/s10867-013-9305-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Accepted: 02/07/2013] [Indexed: 12/23/2022] Open
Abstract
The amount and type of self-entanglement of DNA filaments is significantly affected by spatial confinement, which is ubiquitous in biological systems. Motivated by recent advancements in single DNA molecule experiments based on nanofluidic devices and by the introduction of algorithms capable of detecting knots in open chains, we investigate numerically the entanglement of linear, open DNA chains confined inside nano-slits. The results regard the abundance, type, and length of occurring knots and are compared with recent findings for DNA inside nano-channels. In both cases, the width of the confining region, D, spans the 30 nm-1 μm range and the confined DNA chains are 1-4 μm long. It is found that the knotting probability is maximum for slit widths in the 70-100 nm range. However, over the considered DNA contour lengths, the maximum incidence of knots remains below 20%, while for channel confinement it tops 50%. Further differences of the entanglement are seen for the average contour length of the knotted region, which drops significantly below D ~100 nm for channel-confinement, while it stays approximately constant for slit-like confinement. These properties ought to reverberate in different kinetic properties of linear DNA depending on confinement and could be detectable experimentally or exploitable in nano-technological applications.
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Affiliation(s)
- Enzo Orlandini
- />Dipartimento di Fisica e Astronomia and Sezione INFN, Università di Padova, Via Marzolo 8, 35131 Padova, Italy
| | - Cristian Micheletti
- />SISSA - Scuola Internazionale Superiore di Studi Avanzati and CNR-IOM Democritos, Via Bonomea 265, 34136 Trieste, Italy
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