1
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Moed DE, Dimitriyev MS, Greenvall BR, Grason GM, Crosby AJ. Mesoscale polymer arrays: high aspect ratio surface structures and their digital reconstruction. SOFT MATTER 2024. [PMID: 39145479 DOI: 10.1039/d4sm00324a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Inspired by adhesive bio-filamentous structure, such as bacterial pili, this work details the methods used to fabricate and characterize a surface-anchored array of thin, flexible and shape-responsive mesoscale polymer ribbons with a length-to-thickness aspect ratio of up to 100 000. The resulting structures exhibit geometrically complex and dynamic morphologies consistent with elastocapillary bending that experience an increase in curvature over hours of aging due to creep. We develop a computational image analysis framework to generate 3D reconstructions of these densely crowded geometries and extract quantitative descriptors to demonstrate morphological changes due to aging. We demonstrate the robustness of this quantitative method by characterizing the creep-induced change in an aging ribbon array's shape and develop a scaling relationship to describe the importance of ribbon thickness for shape and dynamical observations. These methods demonstrate an essential baseline to probe morphology-property relationships of mesoscale polymer ribbon arrays fabricated from a variety of materials in numerous environments. Through the introduction of perfluorodecalin droplets, we illustrate the potential of these ribbon arrays towards applications in adhesive, microrobotic, and biomedical devices.
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Affiliation(s)
- Demi E Moed
- Department of Polymer Science & Engineering, University of Massachusetts Amherst, 120 Governors Dr, Amherst, Massachusetts, 01003, USA.
| | - Michael S Dimitriyev
- Department of Polymer Science & Engineering, University of Massachusetts Amherst, 120 Governors Dr, Amherst, Massachusetts, 01003, USA.
- Department of Materials Science and Engineering, Texas A&M University, 575 Ross St., College Station, Texas, 77840, USA
| | - Benjamin R Greenvall
- Department of Polymer Science & Engineering, University of Massachusetts Amherst, 120 Governors Dr, Amherst, Massachusetts, 01003, USA.
| | - Gregory M Grason
- Department of Polymer Science & Engineering, University of Massachusetts Amherst, 120 Governors Dr, Amherst, Massachusetts, 01003, USA.
| | - Alfred J Crosby
- Department of Polymer Science & Engineering, University of Massachusetts Amherst, 120 Governors Dr, Amherst, Massachusetts, 01003, USA.
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2
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Goto S, Kim K, Matubayasi N. Unraveling the Glass-like Dynamic Heterogeneity in Ring Polymer Melts: From Semiflexible to Stiff Chain. ACS POLYMERS AU 2023; 3:437-446. [PMID: 38107414 PMCID: PMC10722566 DOI: 10.1021/acspolymersau.3c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/08/2023] [Accepted: 08/08/2023] [Indexed: 12/19/2023]
Abstract
Ring polymers are an intriguing class of polymers with unique physical properties, and understanding their behavior is important for developing accurate theoretical models. In this study, we investigate the effect of chain stiffness and monomer density on the static and dynamic behaviors of ring polymer melts using molecular dynamics simulations. Our first focus is on the non-Gaussian parameter of center-of-mass displacement as a measure of dynamic heterogeneity, which is commonly observed in glass-forming liquids. We find that the non-Gaussianity in the displacement distribution increases with the monomer density and stiffness of the polymer chains, suggesting that excluded volume interactions between centers of mass have a strong effect on the dynamics of ring polymers. We then analyze the relationship between the radius of gyration and monomer density for semiflexible and stiff ring polymers. Our results indicate that the relationship between the two varies with chain stiffness, which can be attributed to the competition between repulsive forces inside the ring and from adjacent rings. Finally, we study the dynamics of bond-breakage virtually connected between the centers of mass of rings to analyze the exchanges of intermolecular networks of bonds. Our results demonstrate that the dynamic heterogeneity of bond-breakage is coupled with the non-Gaussianity in ring polymer melts, highlighting the importance of the bond-breaking method in determining the intermolecular dynamics of ring polymer melts. Overall, our study sheds light on the factors that govern the dynamic behaviors of ring polymers.
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Affiliation(s)
- Shota Goto
- Division of Chemical Engineering, Department
of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Kang Kim
- Division of Chemical Engineering, Department
of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Department
of Materials Engineering Science, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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3
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Vega DA, Lance P, Zorzi E, Register RA, Gómez LR. Shock compression of semiflexible polymers. SOFT MATTER 2023; 19:6131-6139. [PMID: 37540128 DOI: 10.1039/d3sm00765k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
We employ molecular dynamics simulations to investigate the shock compression of linear semiflexible polymers. While the propagation velocity of a shock primarily depends on density, both chain rigidity and chain orientation significantly influence the shock width and the final temperature of the system. In general, the shock wave triggers molecular buckling in chains oriented perpendicular to the compression front. Following the passage of the front, the semiflexible chains buckle with a wavelength that decreases with the compression speed as λm ∼ up-0.2, and subsequent relaxation leads to a banana-like liquid crystal phase. In ordered systems with molecules oriented perpendicular to the compression front, the shock width increases by a factor of up to 10 compared to a similar isotropic system, resulting in enhanced shock energy absorption. These findings indicate that chain stiffness plays a critical role in the impact absorption properties of polymeric materials.
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Affiliation(s)
- Daniel A Vega
- Department of Physics, Universidad Nacional del Sur-IFISUR-CONICET, 8000 Bahía Blanca, Argentina.
| | - Pedro Lance
- Department of Physics, Universidad Nacional del Sur-IFISUR-CONICET, 8000 Bahía Blanca, Argentina.
| | - Enzo Zorzi
- Department of Physics, Universidad Nacional del Sur-IFISUR-CONICET, 8000 Bahía Blanca, Argentina.
| | - Richard A Register
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, 08544, USA
| | - Leopoldo R Gómez
- Department of Physics, Universidad Nacional del Sur-IFISUR-CONICET, 8000 Bahía Blanca, Argentina.
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4
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Gómez LR, García NA, Pöschel T. Macroscopic analogue to entangled polymers. SOFT MATTER 2023; 19:3538-3542. [PMID: 37114347 DOI: 10.1039/d3sm00148b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The entangled structure of polymeric materials is often described as resembling a bowl of spaghetti, swarms of earthworms, or snakes. These analogies not only illustrate the concept, but form the foundation of polymer physics. However, the similarity between these macroscopic, athermal systems and polymers in terms of topology remains uncertain. To better understand this relationship, we conducted an experiment using X-ray tomography to study the structure of arrays of linear rubber bands. We found that, similar to linear polymers, the average number of entanglements increases linearly with the length of the ribbons. Additionally, we observed that entanglements are less frequent near the surface of the container, where there are also more ends, similar to what has been seen in trapped polymers. These findings provide the first experimental evidence supporting the visualization of polymer structures using macroscopic, athermal analogues, confirming the initial intuitive insights of the pioneers of polymer physics.
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Affiliation(s)
- Leopoldo R Gómez
- Institut für Multiscale Simulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91052, Erlangen, Germany.
- Department of Physics, Universidad Nacional del Sur - IFISUR - CONICET, Bahía Blanca 8000, Argentina
| | - Nicolás A García
- Department of Physics, Universidad Nacional del Sur - IFISUR - CONICET, Bahía Blanca 8000, Argentina
- Institut Laue-Langevin, 71 Avenue des Martyrs, Grenoble 38042, France
| | - Thorsten Pöschel
- Institut für Multiscale Simulation, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91052, Erlangen, Germany.
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5
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Li J, Zhang B, Li Y. Glass Formation in Mechanically Interlocked Ring Polymers: The Role of Induced Chain Stiffness. Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c01368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Jian Li
- Department of Physics and Electronic Engineering, Heze University, Heze274015, China
| | - Bokai Zhang
- School of Physical Science and Technology, Southwest University, Chongqing400715, China
- Department of Physics, Zhejiang Sci-Tech University, Hangzhou310018, China
| | - Yushan Li
- Department of Physics and Electronic Engineering, Heze University, Heze274015, China
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6
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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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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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8
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Roy PK, Chaudhuri P, Vemparala S. Effect of ring stiffness and ambient pressure on the dynamical slowdown in ring polymers. SOFT MATTER 2022; 18:2959-2967. [PMID: 35348146 DOI: 10.1039/d1sm01754c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Using extensive molecular dynamics simulations, we investigate the slowdown of dynamics in a 3D system of ring polymers by varying the ambient pressure and the stiffness of the rings. Our study demonstrates that the stiffness of the rings determines the dynamics of the ring polymers, leading to glassiness at lower pressures for stiffer rings. The threading of the ring polymers, a unique feature that emerges only due to the topological nature of such polymers in three dimensions, is shown to be the determinant feature of dynamical slowdown, albeit only in a certain stiffness range. Our results suggest a possible framework for exploring the phase space spanned by ring stiffness and pressure to obtain spontaneously emerging topologically constrained polymer glasses.
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Affiliation(s)
- Projesh Kumar Roy
- The Institute of Mathematical Sciences, C. I. T. Campus, Taramani, Chennai 600113, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Pinaki Chaudhuri
- The Institute of Mathematical Sciences, C. I. T. Campus, Taramani, Chennai 600113, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C. I. T. Campus, Taramani, Chennai 600113, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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9
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Affiliation(s)
- Peter Cifra
- Polymer Institute Slovak Academy of Sciences Bratislava 84541 Slovakia
| | - Tomáš Bleha
- Polymer Institute Slovak Academy of Sciences Bratislava 84541 Slovakia
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10
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Smrek J, Garamella J, Robertson-Anderson R, Michieletto D. Topological tuning of DNA mobility in entangled solutions of supercoiled plasmids. SCIENCE ADVANCES 2021; 7:eabf9260. [PMID: 33980492 PMCID: PMC8115916 DOI: 10.1126/sciadv.abf9260] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/26/2021] [Indexed: 05/04/2023]
Abstract
Ring polymers in dense solutions are among the most intriguing problems in polymer physics. Because of its natural occurrence in circular form, DNA has been extensively used as a proxy to study the fundamental physics of ring polymers in different topological states. Yet, torsionally constrained-such as supercoiled-topologies have been largely neglected so far. The applicability of existing theoretical models to dense supercoiled DNA is thus unknown. Here, we address this gap by coupling large-scale molecular dynamics simulations with differential dynamic microscopy of entangled supercoiled DNA plasmids. We find that, unexpectedly, larger supercoiling increases the size of entangled plasmids and concomitantly induces an enhancement in DNA mobility. These findings are reconciled as due to supercoiling-driven asymmetric and double-folded plasmid conformations that reduce interplasmid entanglements and threadings. Our results suggest a way to topologically tune DNA mobility via supercoiling, thus enabling topological control over the (micro)rheology of DNA-based complex fluids.
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Affiliation(s)
- Jan Smrek
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Jonathan Garamella
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92110, USA
| | | | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine University of Edinburgh, Edinburgh EH4 2XU, UK
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11
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Hagita K, Murashima T. Effect of chain-penetration on ring shape for mixtures of rings and linear polymers. POLYMER 2021. [DOI: 10.1016/j.polymer.2021.123493] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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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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13
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Borger A, Wang W, O'Connor TC, Ge T, Grest GS, Jensen GV, Ahn J, Chang T, Hassager O, Mortensen K, Vlassopoulos D, Huang Q. Threading-Unthreading Transition of Linear-Ring Polymer Blends in Extensional Flow. ACS Macro Lett 2020; 9:1452-1457. [PMID: 35653662 DOI: 10.1021/acsmacrolett.0c00607] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Adding small amounts of ring polymers to a matrix of their linear counterparts is known to increase the zero-shear-rate viscosity because of linear-ring threading. Uniaxial extensional rheology measurements show that, unlike its pure linear and ring constituents, the blend exhibits an overshoot in the stress growth coefficient. By combining these measurements with ex-situ small-angle neutron scattering and nonequilibrium molecular dynamics simulations, this overshoot is shown to be driven by a transient threading-unthreading transition of rings embedded within the linear entanglement network. Prior to unthreading, embedded rings deform affinely with the linear entanglement network and produce a measurably stronger elongation of the linear chains in the blend compared to the pure linear melt. Thus, rings uniquely alter the mechanisms of transient elongation in linear polymers.
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Affiliation(s)
- Anine Borger
- Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Wendi Wang
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Thomas C O'Connor
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Ting Ge
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Gary S Grest
- Sandia National Laboratories, Albuquerque, New Mexico 87185, United States
| | - Grethe V Jensen
- The NIST Center for Neutron Research, Gaithersburg, Maryland 20899, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Junyoung Ahn
- Division of Advanced Materials Science and Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Taihyun Chang
- Division of Advanced Materials Science and Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Korea
| | - Ole Hassager
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Kell Mortensen
- Niels Bohr Institute, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Dimitris Vlassopoulos
- Institute of Electronic Structure and Laser, Foundation for Research and Technology Hellas (FORTH), Heraklion, Crete 70013, Greece.,Department of Materials Science and Technology, University of Crete, Heraklion, Crete 71003, Greece
| | - Qian Huang
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Lyngby, Denmark
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14
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Pachong SM, Chubak I, Kremer K, Smrek J. Melts of nonconcatenated rings in spherical confinement. J Chem Phys 2020; 153:064903. [DOI: 10.1063/5.0013929] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
| | - Iurii Chubak
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Jan Smrek
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
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