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Blovský T, Šindelka K, Limpouchová Z, Procházka K. Self-Assembly of Symmetric Copolymers in Slits with Inert and Attractive Walls. Polymers (Basel) 2023; 15:4458. [PMID: 38006182 PMCID: PMC10675682 DOI: 10.3390/polym15224458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/01/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Although the behavior of the confined semi-dilute solutions of self-assembling copolymers represents an important topic of basic and applied research, it has eluded the interest of scientists. Extensive series of dissipative particle dynamics simulations have been performed on semi-dilute solutions of A5B5 chains in a selective solvent for A in slits using a DL-MESO simulation package. Simulations of corresponding bulk systems were performed for comparison. This study shows that the associates in the semi-dilute bulk solutions are partly structurally organized. Mild steric constraints in slits with non-attractive walls hardly affect the size of the associates, but they promote their structural arrangement in layers parallel to the slit walls. Attractive walls noticeably affect the association process. In slits with mildly attractive walls, the adsorption competes with the association process. At elevated concentrations, the associates start to form in wide slits when the walls are sparsely covered by separated associates, and the association process prevents the full coverage of the surface. In slits with strongly attractive walls, adsorption is the dominant behavior. The associates form in wide slits at elevated concentrations only after the walls are completely and continuously covered by the adsorbed chains.
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Affiliation(s)
- Tomáš Blovský
- The Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague, Czech Republic;
| | - Karel Šindelka
- Department of Molecular and Mesoscopic Modelling, Institute of Chemical Process Fundamentals, Czech Academy of Sciences, Rozvojová 135, 165 02 Prague, Czech Republic;
| | - Zuzana Limpouchová
- The Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague, Czech Republic;
| | - Karel Procházka
- The Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030, 128 40 Prague, Czech Republic;
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Rusková R, Račko D. Knot Formation on DNA Pushed Inside Chiral Nanochannels. Polymers (Basel) 2023; 15:4185. [PMID: 37896430 PMCID: PMC10611388 DOI: 10.3390/polym15204185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/29/2023] Open
Abstract
We performed coarse-grained molecular dynamics simulations of DNA polymers pushed inside infinite open chiral and achiral channels. We investigated the behavior of the polymer metrics in terms of span, monomer distributions and changes of topological state of the polymer in the channels. We also compared the regime of pushing a polymer inside the infinite channel to the case of polymer compression in finite channels of knot factories investigated in earlier works. We observed that the compression in the open channels affects the polymer metrics to different extents in chiral and achiral channels. We also observed that the chiral channels give rise to the formation of equichiral knots with the same handedness as the handedness of the chiral channels.
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Affiliation(s)
- Renáta Rusková
- Polymer Institute of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia
| | - Dušan Račko
- Polymer Institute of the Slovak Academy of Sciences, Dúbravská cesta 9, 845 41 Bratislava, Slovakia
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Cifra P, Bleha T. Pressure of Linear and Ring Polymers Confined in a Cavity. J Phys Chem B 2023; 127:4646-4657. [PMID: 37192395 DOI: 10.1021/acs.jpcb.3c01585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Nanoscale confinement of polymers in a cavity is central to a variety of biological and nanotechnology processes. Using the discrete WLC model we simulate the compression of flexible and semiflexible polymers of linear and ring topology in a closed cavity. Simulation reveals that polymer pressure inside the cavity increases with the chain stiffness but is practically unaffected by the chain topology. For flexible polymers, the computed dependence of pressure on the cavity size and polymer concentration is consistent with the scaling behavior expected for bulk polymers in a good solvent. However, the scaling behavior of semiflexible polymers is only in partial agreement with the theory prediction, with discrepancies arising from a continuous transition between regimes in chains of moderate lengths. The computed segment density profiles endorse the propensity of semiflexible polymers to concentrate beneath the cavity surface and thus elevate the pressure. The compaction of polymers by compression into the disordered globule or growing toroidal structure is documented.
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Affiliation(s)
- Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
| | - Tomáš Bleha
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
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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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Mondal A, Morrison G. Compression-induced buckling of a semiflexible filament in two and three dimensions. J Chem Phys 2022; 157:104903. [DOI: 10.1063/5.0104910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ability of biomolecules to exert forces on their surroundings or resist compression from the environment is essential in a variety of biologically relevant contexts. For filaments in the low-temperature limit and under a constant compressive force, Euler buckling theory predicts a sudden transition from a compressed to a bent state in these slender rods. In this paper, we use a mean-field theory to show that if a semiflexible chain is compressed at a finite temperature with a fixed end-to-end distance (permitting fluctuations in the compressive forces), it exhibits a continuous phase transition to a buckled state at a critical level of compression. We determine a quantitatively accurate prediction of the transverse position distribution function of the midpoint of the chain that indicates this transition. We find the mean compressive forces are non-monotonic as the extension of the filament varies, consistent with the observation that strongly buckled filaments are less able to bear an external load. We also find that for the fixed extension (isometric) ensemble, the buckling transition does not coincide with the local minimum of the mean force (in contrast to Euler buckling). We also show the theory is highly sensitive to fluctuations in length in two dimensions, and that the buckling transition can still be accurately recovered by accounting for those fluctuations. These predictions may be useful in understanding the behavior of filamentous biomolecules compressed by fluctuating forces, relevant in a variety of biological contexts.
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Affiliation(s)
- Ananya Mondal
- Physics, University of Houston, United States of America
| | - Greg Morrison
- Physics, University of Houston, United States of America
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Janse van Rensburg EJ, Orlandini E. Phase diagrams of confined square lattice linked polygons. Phys Rev E 2021; 104:064134. [PMID: 35030883 DOI: 10.1103/physreve.104.064134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/10/2021] [Indexed: 11/07/2022]
Abstract
The phase diagrams of two models of two confined and dense two-dimensional ring polymers are examined numerically. The ring polymers are modeled by square lattice polygons in a square cavity and are placed to be either unlinked or linked in the plane. The phase diagrams of the two models are found to be a function of the placement of the ring polymers and include multicritical points where first-order and continuous phase boundaries meet. We estimate numerically the critical exponents associated with the phase boundaries and the multicritical points.
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Affiliation(s)
- E J Janse van Rensburg
- Department of Mathematics and Statistics, York University, Toronto, Ontario M3J 1P3, Canada
| | - E Orlandini
- Dipartimento di Fisica e Astronomia "Galileo Galilei", Universitá degli studi di Padova, 8-35131 Padova, Italia
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Chen W, Kong X, Wei Q, Chen H, Liu J, Jiang D. Compression and Stretching of Confined Linear and Ring Polymers by Applying Force. Polymers (Basel) 2021; 13:polym13234193. [PMID: 34883696 PMCID: PMC8659573 DOI: 10.3390/polym13234193] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/17/2021] [Accepted: 11/19/2021] [Indexed: 11/16/2022] Open
Abstract
We use Langevin dynamics to study the deformations of linear and ring polymers in different confinements by applying compression and stretching forces on their two sides. Our results show that the compression deformations are the results of an interplay among of polymer rigidity, degree of confinement, and force applied. When the applied force is beyond the threshold required for the buckling transition, the semiflexible chain under the strong confinement firstly buckles; then comes helical deformation. However, under the same force loading, the semiflexible chain under the weaker confinement exhibits buckling instability and shrinks from the folded ends/sides until it becomes three-folded structures. This happens because the strong confinement not only strongly reduces the buckling wavelength, but also increases the critical buckling force threshold. For the weakly confined polymers, in compression process, the flexible linear polymer collapses into condensed states under a small external force, whereas the ring polymer only shows slight shrinkage, due to the excluded volume interactions of two strands in the crowded states. These results are essential for understanding the deformations of the ring biomacromolecules and polymer chains in mechanical compression or driven transport.
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Affiliation(s)
- Wenduo Chen
- School of Materials, Sun Yat-sen University, No. 135, Xingang Xi Road, Guangzhou 510275, China; (Q.W.); (H.C.); (J.L.); (D.J.)
- School of Materials, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen 518107, China
- Correspondence:
| | - Xiangxin Kong
- Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China;
| | - Qianqian Wei
- School of Materials, Sun Yat-sen University, No. 135, Xingang Xi Road, Guangzhou 510275, China; (Q.W.); (H.C.); (J.L.); (D.J.)
- School of Materials, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Huaiyu Chen
- School of Materials, Sun Yat-sen University, No. 135, Xingang Xi Road, Guangzhou 510275, China; (Q.W.); (H.C.); (J.L.); (D.J.)
- School of Materials, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Jiayin Liu
- School of Materials, Sun Yat-sen University, No. 135, Xingang Xi Road, Guangzhou 510275, China; (Q.W.); (H.C.); (J.L.); (D.J.)
- School of Materials, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen 518107, China
| | - Dazhi Jiang
- School of Materials, Sun Yat-sen University, No. 135, Xingang Xi Road, Guangzhou 510275, China; (Q.W.); (H.C.); (J.L.); (D.J.)
- School of Materials, Shenzhen Campus of Sun Yat-sen University, No. 66, Gongchang Road, Guangming District, Shenzhen 518107, China
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