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Wang Z, Ziolek RM, Tsige M. Constraints on Knot Insertion, Not Internal Jamming, Control Polycatenane Translocation Dynamics through Crystalline Pores. Macromolecules 2023; 56:3238-3245. [PMID: 37128623 PMCID: PMC10141125 DOI: 10.1021/acs.macromol.2c02565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/15/2023] [Indexed: 05/03/2023]
Abstract
The translocation of polymers through pores and channels is an archetypal process in biology and is widely studied and exploited for applications in bio- and nanotechnology. In recent times, the translocation of polymers of various different topologies has been studied both experimentally and by computer simulation. However, in some cases, a clear understanding of the precise mechanisms that drive their translocation dynamics can be challenging to derive. Experimental methods are able to provide statistical details of polymer translocation, but computer simulations are uniquely placed to uncover a finer level of mechanistic understanding. In this work, we use high-throughput molecular simulations to reveal the importance that knot insertion rates play in controlling translocation dynamics in the small pore limit, where unexpected nonpower law behavior emerges. This work both provides new predictive understanding of polycatenane translocation and shows the importance of carefully considering the role of the definition of translocation itself.
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Affiliation(s)
- Zifeng Wang
- School
of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325-3909, United States
| | - Robert M. Ziolek
- Biological
Physics and Soft Matter Group, Department of Physics, King’s College London, London WC2R 2LS, United Kingdom
| | - Mesfin Tsige
- School
of Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325-3909, United States
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2
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Ding M, Li L. Flow-Induced Translocation and Conformational Transition of Polymer Chains through Nanochannels: Recent Advances and Future Perspectives. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00909] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mingming Ding
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, China
| | - Lianwei Li
- Food Science and Processing Research Center, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
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3
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Affiliation(s)
- Karthik Nagarajan
- K. Nagarajan, Prof. S. B. ChenDepartment of Chemical & Biomolecular EngineeringNational University of Singapore Singapore 117585 Singapore
| | - Shing Bor Chen
- K. Nagarajan, Prof. S. B. ChenDepartment of Chemical & Biomolecular EngineeringNational University of Singapore Singapore 117585 Singapore
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Ding M, Chen Q, Duan X, Shi T. Flow-Driven Translocation of a Diblock Copolymer through a Nanopore. J Phys Chem B 2019; 123:8848-8852. [PMID: 31566376 DOI: 10.1021/acs.jpcb.9b07481] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using a hybrid molecular dynamic and lattice Boltzmann simulation method, we investigate the flow-driven translocation of a diblock copolymer which is composed of a hydrophilic block and a hydrophobic block through a nanopore. Our results illustrate the nontrivial translocation dynamics of diblock copolymers. We find that the increase in the number of hydrophobic segments requires a larger critical flow rate and a reduced translocation time, which implies that the separation of diblock copolymers with different fractions of hydrophobic segments can be achieved by adjusting the flow rate. Our work deepens the understanding of copolymer translocation through a nanopore and provides an insight into designing related microscaled separation devices.
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Affiliation(s)
- Mingming Ding
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun 130022 , P. R. China
| | - Qiaoyue Chen
- Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology , Yili Normal University , Yining 835000 , P. R. China
| | - Xiaozheng Duan
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun 130022 , P. R. China
| | - Tongfei Shi
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun 130022 , P. R. China.,School of Applied Chemistry and Engineering , University of Science and Technology of China , Hefei 230026 , P. R. China
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Nagarajan K, Chen SB. Flow-Induced Translocation of Star Polymers through a Nanopore. J Phys Chem B 2019; 123:7919-7925. [PMID: 31461281 DOI: 10.1021/acs.jpcb.9b07066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The flow-induced translocation of star polymers through a cylindrical nanopore has been studied using dissipative particle dynamics (DPD) simulations. The number of arms, f, was varied with the total number of monomers, N, kept constant. The effect of simulating the capture of the polymer into the pore upon the mean translocation time, <τt>, has been investigated by varying the chain's initial location. The results indicate that the incorporation of the capture process results in a reduction of <τt> by up to 15%. This is because the chain's initial location affects the extent of its stretching along the flow direction during translocation. <τt> exhibits nonmonotonic variation with f, in agreement with recently reported results for electric field-driven translocation of star polymers. Its value is larger and shows greater variation with f when the solvent quality is better. For the same value of f, the capture occurs faster in a good solvent. In addition, <τt> is greater for a semiflexible chain than its flexible counterpart as the time required for the branch point to enter the nanopore is longer in the former case.
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Affiliation(s)
- Karthik Nagarajan
- Department of Chemical & Biomolecular Engineering , National University of Singapore , 117585 Singapore
| | - Shing Bor Chen
- Department of Chemical & Biomolecular Engineering , National University of Singapore , 117585 Singapore
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Abstract
The electric field driven translocation of charged star polymers through a cylindrical nanopore has been studied using dissipative particle dynamics simulations. The critical field strength required to induce translocation depends on both the number of arms and the number of beads per arm. It may therefore be possible to separate star polyelectrolytes of different arm lengths using electric field driven translocation through a nanopore. The average translocation time exhibits nonmonotonic variation with the number of arms for good solvent conditions. During translocation, a star polymer with many arms is stretched along the pore axis to a lesser extent as compared to its linear counterpart. Unlike a linear chain that shows tension propagation with large tensions for bonds about to enter the pore, a star has the tensest bonds closest to the branch point whose connectivity to multiple arms raises difficulty for its entry and passage.
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Affiliation(s)
- Karthik Nagarajan
- Department of Chemical & Biomolecular Engineering , National University of Singapore , 117585 , Singapore
| | - Shing Bor Chen
- Department of Chemical & Biomolecular Engineering , National University of Singapore , 117585 , Singapore
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7
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Katkar HH, Muthukumar M. Single molecule electrophoresis of star polymers through nanopores: Simulations. J Chem Phys 2018; 149:163306. [PMID: 30384726 DOI: 10.1063/1.5029980] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We study the translocation of charged star polymers through a solid-state nanopore using coarse-grained Langevin dynamics simulations, in the context of using nanopores as high-throughput devices to characterize polymers based on their architecture. The translocation is driven by an externally applied electric field. Our key observation is that translocation kinetics is highly sensitive to the functionality (number of arms) of the star polymer. The mean translocation time is found to vary non-monotonically with polymer functionality, exhibiting a critical value for which translocation is the fastest. The origin of this effect lies in the competition between the higher driving force inside the nanopore and inter-arm electrostatic repulsion in entering the pore, as the functionality is increased. Our simulations also show that the value of the critical functionality can be tuned by varying nanopore dimensions. Moreover, for narrow nanopores, star polymers above a threshold functionality do not translocate at all. These observations suggest the use of nanopores as a high-throughput low-cost analytical tool to characterize and separate star polymers.
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Affiliation(s)
- H H Katkar
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
| | - M Muthukumar
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
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Ding M, Duan X, Shi T. Flow-induced polymer separation through a nanopore: effects of solvent quality. SOFT MATTER 2017; 13:7239-7243. [PMID: 28930354 DOI: 10.1039/c7sm00784a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Using a hybrid simulation method that combines a lattice-Boltzmann approach for the flow and a molecular dynamics model for the polymer, we investigated the effect of solvent quality on the flow-induced polymer translocation through a nanopore. We demonstrate the nontrivial dependence of the translocation dynamics of polymers on the solvent quality, i.e., the enhancement in the polymer insolubility increases the critical velocity flux and shortens the translocation time. Accordingly, we propose a new strategy to separate polymers with different solubilities via their translocations in the nanopore by adjusting the velocity flux of the flow, which appears to be promising for the design of micro-scaled polymer separation devices.
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Affiliation(s)
- Mingming Ding
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China.
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9
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Affiliation(s)
- Mingming Ding
- State Key Laboratory of Polymer
Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Xiaozheng Duan
- State Key Laboratory of Polymer
Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
| | - Tongfei Shi
- State Key Laboratory of Polymer
Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P. R. China
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