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Tilahun M, Tatek YB. End‐Pulled Translocation of a Star Polymer Out of a Confining Cylindrical Cavity. MACROMOL THEOR SIMUL 2021. [DOI: 10.1002/mats.202000090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mesay Tilahun
- Department of Physics Addis Ababa University Addis Ababa 1176 Ethiopia
| | - Yergou B. Tatek
- Department of Physics Addis Ababa University Addis Ababa 1176 Ethiopia
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Tan F, Chen Y, Zhao N. Effects of active crowder size and activity-crowding coupling on polymer translocation. SOFT MATTER 2021; 17:1940-1954. [PMID: 33427276 DOI: 10.1039/d0sm01906b] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Polymer translocation in complex environments is crucially important to many biological processes in life. In the present work, we adopted two-dimensional Langevin dynamics simulations to study the forced and unbiased polymer translocation dynamics in active and crowded media. The translocation time and probability are analyzed in terms of active force Fa, volume fraction φ and also the crowder size. The non-trivial active crowder size effect and activity-crowding coupling effect as well as the novel mechanism of unbiased translocation between two active environments with different active particle sizes are clarified. Firstly, for forced translocation, we reveal an intriguing non-monotonic dependence of the translocation time on the crowder size in the case of large activity. In particular, crowders of intermediate size similar to the polymer segment are proven to be the most favorable for translocation. Moreover, a facilitation-inhibition crossover of the translocation time with increasing volume fraction is observed, indicating a crucial activity-crowding coupling effect. Secondly, for unbiased translocation driven by different active crowder sizes, the translocation probability demonstrates a novel turnover phenomenon, implying the appearance of an opposite directional preference as the active force exceeds a critical value. The translocation time in both directions decreases monotonically with the active force. The asymmetric activity effect together with the entropic driving scenario provides a reasonable picture for the peculiar behavior observed in unbiased translocation.
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Affiliation(s)
- Fei Tan
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Ying Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China.
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Scaling Theory of a Polymer Ejecting from a Cavity into a Semi-Space. Polymers (Basel) 2020; 12:polym12123014. [PMID: 33339450 PMCID: PMC7766115 DOI: 10.3390/polym12123014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 12/23/2022] Open
Abstract
A two-stage model is developed in order to understand the scaling behaviors of single polymers ejecting from a spherical cavity through a nanopore. The dynamics of ejection is derived by balancing the free energy change with the energy dissipation during a process. The ejection velocity is found to vary with the number of monomers in the cavity, m, as mz1/(Nx1D3z1) at the confined stage, and it turns to be m−z2 at the non-confined stage, where N is the chain length and D the cavity diameter. The exponents are shown to be z1=(3ν−1)−1, z2=2ν and x1=1/3, with ν being the Flory exponent. The profile of the velocity is carefully verified by performing Langevin dynamics simulations. The simulations further reveal that, at the starting point, the decreasing of m can be stalled for a good moment. It suggests the existence of a pre-stage that can be explained by using the concept of a classical nucleation theory. By trimming the pre-stage, the ejection time are properly studied by varying N, D, and ϕ0 (the initial volume fraction). The scaling properties of the nucleation time are also analyzed. The results fully support the predictions of the theory. The physical pictures are given for various ejection conditions that cover the entire parameter space.
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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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Polson JM, Heckbert DR. Polymer translocation into cavities: Effects of confinement geometry, crowding, and bending rigidity on the free energy. Phys Rev E 2019; 100:012504. [PMID: 31499877 DOI: 10.1103/physreve.100.012504] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Indexed: 06/10/2023]
Abstract
Monte Carlo simulations are used to study the translocation of a polymer into a cavity. Modeling the polymer as a hard-sphere chain with a length up to N=601 monomers, we use a multiple-histogram method to measure the variation of the conformational free energy of the polymer with respect to the number of translocated monomers. The resulting free-energy functions are then used to obtain the confinement free energy for the translocated portion of the polymer. We characterize the confinement free energy for a flexible polymer in cavities with constant cross-sectional area A for various cavity shapes (cylindrical, rectangular, and triangular) as well as for tapered cavities with pyramidal and conical shape. The scaling of the free energy with cavity volume and translocated polymer subchain length is generally consistent with predictions from simple scaling arguments, with small deviations in the scaling exponents likely due to finite-size effects. The confinement free energy depends strongly on cavity shape anisometry and is a minimum for an isometric cavity shape with a length-to-width ratio of unity. Entropic depletion at the edges or vertices of the confining cavity are evident in the results for constant-A and pyramidal cavities. For translocation into infinitely long cones, the scaling of the free energy with taper angle is consistent with a theoretical prediction employing the blob model. We also examine the effects of polymer bending rigidity on the translocation free energy for cylindrical cavities. For isometric cavities, the observed scaling behavior is in partial agreement with theoretical predictions, with discrepancies arising from finite-size effects that prevent the emergence of well-defined scaling regimes. In addition, translocation into highly anisometric cylindrical cavities leads to a multistage folding process for stiff polymers. Finally, we examine the effects of crowding agents inside the cavity. We find that the confinement free energy increases with crowder density. At constant packing fraction the magnitude of this effect lessens with increasing crowder size for a crowder-to-monomer size ratio ≥1.
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Affiliation(s)
- James M Polson
- Department of Physics, University of Prince Edward Island, 550 University Avenue, Charlottetown, Prince Edward Island, Canada C1A 4P3
| | - David R Heckbert
- Department of Physics, University of Prince Edward Island, 550 University Avenue, Charlottetown, Prince Edward Island, Canada C1A 4P3
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Sun LZ, Wang CH, Luo MB, Li H. Trapped and non-trapped polymer translocations through a spherical pore. J Chem Phys 2019; 150:024904. [PMID: 30646715 DOI: 10.1063/1.5063331] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The polymer translocation through a spherical pore is studied using the Langevin dynamics simulation. The translocation events are classified into two types: one is the trapped translocation in which the entire polymer is trapped in the pore and the other is the non-trapped translocation where the pore cannot hold the whole polymer. We find that the trapped translocation is favored at large spheres and small external voltages. However, the monomer-pore attraction would lead to the non-monotonic behavior of the trapped translocation possibility out of all translocation events. Moreover, both the trapped and non-trapped translocation times are dependent on the polymer length, pore size, external voltage, and the monomer-pore attraction. There exist two pathways for the polymer in the trapped translocation: an actively trapped pathway for the polymer trapped in the pore before the head monomer arrives at the pore exit, and a passively trapped pathway for the polymer trapped in the pore while the head monomer is struggling to move out of the pore. The studies of trapped pathways can provide a deep understanding of the polymer translocation behavior.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Chang-Hui Wang
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Haibin Li
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
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Sun LZ, Luo MB, Cao WP, Li H. Theoretical study on the polymer translocation into an attractive sphere. J Chem Phys 2018; 149:024901. [PMID: 30007381 DOI: 10.1063/1.5025609] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We report a non-sampling model, combining the blob method with the standard lattice-based approximation, to calculate the free energy for the polymer translocation into an attractive sphere (i.e., spherical confined trans side) through a small pore. The translocation time is then calculated by the Fokker-Planck equation based on the free energy profile. There is a competition between the confinement effect of the sphere and the polymer-sphere attraction. The translocation time is increased due to the confinement effect of the sphere, whereas it is reduced by the polymer-sphere attraction. The two effects offset each other at a special polymer-sphere attraction which is dependent on the sphere size, the polymer length, and the driving force. Moreover, the entire translocation process can be divided into an uncrowded stage where the polymer does not experience the confinement effect of the sphere and a crowded stage where the polymer is confined by the sphere. At the critical sphere radius, the durations of the two (uncrowded and crowded) stages are the same. The critical sphere radius R* has a scaling relation with the polymer length N as R* ∼ Nβ. The calculation results show that the current model can effectively treat the translocation of a three-dimensional self-avoiding polymer into the spherical confined trans side.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
| | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
| | - Wei-Ping Cao
- Institute of Optoelectronic Technology, Lishui University, Lishui 323000, China
| | - Haibin Li
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China
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Ding M, Chen Q, Duan X, Shi T. Flow-induced polymer translocation through a nanopore from a confining nanotube. J Chem Phys 2017; 144:174903. [PMID: 27155652 DOI: 10.1063/1.4948551] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We study the flow-induced polymer translocation through a nanopore from a confining nanotube, using a hybrid simulation method that couples point particles into a fluctuating lattice-Boltzmann fluid. Our simulation illustrates that the critical velocity flux of the polymer linearly decreases with the decrease in the size of the confining nanotube, which corresponds well with our theoretical analysis based on the blob model of the polymer translocation. Moreover, by decreasing the size of the confining nanotube, we find a significantly favorable capture of the polymer near its ends, as well as a longer translocation time. Our results provide the computational and theoretical support for the development of nanotechnologies based on the ultrafiltration and the single-molecule sequencing.
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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, People's Republic of China
| | - Qiaoyue Chen
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Xiaozheng Duan
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Tongfei Shi
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
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Sean D, Slater GW. Highly driven polymer translocation from a cylindrical cavity with a finite length. J Chem Phys 2017; 146:054903. [DOI: 10.1063/1.4975091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- David Sean
- University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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The Semiflexible Polymer Translocation into Laterally Unbounded Region between Two Parallel Flat Membranes. Polymers (Basel) 2016; 8:polym8090332. [PMID: 30974609 PMCID: PMC6431992 DOI: 10.3390/polym8090332] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 08/28/2016] [Accepted: 08/30/2016] [Indexed: 11/17/2022] Open
Abstract
Using the dynamic Monte Carlo method, we investigate dynamics of semiflexible polymer translocation through a nanopore into laterally unbounded region between two parallel flat membranes with separation R in presence of an electric field inside the pore. The average translocation time τ initially decreases rapidly with increase of R in the range of R < 10 and then almost keeps constant for R ≥ 10, and the decline range increases with increase of dimensionless bending stiffness κ. We mainly study the effect of chain length N, κ and electric field strength E on the translocation process for R = 5. The translocation dynamics is significantly altered in comparison to an unconfined environment. We find τ ~ Nα, where the exponent α increases with increase of E for small κ. α initially increases slowly with increase of E and then keeps constant for moderate κ. α decreases with increase of E for large κ. However, α decreases with increase of κ under various E. In addition, we find τ ~ κβ. β decreases with increase of N under various E. These behaviors are interpreted in terms of the probability distribution of translocation time and the waiting time of an individual monomer segment passing through the pore during translocation.
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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
| | - Yuyuan Lu
- 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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Polson JM. Polymer translocation into and out of an ellipsoidal cavity. J Chem Phys 2015; 142:174903. [DOI: 10.1063/1.4919642] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- James M. Polson
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island C1A 4P3, Canada
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