1
|
Upadhyay G, Kapri R, Chaudhuri A. Homopolymer and heteropolymer translocation through patterned pores under fluctuating forces. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2024; 47:23. [PMID: 38573533 DOI: 10.1140/epje/s10189-024-00417-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
We investigate the translocation of a semiflexible polymer through extended patterned pores using Langevin dynamics simulations, specifically focusing on the influence of a time-dependent driving force. Our findings reveal that, akin to its flexible counterpart, a rigid chain-like molecule translocates faster when subjected to an oscillating force than a constant force of equivalent average magnitude. The enhanced translocation is strongly correlated with the stiffness of the polymer and the stickiness of the pores. The arrangement of the pores plays a pivotal role in translocation dynamics, deeply influenced by the interplay between polymer stiffness and pore-polymer interactions. For heterogeneous polymers with periodically varying stiffness, the oscillating force introduces significant variations in the translocation time distributions based on segment sizes and orientations. On the basis of these insights, we propose a sequencing approach that harnesses distinct pore surface properties that are capable of accurately predicting sequences in heteropolymers with diverse bending rigidities.
Collapse
Affiliation(s)
- Gokul Upadhyay
- Department of Physical Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, Knowledge City, S. A. S. Nagar, Manauli, 140306, India
| | - Rajeev Kapri
- Department of Physical Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, Knowledge City, S. A. S. Nagar, Manauli, 140306, India
| | - Abhishek Chaudhuri
- Department of Physical Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, Knowledge City, S. A. S. Nagar, Manauli, 140306, India.
| |
Collapse
|
2
|
Upadhyay G, Kapri R, Chaudhuri A. Gain reversal in the translocation dynamics of a semiflexible polymer through a flickering pore. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2024; 36:185101. [PMID: 38262064 DOI: 10.1088/1361-648x/ad21a9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/23/2024] [Indexed: 01/25/2024]
Abstract
We study the driven translocation of a semiflexible polymer through an attractive extended pore with a periodically oscillating width. Similar to its flexible counterpart, a stiff polymer translocates through an oscillating pore more quickly than a static pore whose width is equal to the oscillating pore's mean width. This efficiency quantified as a gain in the translocation time, highlights a considerable dependence of the translocation dynamics on the stiffness of the polymer and the attractive nature of the pore. The gain characteristics for various polymer stiffness exhibit a trend reversal when the stickiness of the pore is changed. The gain reduces with increasing stiffness for a lower attractive strength of the pore, whereas it increases with increasing stiffness for higher attractive strengths. Such a dependence leads to the possibility of a high degree of robust selectivity in the translocation process.
Collapse
Affiliation(s)
- Gokul Upadhyay
- Department of Physical Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, Knowledge City, S. A. S. Nagar, Manauli 140306, India
| | - Rajeev Kapri
- Department of Physical Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, Knowledge City, S. A. S. Nagar, Manauli 140306, India
| | - Abhishek Chaudhuri
- Department of Physical Sciences, Indian Institute of Science Education and Research Mohali, Sector 81, Knowledge City, S. A. S. Nagar, Manauli 140306, India
| |
Collapse
|
3
|
Tan F, Wang J, Yan R, Zhao N. Forced and spontaneous translocation dynamics of a semiflexible active polymer in two dimensions. SOFT MATTER 2024; 20:1120-1132. [PMID: 38224190 DOI: 10.1039/d3sm01409f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Polymer translocation is a fundamental topic in non-equilibrium physics and is crucially important to many biological processes in life. In the present work, we adopt two-dimensional Langevin dynamics simulations to study the forced and spontaneous translocation dynamics of an active filament. The influence of polymer stiffness on the underlying dynamics is explicitly analyzed. For the forced translocation, the results show a robust stiffness-induced inhibition, and the translocation time exhibits a dual-exponent scaling relationship with the bending modulus. Tension propagation (TP) is also examined, where we find prominent modifications in terms of both activity and stiffness. For spontaneous translocation into a pure solvent, the translocation time is almost independent of the polymer stiffness. However, when the polymer is translocated into a porous medium, an intriguing non-monotonic alteration of translocation time with increasing chain stiffness is demonstrated. The semiflexible chain is beneficial for translocation while the rigid chain is not conducive. Stiffness regulation on the diffusion dynamics of the polymer in porous media shows a consistent scenario. The interplay of activity, stiffness, and porous crowding provides a new mechanism for understanding the non-trivial translocation dynamics of an active filament in complex environments.
Collapse
Affiliation(s)
- Fei Tan
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Jingli Wang
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Ran Yan
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| |
Collapse
|
4
|
Lu LW, Wang ZH, Shi AC, Lu YY, An LJ. Polymer Translocation. CHINESE JOURNAL OF POLYMER SCIENCE 2023. [DOI: 10.1007/s10118-023-2975-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
|
5
|
Hu HX, Shen YF, Wang C, Luo MB. Dynamics of a two-dimensional active polymer chain with a rotation-restricted active head. SOFT MATTER 2022; 18:8820-8829. [PMID: 36367147 DOI: 10.1039/d2sm01139e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The dynamics of a two-dimensional active polymer composed of an active Brownian particle (ABP) at the head and a passive polymer chain is investigated using Langevin dynamics simulation. The ABP experiences a self-propulsion force fs and a resistance torque M as the passive polymer chain is bonded to the edge of the ABP. M restricts the rotation of the ABP, and thus the dynamics of the ABP and that of the whole active polymer are influenced significantly. Due to this restriction, the persistence time τr, which characterizes the random rotation of the ABP, is increased significantly and changes non-monotonically with the rotational friction coefficient ηr. Our simulation results show that the effect of M on the dynamics of the active polymer can be characterized mainly by the change of τr. Moreover, the propulsive diffusion coefficient DP of the whole polymer chain originated from the self-propulsion force can be described by a scaling relation DP ∝ fs2τr/N2ηt2 with ηt the translational friction coefficient and N the polymer length. Our results show that the diffusion is promoted by the resistance torque M and τr is a key factor for the diffusion of active polymers.
Collapse
Affiliation(s)
- Han-Xian Hu
- Department of Physics, Zhejiang University, Hangzhou 310027, Zhejiang, China.
| | - Yi-Fan Shen
- Department of Physics, Zhejiang University, Hangzhou 310027, Zhejiang, China.
| | - Chao Wang
- Department of Physics, Taizhou University, Taizhou 318000, Zhejiang, China.
| | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, Zhejiang, China.
| |
Collapse
|
6
|
Sharma A, Kapri R, Chaudhuri A. Driven translocation of a semiflexible polymer through a conical channel in the presence of attractive surface interactions. Sci Rep 2022; 12:19081. [PMID: 36351960 PMCID: PMC9646819 DOI: 10.1038/s41598-022-21845-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/04/2022] [Indexed: 11/11/2022] Open
Abstract
We study the translocation of a semiflexible polymer through a conical channel with attractive surface interactions and a driving force which varies spatially inside the channel. Using the results of the translocation dynamics of a flexible polymer through an extended channel as control, we first show that the asymmetric shape of the channel gives rise to non-monotonic features in the total translocation time as a function of the apex angle of the channel. The waiting time distributions of individual monomer beads inside the channel show unique features strongly dependent on the driving force and the surface interactions. Polymer stiffness results in longer translocation times for all angles of the channel. Further, non-monotonic features in the translocation time as a function of the channel angle changes substantially as the polymer becomes stiffer, which is reflected in the changing features of the waiting time distributions. We construct a free energy description of the system incorporating entropic and energetic contributions in the low force regime to explain the simulation results.
Collapse
Affiliation(s)
- Andri Sharma
- grid.458435.b0000 0004 0406 1521Department of Physical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, S. A. S. Nagar, Mohali, 140306 Punjab India
| | - Rajeev Kapri
- grid.458435.b0000 0004 0406 1521Department of Physical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, S. A. S. Nagar, Mohali, 140306 Punjab India
| | - Abhishek Chaudhuri
- grid.458435.b0000 0004 0406 1521Department of Physical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, S. A. S. Nagar, Mohali, 140306 Punjab India
| |
Collapse
|
7
|
Effect of Solvent Viscosity on the Driven Translocation of Charged Polymers through Nanopores. CHINESE JOURNAL OF POLYMER SCIENCE 2022. [DOI: 10.1007/s10118-022-2696-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
8
|
Abstract
The force- and flow-induced translocation processes of linear and ring polymers are studied using a combination of multiparticle collision dynamics and molecular dynamics, focusing on the behavior of the polymer translocation time. We compare the force- and flow-induced translocations of linear and ring polymers. It is found that when the translocation time (τ*) is characterized by scaling exponents, δ, δ', and α, via the relations τ* ∼ fδNα and τ* ∼ Jδ'Nα, the scaling exponents are not constants. For long chains tested, α = 1.0 for both force- and flow-induced translocations. The difference between the force- and flow-induced translocations stems from different monomer crowding effects due to distinct flow patterns outside the channel. Furthermore, general relations for polymer translocation time are derived for these two translocation processes, which are in good agreement with the simulation results. Our results provide clear molecular pictures for the force- and flow-induced translocations, which shed light on the understanding of translocation dynamics and provide guidance for practical applications such as molecular sequencing and ultrafiltration.
Collapse
Affiliation(s)
- Yuyuan Lu
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Zhenhua Wang
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
| | - Lijia An
- State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - An-Chang Shi
- Department of Physics and Astronomy, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Zhang JZ, Peng XY, Liu S, Jiang BP, Ji SC, Shen XC. The Persistence Length of Semiflexible Polymers in Lattice Monte Carlo Simulations. Polymers (Basel) 2019; 11:E295. [PMID: 30960279 PMCID: PMC6419224 DOI: 10.3390/polym11020295] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/01/2019] [Accepted: 02/05/2019] [Indexed: 01/10/2023] Open
Abstract
While applying computer simulations to study semiflexible polymers, it is a primary task to determine the persistence length that characterizes the chain stiffness. One frequently asked question concerns the relationship between persistence length and the bending constant of applied bending potential. In this paper, theoretical persistence lengths of polymers with two different bending potentials were analyzed and examined by using lattice Monte Carlo simulations. We found that the persistence length was consistent with theoretical predictions only in bond fluctuation model with cosine squared angle potential. The reason for this is that the theoretical persistence length is calculated according to a continuous bond angle, which is discrete in lattice simulations. In lattice simulations, the theoretical persistence length is larger than that in continuous simulations.
Collapse
Affiliation(s)
- Jing-Zi Zhang
- State Key Laboratory for Chemistry and Molecular Engineering of Medical Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China.
| | - Xiang-Yao Peng
- State Key Laboratory for Chemistry and Molecular Engineering of Medical Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China.
| | - Shan Liu
- State Key Laboratory for Chemistry and Molecular Engineering of Medical Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China.
| | - Bang-Ping Jiang
- State Key Laboratory for Chemistry and Molecular Engineering of Medical Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China.
| | - Shi-Chen Ji
- State Key Laboratory for Chemistry and Molecular Engineering of Medical Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China.
| | - Xing-Can Shen
- State Key Laboratory for Chemistry and Molecular Engineering of Medical Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, China.
| |
Collapse
|
12
|
Hsiao PY. Translocation of Charged Polymers through a Nanopore in Monovalent and Divalent Salt Solutions: A Scaling Study Exploring over the Entire Driving Force Regimes. Polymers (Basel) 2018; 10:E1229. [PMID: 30961154 PMCID: PMC6290626 DOI: 10.3390/polym10111229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 10/31/2018] [Accepted: 11/02/2018] [Indexed: 11/16/2022] Open
Abstract
Langevin dynamics simulations are performed to study polyelectrolytes driven through a nanopore in monovalent and divalent salt solutions. The driving electric field E is applied inside the pore, and the strength is varied to cover the four characteristic force regimes depicted by a rederived scaling theory, namely the unbiased (UB) regime, the weakly-driven (WD) regime, the strongly-driven trumpet (SD(T)) regime and the strongly-driven isoflux (SD(I)) regime. By changing the chain length N, the mean translocation time is studied under the scaling form 〈 τ 〉 ∼ N α E - δ . The exponents α and δ are calculated in each force regime for the two studied salt cases. Both of them are found to vary with E and N and, hence, are not universal in the parameter's space. We further investigate the diffusion behavior of translocation. The subdiffusion exponent γ p is extracted. The three essential exponents ν s , q, z p are then obtained from the simulations. Together with γ p , the validness of the scaling theory is verified. Through a comparison with experiments, the location of a usual experimental condition on the scaling plot is pinpointed.
Collapse
Affiliation(s)
- Pai-Yi Hsiao
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
- Institute of Nuclear Engineering and Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
| |
Collapse
|