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
|
Seth S, Bhattacharya A. DNA Barcodes Using a Dual Nanopore Device. Methods Mol Biol 2024; 2744:197-211. [PMID: 38683320 DOI: 10.1007/978-1-0716-3581-0_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
We report a novel method based on the current blockade (CB) characteristics obtained from a dual nanopore device that can determine DNA barcodes with near-perfect accuracy using a Brownian dynamics simulation strategy. The method supersedes our previously reported velocity correction algorithm (S. Seth and A. Bhattacharya, RSC Advances, 11:20781-20787, 2021), taking advantage of the better measurement of the time-of-flight (TOF) protocol offered by the dual nanopore setup. We demonstrate the efficacy of the method by comparing our simulation data from a coarse-grained model of a polymer chain consisting of 2048 excluded volume beads of diameter 𝜎 = 24 bp using with those obtained from experimental CB data from a 48,500 bp λ-phage DNA, providing a 48500 2400 ≅ 24 base pair resolution in simulation. The simulation time scale is compared to the experimental time scale by matching the simulated time-of-flight (TOF) velocity distributions with those obtained experimentally (Rand et al., ACS Nano, 16:5258-5273, 2022). We then use the evolving coordinates of the dsDNA and the molecular features to reconstruct the current blockade characteristics on the fly using a volumetric model based on the effective van der Waal radii of the species inside and in the immediate vicinity of the pore. Our BD simulation mimics the control-zoom-in-logic to understand the origin of the TOF distributions due to the relaxation of the out-of-equilibrium conformations followed by a reversal of the electric fields. The simulation algorithm is quite general and can be applied to differentiate DNA barcodes from different species.
Collapse
|
5
|
Tan F, Yan R, Zhao C, Zhao N. Translocation Dynamics of an Active Filament through a Long-Length Scale Channel. J Phys Chem B 2023; 127:8603-8615. [PMID: 37782905 DOI: 10.1021/acs.jpcb.3c04250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Active filament translocation through a confined space is crucial for diverse biological processes. By using Langevin dynamics simulations, we investigate the translocation dynamics of an axially self-propelled chain through a channel. First, results show a suggestive reciprocal scaling of translocation time versus active force. Second, in the case of a long channel, we demonstrate a very intriguing nonmonotonic change of translocation time with increasing channel width. The driving force shows a similar trend, providing a consistent picture to understand the unexpected channel width effect. In particular, in a moderately broad channel, the disordered chain conformation results in a loss of driving force and thus inhibits translocation dynamics. Chain adsorption might occur in a wide channel, which accounts for a facilitated translocation. Lastly, we connect the translocation process to tension propagation (TP). A modified TP picture is proposed to interpret the waiting time distribution. Our work highlights the new phenomenology owing to the crucial interplay of activity and spacial confinement, which drives the translocation dynamics, going beyond the traditional entropic barrier scenario.
Collapse
Affiliation(s)
- Fei Tan
- College of Chemistry, Sichuan University, Chengdu 610065, China
| | - Ran Yan
- College of Chemistry, Sichuan University, Chengdu 610065, China
| | - Chaonan Zhao
- College of Chemistry, Sichuan University, Chengdu 610065, China
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610065, China
| |
Collapse
|
6
|
Sáinz-Agost A, Falo F, Fiasconaro A. Polymer translocation driven by longitudinal and transversal time-dependent end-pulling forces. Phys Rev E 2023; 108:034501. [PMID: 37849105 DOI: 10.1103/physreve.108.034501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 08/07/2023] [Indexed: 10/19/2023]
Abstract
In this article, we simulate the translocation of a semiflexible homopolymer through an extended pore, driven by both a constant and a time-dependent end-pulled force, employing a model introduced in previous studies. The time dependence is simplistically modeled as a cosine function, and we distinguish between two scenarios for the driving--longitudinal force and transversal force-depending on the relative orientation of the force, parallel or perpendicular, respectively, with respect to the pore axis. Besides some key differences between the two drivings, the mean translocation times present a large minimum region as a function of the frequency of the force that is typical of the resonant activation effect. The presence of the minimum is independent on the elastic characteristics of the polymeric chains and reveals a linear relation between the optimum mean translocation time and the corresponding period of the driving. The mean translocation times show different scaling exponents with the polymer length for different flexibilities. Lastly, we derive an analytical expression of the mean translocation time for low driving frequency, which clearly agrees with the simulations.
Collapse
Affiliation(s)
- A Sáinz-Agost
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, Zaragoza 50009, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Zaragoza 50018, Spain
| | - F Falo
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, Zaragoza 50009, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Zaragoza 50018, Spain
| | - A Fiasconaro
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, Zaragoza 50009, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, Zaragoza 50018, Spain
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Palermo 90146, Italy
| |
Collapse
|
7
|
Singh SL, Chauhan K, Bharadwaj AS, Kishore V, Laux P, Luch A, Singh AV. Polymer Translocation and Nanopore Sequencing: A Review of Advances and Challenges. Int J Mol Sci 2023; 24:6153. [PMID: 37047125 PMCID: PMC10094227 DOI: 10.3390/ijms24076153] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/01/2023] [Accepted: 02/28/2023] [Indexed: 03/31/2023] Open
Abstract
Various biological processes involve the translocation of macromolecules across nanopores; these pores are basically protein channels embedded in membranes. Understanding the mechanism of translocation is crucial to a range of technological applications, including DNA sequencing, single molecule detection, and controlled drug delivery. In this spirit, numerous efforts have been made to develop polymer translocation-based sequencing devices, these efforts include findings and insights from theoretical modeling, simulations, and experimental studies. As much as the past and ongoing studies have added to the knowledge, the practical realization of low-cost, high-throughput sequencing devices, however, has still not been realized. There are challenges, the foremost of which is controlling the speed of translocation at the single monomer level, which remain to be addressed in order to use polymer translocation-based methods for sensing applications. In this article, we review the recent studies aimed at developing control over the dynamics of polymer translocation through nanopores.
Collapse
Affiliation(s)
- Swarn Lata Singh
- Department of Physics, Mahila Mahavidyalaya (MMV), Banaras Hindu University, Varanasi 221005, UP, India
| | - Keerti Chauhan
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Atul S. Bharadwaj
- Department of Physics, CMP Degree College, University of Allahabad, Prayagraj 211002, UP, India
| | - Vimal Kishore
- Department of Physics, Banaras Hindu University, Varanasi 221005, UP, India
| | - Peter Laux
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Andreas Luch
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| | - Ajay Vikram Singh
- Department of Chemical and Product Safety, German Federal Institute of Risk Assessment (BfR) Maxdohrnstrasse 8-10, 10589 Berlin, Germany
| |
Collapse
|
8
|
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
|
9
|
Discriminating protein tags on a dsDNA construct using a Dual Nanopore Device. Sci Rep 2022; 12:11305. [PMID: 35787637 PMCID: PMC9253098 DOI: 10.1038/s41598-022-14609-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/09/2022] [Indexed: 11/08/2022] Open
Abstract
We report Brownian dynamics simulation results with the specific goal to identify key parameters controlling the experimentally measurable characteristics of protein tags on a dsDNA construct translocating through a double nanopore setup. First, we validate the simulation scheme in silico by reproducing and explaining the physical origin of the asymmetric experimental dwell time distributions of the oligonucleotide flap markers on a 48 kbp long dsDNA at the left and the right pore. We study the effect of the electric field inside and beyond the pores, critical to discriminate the protein tags based on their effective charges and masses revealed through a generic power-law dependence of the average dwell time at each pore. The simulation protocols monitor piecewise dynamics at a sub-nanometer length scale and explain the disparate velocity using the concepts of nonequilibrium tension propagation theory. We further justify the model and the chosen simulation parameters by calculating the Péclet number which is in close agreement with the experiment. We demonstrate that our carefully chosen simulation strategies can serve as a powerful tool to discriminate different types of neutral and charged tags of different origins on a dsDNA construct in terms of their physical characteristics and can provide insights to increase both the efficiency and accuracy of an experimental dual-nanopore setup.
Collapse
|
10
|
Seth S, Bhattacharya A. How capture affects polymer translocation in a solitary nanopore. J Chem Phys 2022; 156:244902. [DOI: 10.1063/5.0094221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in the presence of an extended electric field using the Brownian dynamics simulation that enables us to record statistics of the conformations at every stage of the translocation process. By releasing the equilibrated DNAs from different equipotentials, we observe that the capture time distribution depends on the initial starting point and follows a Poisson process. The field gradient elongates the DNA on its way toward the nanopore and favors a successful translocation even after multiple failed threading attempts. Even in the limit of an extremely narrow pore, a fully flexible chain has a finite probability of hairpin-loop capture, while this probability decreases for a stiffer chain and promotes single file translocation. Our in silico studies identify and differentiate characteristic distributions of the mean first passage time due to single file translocation from those due to translocation of different types of folds and provide direct evidence of the interpretation of the experimentally observed folds [M. Gershow and J. A. Golovchenko, Nat. Nanotechnol. 2, 775 (2007) and Mihovilovic et al., Phys. Rev. Lett. 110, 028102 (2013)] in a solitary nanopore. Finally, we show a new finding—that a charged tag attached at the 5′ end of the DNA enhances both the multi-scan rate and the uni-directional translocation (5′ → 3′) probability that would benefit the genomic barcoding and sequencing experiments.
Collapse
Affiliation(s)
- Swarnadeep Seth
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| | - Aniket Bhattacharya
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| |
Collapse
|
11
|
Seth S, Bhattacharya A. DNA barcode by flossing through a cylindrical nanopore. RSC Adv 2021; 11:20781-20787. [PMID: 34178311 PMCID: PMC8190898 DOI: 10.1039/d1ra00349f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
We report an accurate method to determine DNA barcodes from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive theoretical scheme which improves the measurements to almost 100% accuracy. The heavier protein tags along the DNA backbone introduce a large speed variation in the chain that can be understood using the idea of non-equilibrium tension propagation theory. However, from an initial rough characterization of velocities into “fast” (nucleotides) and “slow” (protein tags) domains, we introduce a physically motivated interpolation scheme that enables us to determine the barcode velocities rather accurately. Our theoretical analysis of the motion of the DNA through a cylindrical nanopore opens up the possibility of its experimental realization and carries over to multi-nanopore devices used for barcoding. We report a method for DNA barcoding from the dwell time measurement of protein tags (barcodes) along the DNA backbone using Brownian dynamics simulation of a model DNA and use a recursive scheme to improve the measurements to almost 100% accuracy.![]()
Collapse
Affiliation(s)
- Swarnadeep Seth
- Department of Physics, University of Central Florida Orlando FL 32816-2385 USA
| | - Aniket Bhattacharya
- Department of Physics, University of Central Florida Orlando FL 32816-2385 USA
| |
Collapse
|
12
|
Abstract
The potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the chain backbone, we demonstrate that due to large variation of velocities of the chain segments between the tags, it is inevitable to under/overestimate the genetic lengths from the experimental current blockade and time of flight data. We demonstrate that it is the tension propagation along the chain's backbone that governs the motion of the entire chain and is the key element to explain the non uniformity and disparate velocities of the tags and DNA monomers under translocation that introduce errors in measurement of the length segments between protein tags. Using simulation data we further demonstrate that it is important to consider the dynamics of the entire chain and suggest methods to accurately decipher barcodes. We introduce and validate an interpolation scheme using simulation data for a broad distribution of tag separations and suggest how to implement the scheme experimentally.
Collapse
|
13
|
Seth S, Bhattacharya A. Polymer escape through a three dimensional double-nanopore system. J Chem Phys 2021; 153:104901. [PMID: 32933266 DOI: 10.1063/5.0015310] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the escape dynamics of a double-stranded DNA (dsDNA) through an idealized double nanopore geometry subject to two equal and opposite forces (tug-of-war) using Brownian dynamics (BD) simulation. In addition to the geometrical restrictions imposed on the cocaptured dsDNA segment in between the pores, the presence of tug-of-war forces at each pore results in a variation of the local chain stiffness for the segment of the chain in between the pores, which increases the overall stiffness of the chain. We use the BD simulation results to understand how the intrinsic chain stiffness and the tug-of-war forces affect the escape dynamics by monitoring the local chain persistence length ℓp, the residence time of the individual monomers W(m) in the nanopores, and the chain length dependence of the escape time ⟨τ⟩ and its distribution. Finally, we generalize the scaling theory for the unbiased single nanopore translocation for a fully flexible chain for the escape of a semi-flexible chain through a double nanopore in the presence of tug-of-war forces. We establish that the stiffness dependent part of the escape time is approximately independent of the translocation mechanism so that ⟨τ⟩∼ℓp 2/D+2, and therefore, the generalized escape time for a semi-flexible chain can be written as ⟨τ⟩=ANαℓp 2/D+2. We use the BD simulation results to compare the predictions of the scaling theory. Our numerical studies supplemented by scaling analysis provide fundamental insights to design new experiments where a dsDNA moves slowly through a series of graphene nanopores.
Collapse
Affiliation(s)
- Swarnadeep Seth
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| | - Aniket Bhattacharya
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| |
Collapse
|
14
|
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
|
15
|
Bhattacharya A, Seth S. Tug of war in a double-nanopore system. Phys Rev E 2020; 101:052407. [PMID: 32575312 DOI: 10.1103/physreve.101.052407] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/30/2020] [Indexed: 02/02/2023]
Abstract
We simulate a tug-of-war (TOW) scenario for a model double-stranded DNA threading through a double nanopore (DNP) system. The DNA, simultaneously captured at both pores, is subject to two equal and opposite forces -f[over ⃗]_{L}=f[over ⃗]_{R} (TOW), where f[over ⃗]_{L} and f[over ⃗]_{R} are the forces applied to the left and the right pore, respectively. Even though the net force on the DNA polymer Δf[over ⃗]_{LR}=f[over ⃗]_{L}+f[over ⃗]_{R}=0, the mean first passage time (MFPT) 〈τ〉 depends on the magnitude of the TOW forces |f_{L}|=|f_{R}|=f_{LR}. We qualitatively explain this dependence of 〈τ〉 on f_{LR} from the known results for the single-pore translocation of a triblock copolymer A-B-A with ℓ_{pB}>ℓ_{pA}, where ℓ_{pA} and ℓ_{pB} are the persistence length of the A and B segments, respectively. We demonstrate that the time of flight of a monomer with index m [〈τ_{LR}(m)〉] from one pore to the other exhibits quasiperiodic structure commensurate with the distance between the pores d_{LR}. Finally, we study the situation where we offset the TOW biases so that Δf[over ⃗]_{LR}=f[over ⃗]_{L}+f[over ⃗]_{R}≠0, and qualitatively reproduce the experimental result of the dependence of the MFPT on Δf[over ⃗]_{LR}. We demonstrate that, for a moderate bias, the MFPT for the DNP system for a chain length N follows the same scaling ansatz as that for the single nanopore, 〈τ〉=(AN^{1+ν}+η_{pore}N)(Δf_{LR})^{-1}, where η_{pore} is the pore friction, which enables us to estimate 〈τ〉 for a long chain. Our Brownian dynamics simulation studies provide fundamental insights and valuable information about the details of the translocation speed obtained from 〈τ_{LR}(m)〉, and accuracy of the translation of the data obtained in the time domain to units of genomic distances.
Collapse
Affiliation(s)
- Aniket Bhattacharya
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| | - Swarnadeep Seth
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| |
Collapse
|
16
|
Suhonen PM, Linna RP. Dynamics of driven translocation of semiflexible polymers. Phys Rev E 2018; 97:062413. [PMID: 30011459 DOI: 10.1103/physreve.97.062413] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Indexed: 11/07/2022]
Abstract
We study translocation of semiflexible polymers driven by force f_{d} inside a nanometer-scale pore using our three-dimensional Langevin dynamics model. We show that the translocation time τ increases with increasing bending rigidity κ. Similarly, the exponent β for the scaling of τ with polymer length N,τ∼N^{β}, increases with increasing κ as well as with increasing f_{d}. By comparing waiting times between semiflexible and fully flexible polymers we show that for realistic f_{d} translocation dynamics is to a large extent, but not completely, determined by the polymer's elastic length measured in number of Kuhn segments N_{Kuhn}. Unlike in driven translocation of flexible polymers, friction related to the polymer segment on the trans side has a considerable effect on the resulting dynamics. This friction is intermittently reduced by buckling of the polymer segment in the vicinity of the pore opening on the trans side. We show that in the experimentally relevant regime where viscosity is higher than in computer simulation models, the probability for this buckling increases with increasing f_{d}, giving rise to a larger contribution to the trans side friction at small f_{d}. Similarly to flexible polymers, we find significant center-of-mass diffusion of the cis side polymer segment which speeds up translocation. This effect is larger for smaller f_{d}. However, this speedup is smaller than the slowing down due to the trans side friction. At large enough N_{Kuhn}, the roles can be seen to be reversed, and the dynamics of flexible polymers can be reached. However, for example, polymers used in translocation experiments of DNA are elastically so short that the finite-length dynamics outlined here applies.
Collapse
Affiliation(s)
- P M Suhonen
- Department of Computer Science, Aalto University, P.O. Box 15400, FI-00076 Aalto, Finland
| | - R P Linna
- Department of Computer Science, Aalto University, P.O. Box 15400, FI-00076 Aalto, Finland
| |
Collapse
|
17
|
Kumar R, Chaudhuri A, Kapri R. Sequencing of semiflexible polymers of varying bending rigidity using patterned pores. J Chem Phys 2018; 148:164901. [PMID: 29716219 DOI: 10.1063/1.5036529] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the translocation of a semiflexible polymer through extended pores with patterned stickiness, using Langevin dynamics simulations. We find that the consequence of pore patterning on the translocation time dynamics is dramatic and depends strongly on the interplay of polymer stiffness and pore-polymer interactions. For heterogeneous polymers with periodically varying stiffness along their lengths, we find that variation of the block size of the sequences and the orientation results in large variations in the translocation time distributions. We show how this fact may be utilized to develop an effective sequencing strategy. This strategy involving multiple pores with patterned surface energetics can predict heteropolymer sequences having different bending rigidity to a high degree of accuracy.
Collapse
Affiliation(s)
- Rajneesh Kumar
- 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
| | - 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
| |
Collapse
|
18
|
Katkar HH, Muthukumar M. Role of non-equilibrium conformations on driven polymer translocation. J Chem Phys 2018; 148:024903. [PMID: 29331138 PMCID: PMC5764753 DOI: 10.1063/1.4994204] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/28/2017] [Indexed: 11/14/2022] Open
Abstract
One of the major theoretical methods in understanding polymer translocation through a nanopore is the Fokker-Planck formalism based on the assumption of quasi-equilibrium of polymer conformations. The criterion for applicability of the quasi-equilibrium approximation for polymer translocation is that the average translocation time per Kuhn segment, ⟨τ⟩/NK, is longer than the relaxation time τ0 of the polymer. Toward an understanding of conditions that would satisfy this criterion, we have performed coarse-grained three dimensional Langevin dynamics and multi-particle collision dynamics simulations. We have studied the role of initial conformations of a polyelectrolyte chain (which were artificially generated with a flow field) on the kinetics of its translocation across a nanopore under the action of an externally applied transmembrane voltage V (in the absence of the initial flow field). Stretched (out-of-equilibrium) polyelectrolyte chain conformations are deliberately and systematically generated and used as initial conformations in translocation simulations. Independent simulations are performed to study the relaxation behavior of these stretched chains, and a comparison is made between the relaxation time scale and the mean translocation time (⟨τ⟩). For such artificially stretched initial states, ⟨τ⟩/NK < τ0, demonstrating the inapplicability of the quasi-equilibrium approximation. Nevertheless, we observe a scaling of ⟨τ⟩ ∼ 1/V over the entire range of chain stretching studied, in agreement with the predictions of the Fokker-Planck model. On the other hand, for realistic situations where the initial artificially imposed flow field is absent, a comparison of experimental data reported in the literature with the theory of polyelectrolyte dynamics reveals that the Zimm relaxation time (τZimm) is shorter than the mean translocation time for several polymers including single stranded DNA (ssDNA), double stranded DNA (dsDNA), and synthetic polymers. Even when these data are rescaled assuming a constant effective velocity of translocation, it is found that for flexible (ssDNA and synthetic) polymers with NK Kuhn segments, the condition ⟨τ⟩/NK < τZimm is satisfied. We predict that for flexible polymers such as ssDNA, a crossover from quasi-equilibrium to non-equilibrium behavior would occur at NK ∼ O(1000).
Collapse
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
| |
Collapse
|
19
|
Sarabadani J, Ikonen T, Mökkönen H, Ala-Nissila T, Carson S, Wanunu M. Driven translocation of a semi-flexible polymer through a nanopore. Sci Rep 2017; 7:7423. [PMID: 28785040 PMCID: PMC5547125 DOI: 10.1038/s41598-017-07227-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 06/26/2017] [Indexed: 01/05/2023] Open
Abstract
We study the driven translocation of a semi-flexible polymer through a nanopore by means of a modified version of the iso-flux tension propagation theory, and extensive molecular dynamics (MD) simulations. We show that in contrast to fully flexible chains, for semi-flexible polymers with a finite persistence length [Formula: see text] the trans side friction must be explicitly taken into account to properly describe the translocation process. In addition, the scaling of the end-to-end distance R N as a function of the chain length N must be known. To this end, we first derive a semi-analytic scaling form for R N, which reproduces the limits of a rod, an ideal chain, and an excluded volume chain in the appropriate limits. We then quantitatively characterize the nature of the trans side friction based on MD simulations. Augmented with these two factors, the theory shows that there are three main regimes for the scaling of the average translocation time τ ∝ N α . In the rod [Formula: see text], Gaussian [Formula: see text] and excluded volume chain [Formula: see text] ≫ 10 6 limits, α = 2, 3/2 and 1 + ν, respectively, where ν is the Flory exponent. Our results are in good agreement with available simulations and experimental data.
Collapse
Affiliation(s)
- Jalal Sarabadani
- Department of Applied Physics and COMP Center of Excellence, Aalto University School of Science, P.O. Box 11000, FI-00076, Aalto, Espoo, Finland.
| | - Timo Ikonen
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, FI-02044, VTT, Finland
| | - Harri Mökkönen
- Department of Applied Physics and COMP Center of Excellence, Aalto University School of Science, P.O. Box 11000, FI-00076, Aalto, Espoo, Finland
| | - Tapio Ala-Nissila
- Department of Applied Physics and COMP Center of Excellence, Aalto University School of Science, P.O. Box 11000, FI-00076, Aalto, Espoo, Finland
- Department of Mathematical Sciences and Department of Physics, Loughborough University, Loughborough, Leicestershire, LE11 3TU, UK
| | - Spencer Carson
- Department of Physics, Northeastern University, Boston, MA, 02115, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, MA, 02115, United States
| |
Collapse
|
20
|
Abstract
In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a fixed amount of time, while it waits for an ATP molecule which triggers the motor, during an exponentially distributed time lapse. The polymer is modelled as a beads-springs chain with both excluded volume and bending contributions, and moves in a stochastic three dimensional environment modelled with a Langevin dynamics at a fixed temperature. The resulting dynamics shows a Michaelis-Menten translocation velocity that depends on the chain flexibility. The scaling behavior of the mean translocation time with the polymer length for different bending values is also investigated.
Collapse
|
21
|
Sean D, Slater GW. Langevin dynamcis simulations of driven polymer translocation into a cross-linked gel. Electrophoresis 2017; 38:653-658. [DOI: 10.1002/elps.201600438] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/12/2016] [Accepted: 12/12/2016] [Indexed: 11/10/2022]
Affiliation(s)
- David Sean
- Department of Physics; University of Ottawa; Ottawa ON Canada
| | - Gary W. Slater
- Department of Physics; University of Ottawa; Ottawa ON Canada
| |
Collapse
|
22
|
Gooneie A, Schuschnigg S, Holzer C. A Review of Multiscale Computational Methods in Polymeric Materials. Polymers (Basel) 2017; 9:E16. [PMID: 30970697 PMCID: PMC6432151 DOI: 10.3390/polym9010016] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/07/2016] [Accepted: 12/22/2016] [Indexed: 11/17/2022] Open
Abstract
Polymeric materials display distinguished characteristics which stem from the interplay of phenomena at various length and time scales. Further development of polymer systems critically relies on a comprehensive understanding of the fundamentals of their hierarchical structure and behaviors. As such, the inherent multiscale nature of polymer systems is only reflected by a multiscale analysis which accounts for all important mechanisms. Since multiscale modelling is a rapidly growing multidisciplinary field, the emerging possibilities and challenges can be of a truly diverse nature. The present review attempts to provide a rather comprehensive overview of the recent developments in the field of multiscale modelling and simulation of polymeric materials. In order to understand the characteristics of the building blocks of multiscale methods, first a brief review of some significant computational methods at individual length and time scales is provided. These methods cover quantum mechanical scale, atomistic domain (Monte Carlo and molecular dynamics), mesoscopic scale (Brownian dynamics, dissipative particle dynamics, and lattice Boltzmann method), and finally macroscopic realm (finite element and volume methods). Afterwards, different prescriptions to envelope these methods in a multiscale strategy are discussed in details. Sequential, concurrent, and adaptive resolution schemes are presented along with the latest updates and ongoing challenges in research. In sequential methods, various systematic coarse-graining and backmapping approaches are addressed. For the concurrent strategy, we aimed to introduce the fundamentals and significant methods including the handshaking concept, energy-based, and force-based coupling approaches. Although such methods are very popular in metals and carbon nanomaterials, their use in polymeric materials is still limited. We have illustrated their applications in polymer science by several examples hoping for raising attention towards the existing possibilities. The relatively new adaptive resolution schemes are then covered including their advantages and shortcomings. Finally, some novel ideas in order to extend the reaches of atomistic techniques are reviewed. We conclude the review by outlining the existing challenges and possibilities for future research.
Collapse
Affiliation(s)
- Ali Gooneie
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
| | - Stephan Schuschnigg
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
| | - Clemens Holzer
- Chair of Polymer Processing, Montanuniversitaet Leoben, Otto Gloeckel-Strasse 2, 8700 Leoben, Austria.
| |
Collapse
|
23
|
Sakaue T. Dynamics of Polymer Translocation: A Short Review with an Introduction of Weakly-Driven Regime. Polymers (Basel) 2016; 8:E424. [PMID: 30974699 PMCID: PMC6432367 DOI: 10.3390/polym8120424] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/25/2016] [Accepted: 12/01/2016] [Indexed: 12/22/2022] Open
Abstract
As emphasized in a recent review (by V.V. Palyulin, T. Ala-Nissila, R. Metzler), theoretical understanding of the unbiased polymer translocation lags behind that of the (strongly) driven translocation. Here, we suggest the introduction of a weakly-driven regime, as described by the linear response theory to the unbiased regime, which is followed by the strongly-driven regime beyond the onset of nonlinear response. This provides a concise crossover scenario, bridging the unbiased to strongly-driven regimes.
Collapse
Affiliation(s)
- Takahiro Sakaue
- Department of Physics, Kyushu University, Fukuoka 819-0395, Japan.
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Honcho Kawaguchi, Saitama 332-0012, Japan.
| |
Collapse
|
24
|
Hsiao PY. Conformation Change, Tension Propagation and Drift-Diffusion Properties of Polyelectrolyte in Nanopore Translocation. Polymers (Basel) 2016; 8:E378. [PMID: 30974654 PMCID: PMC6432159 DOI: 10.3390/polym8100378] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 10/15/2016] [Accepted: 10/19/2016] [Indexed: 12/17/2022] Open
Abstract
Using Langevin dynamics simulations, conformational, mechanical and dynamical properties of charged polymers threading through a nanopore are investigated. The shape descriptors display different variation behaviors for the cis- and trans-side sub-chains, which reflects a strong cis-trans dynamical asymmetry, especially when the driving field is strong. The calculation of bond stretching shows how the bond tension propagates on the chain backbone, and the chain section straightened by the tension force is determined by the ratio of the direct to the contour distances of the monomer to the pore. With the study of the waiting time function, the threading process is divided into the tension-propagation stage and the tail-retraction stage. At the end, the drift velocity, diffusive property and probability density distribution are explored. Owing to the non-equilibrium nature, translocation is not a simple drift-diffusion process, but exhibits several intermediate behaviors, such as ballistic motion, normal diffusion and super diffusion, before ending with the last, negative-diffusion behavior.
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
|
25
|
Hsiao PY. Polyelectrolyte Threading through a Nanopore. Polymers (Basel) 2016; 8:E73. [PMID: 30979169 PMCID: PMC6432567 DOI: 10.3390/polym8030073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 02/23/2016] [Accepted: 02/24/2016] [Indexed: 01/02/2023] Open
Abstract
Threading charged polymers through a nanopore, driven by electric fields E, is investigated by means of Langevin dynamics simulations. The mean translocation time 〈 τ 〉 is shown to follow a scaling law Nα, and the exponent α increases monotonically from 1.16 (4) to 1.40 (3) with E. The result is double-checked by the calculation of mean square displacement of translocation coordinate, which asserts a scaling behavior tβ (for t near τ) with β complying with the relation αβ = 2. At a fixed chain length N, 〈τ〉 displayed a reciprocal scaling behavior E-1 in the weak and also in the strong fields, connected by a transition E-1.64(5) in the intermediate fields. The variations of the radius of gyration of chain and the positions of chain end are monitored during a translocation process; far-from-equilibrium behaviors are observed when the driving field is strong. A strong field can strip off the condensed ions on the chain when it passes the pore. The total charges of condensed ions are hence decreased. The studies for the probability and density distributions reveal that the monomers in the trans-region are gathered near the wall and form a pancake-like density profile with a hump cloud over it in the strong fields, due to fast translocation.
Collapse
Affiliation(s)
- Pai-Yi Hsiao
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu 30013, Taiwan.
| |
Collapse
|
26
|
Zhao X, Yu W, Luo K. Surface-adsorption-induced polymer translocation through a nanopore: Effects of the adsorption strength and the surface corrugation. Phys Rev E 2015; 92:022603. [PMID: 26382422 DOI: 10.1103/physreve.92.022603] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Indexed: 11/07/2022]
Abstract
The surface corrugation plays an important role in single polymer diffusion on attractive surfaces. However, its effect on dynamics of surface adsorption-induced polymer translocation through a nanopore is not clear. Using three-dimensional Langevin dynamics simulations, we investigate the dynamics of a flexible polymer chain translocation through a nanopore induced by the selective adsorption of translocated segments onto the trans side of the membrane. The translocation probability Ptrans increases monotonically, while the mean translocation time τ has a minimum as a function of the adsorption strength ɛ, which are explained from the perspective of the effective driving force for the translocation. With the surface being smoother, τ as well as the scaling exponent α of τ with the chain length N decreases. Finally, we show that the distributions of the translocation time are non-Gaussian even for strong adsorption at a moderate surface corrugation. A nearly Gaussian distribution of the translocation time is observed only for the smoothest surface we studied.
Collapse
Affiliation(s)
- Xiaoyu Zhao
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui Province 230026, P.R. China
| | - Wancheng Yu
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui Province 230026, P.R. China
| | - Kaifu Luo
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui Province 230026, P.R. China
| |
Collapse
|
27
|
Adhikari R, Bhattacharya A. Translocation of a semiflexible polymer through a nanopore in the presence of attractive binding particles. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:032711. [PMID: 26465502 DOI: 10.1103/physreve.92.032711] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Indexed: 06/05/2023]
Abstract
We study the translocation dynamics of a semiflexible polymer through a nanopore from the cis into the trans compartment containing attractive binding particles (BPs) using the Langevin dynamics simulation in two dimensions. The binding particles accelerate the threading process in two ways: (i) reducing the back-sliding of the translocated monomer, and (ii) providing the pulling force toward the translocation direction. We observe that for certain binding strength (ε_{c}) and concentration (ρ) of the BPs, the translocation is faster than the ideal ratcheting condition as elucidated by Simon, Peskin, and Oster [M. Simon, C. S. Peskin, and G. F. Oster, Proc. Natl. Acad. Sci. USA 89, 3770 (1992)PNASA60027-842410.1073/pnas.89.9.3770]. The asymmetry produced by the BPs at the trans-side leads to similarities of this process to that of a driven translocation with an applied force inside the pore manifested in various physical quantities. Furthermore, we provide an analytic expression for the force experienced by the translocating chain as well as for the scaled mean first passage time (MFPT), for which we observe that for various combinations of N, ε, and ρ the scaled MFPT (〈τ〉/N^{1.5}ρ^{0.8}) collapses onto the same master plot. Based on the analysis of our simulation data, we provide plausible arguments with regard to how the scaling theory of driven translocation can be generalized for such a directed diffusion process by replacing the externally applied force with an effective force.
Collapse
Affiliation(s)
- Ramesh Adhikari
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| | - Aniket Bhattacharya
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
| |
Collapse
|
28
|
Fiasconaro A, Mazo JJ, Falo F. Active polymer translocation in the three-dimensional domain. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:022113. [PMID: 25768464 DOI: 10.1103/physreve.91.022113] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Indexed: 06/04/2023]
Abstract
In this work we study the translocation process of a polymer through a nanochannel where a time dependent force is acting. Two conceptually different types of driving are used: a deterministic sinusoidal one and a random telegraph noise force. The mean translocation time presents interesting resonant minima as a function of the frequency of the external driving. For the computed sizes, the translocation time scales with the polymer length according to a power law with the same exponent for almost all the frequencies of the two driving forces. The dependence of the translocation time with the polymer rigidity, which accounts for the persistence length of the molecule, shows a different low frequency dependence for the two drivings.
Collapse
Affiliation(s)
- A Fiasconaro
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Instituto de Ciencia de Materiales de Aragón, C.S.I.C.-Universidad de Zaragoza, 50009 Zaragoza, Spain
- School of Mathematical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - J J Mazo
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Instituto de Ciencia de Materiales de Aragón, C.S.I.C.-Universidad de Zaragoza, 50009 Zaragoza, Spain
| | - F Falo
- Departamento de Física de la Materia Condensada, Universidad de Zaragoza, 50009 Zaragoza, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos, Universidad de Zaragoza, 50018 Zaragoza, Spain
| |
Collapse
|
29
|
de Haan HW, Sean D, Slater GW. Using a Péclet number for the translocation of a polymer through a nanopore to tune coarse-grained simulations to experimental conditions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:022601. [PMID: 25768522 DOI: 10.1103/physreve.91.022601] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Indexed: 06/04/2023]
Abstract
Coarse-grained simulations are often employed to study the translocation of DNA through a nanopore. The majority of these studies investigate the translocation process in a relatively generic sense and do not endeavor to match any particular set of experimental conditions. In this manuscript, we use the concept of a Péclet number for translocation, P(t), to compare the drift-diffusion balance in a typical experiment vs a typical simulation. We find that the standard coarse-grained approach overestimates diffusion effects by anywhere from a factor of 5 to 50 compared to experimental conditions using double stranded DNA (dsDNA). By defining a Péclet control parameter, λ, we are able to correct this and tune the simulations to replicate the experimental P(t) (for dsDNA and other scenarios). To show the effect that a particular P(t) can have on the dynamics of translocation, we perform simulations across a wide range of P(t) values for two different types of driving forces: a force applied in the pore and a pulling force applied to the end of the polymer. As P(t) brings the system from a diffusion dominated to a drift dominated regime, a variety of effects are observed including a non-monotonic dependence of the translocation time τ on P(t) and a steep rise in the probability of translocating. Comparing the two force cases illustrates the impact of the crowding effects that occur on the trans side: a non-monotonic dependence of the width of the τ distributions is obtained for the in-pore force but not for the pulling force.
Collapse
Affiliation(s)
- Hendrick W de Haan
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario L1H 7K4, Canada
| | - David Sean
- Physics Department, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Gary W Slater
- Physics Department, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| |
Collapse
|
30
|
Palyulin VV, Ala-Nissila T, Metzler R. Polymer translocation: the first two decades and the recent diversification. SOFT MATTER 2014; 10:9016-37. [PMID: 25301107 DOI: 10.1039/c4sm01819b] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Probably no other field of statistical physics at the borderline of soft matter and biological physics has caused such a flurry of papers as polymer translocation since the 1994 landmark paper by Bezrukov, Vodyanoy, and Parsegian and the study of Kasianowicz in 1996. Experiments, simulations, and theoretical approaches are still contributing novel insights to date, while no universal consensus on the statistical understanding of polymer translocation has been reached. We here collect the published results, in particular, the famous-infamous debate on the scaling exponents governing the translocation process. We put these results into perspective and discuss where the field is going. In particular, we argue that the phenomenon of polymer translocation is non-universal and highly sensitive to the exact specifications of the models and experiments used towards its analysis.
Collapse
Affiliation(s)
- Vladimir V Palyulin
- Institute for Physics & Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany.
| | | | | |
Collapse
|
31
|
Yu W, Luo K. Polymer translocation through a nanopore driven by binding particles: influence of chain rigidity. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:042708. [PMID: 25375524 DOI: 10.1103/physreve.90.042708] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Indexed: 06/04/2023]
Abstract
We investigate the influence of chain rigidity on the dynamics of polymer translocation in the presence of binding particles (BPs) through a nanopore using two-dimensional Langevin dynamics simulations. With increasing chain rigidity κ, the mean translocation time 〈τ〉 increases monotonically due to an increase in the radius of gyration and a decrease in the center of mass velocity. Particularly for weak binding, we further find that 〈τ〉 shows a power-law behavior with the persistence length lp. Analysis indicates a scaling relation between the average velocity of the center of mass of a chain 〈vc.m.〉 and lp. As the chain becomes stiffer, the distribution of the translocation time τ approximates the Gaussian distribution and gets broader with the peak position being shifted towards longer translocation time. The corresponding translocation coordinate smax of the maximum waiting time gets smaller with increasing chain rigidity. Finally, under an extremely low BP concentration, 〈τ〉 shows a minimum for small κ, while it decreases monotonically for large κ with increasing binding energy. Our results suggest a nontrivial effect of the intrinsic property of chains on the dynamics of polymer translocation driven by BPs.
Collapse
Affiliation(s)
- Wancheng Yu
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui Province 230026, People's Republic of China
| | - Kaifu Luo
- CAS Key Laboratory of Soft Matter Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui Province 230026, People's Republic of China
| |
Collapse
|