51
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Bian Y, Wang Z, Chen A, Zhao N. Fluctuating bottleneck model studies on kinetics of DNA escape from α-hemolysin nanopores. J Chem Phys 2015; 143:184908. [PMID: 26567685 DOI: 10.1063/1.4935118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We have proposed a fluctuation bottleneck (FB) model to investigate the non-exponential kinetics of DNA escape from nanometer-scale pores. The basic idea is that the escape rate is proportional to the fluctuating cross-sectional area of DNA escape channel, the radius r of which undergoes a subdiffusion dynamics subjected to fractional Gaussian noise with power-law memory kernel. Such a FB model facilitates us to obtain the analytical result of the averaged survival probability as a function of time, which can be directly compared to experimental results. Particularly, we have applied our theory to address the escape kinetics of DNA through α-hemolysin nanopores. We find that our theoretical framework can reproduce the experimental results very well in the whole time range with quite reasonable estimation for the intrinsic parameters of the kinetics processes. We believe that FB model has caught some key features regarding the long time kinetics of DNA escape through a nanopore and it might provide a sound starting point to study much wider problems involving anomalous dynamics in confined fluctuating channels.
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Affiliation(s)
- Yukun Bian
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, China
| | - Zilin Wang
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Anpu Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China
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52
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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.
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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
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53
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Sarabadani J, Ikonen T, Ala-Nissila T. Theory of polymer translocation through a flickering nanopore under an alternating driving force. J Chem Phys 2015; 143:074905. [DOI: 10.1063/1.4928743] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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
| | - 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 Physics, Brown University, P.O. Box 1843, Providence, Rhode Island 02912-1843, USA
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54
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Polson JM, Dunn TR. Evaluating the applicability of the Fokker-Planck equation in polymer translocation: a Brownian dynamics study. J Chem Phys 2015; 140:184904. [PMID: 24832303 DOI: 10.1063/1.4874976] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Brownian dynamics (BD) simulations are used to study the translocation dynamics of a coarse-grained polymer through a cylindrical nanopore. We consider the case of short polymers, with a polymer length, N, in the range N = 21-61. The rate of translocation is controlled by a tunable friction coefficient, γ0p, for monomers inside the nanopore. In the case of unforced translocation, the mean translocation time scales with polymer length as <τ1> ∼ (N - Np)(α), where Np is the average number of monomers in the nanopore. The exponent approaches the value α = 2 when the pore friction is sufficiently high, in accord with the prediction for the case of the quasi-static regime where pore friction dominates. In the case of forced translocation, the polymer chain is stretched and compressed on the cis and trans sides, respectively, for low γ0p. However, the chain approaches conformational quasi-equilibrium for sufficiently large γ0p. In this limit the observed scaling of <τ1> with driving force and chain length supports the Fokker-Planck (FP) prediction that <τ> ∝ N/fd for sufficiently strong driving force. Monte Carlo simulations are used to calculate translocation free energy functions for the system. The free energies are used with the FP equation to calculate translocation time distributions. At sufficiently high γ0p, the predicted distributions are in excellent agreement with those calculated from the BD simulations. Thus, the FP equation provides a valid description of translocation dynamics for sufficiently high pore friction for the range of polymer lengths considered here. Increasing N will require a corresponding increase in pore friction to maintain the validity of the FP approach. Outside the regime of low N and high pore friction, the polymer is out of equilibrium, and the FP approach is not valid.
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Affiliation(s)
- James M Polson
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown,Prince Edward Island C1A 4P3, Canada
| | - Taylor R Dunn
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown,Prince Edward Island C1A 4P3, Canada
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55
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Wang J, Wang Y, Luo K. Dynamics of polymer translocation through kinked nanopores. J Chem Phys 2015; 142:084901. [PMID: 25725751 DOI: 10.1063/1.4913468] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Polymer translocation through nanopore has potential technological applications for DNA sequencing, where one challenge problem is to slow down translocation speed. Inspired by experimental findings that kinked nanopores exhibit a large reduction in translocation velocity compared with their straight counterparts, we investigate the dynamics of polymer translocation through kinked nanopores in two dimensions under an applied external field. With increasing the tortuosity of an array of nanopores, our analytical results show that the translocation probability decreases. Langevin dynamics simulation results support this prediction and further indicate that with increasing the tortuosity, translocation time shows a slow increase followed by a rapid increase after a critical tortuosity. This behavior demonstrates that kinked nanopores can effectively reduce translocation speed. These results are interpreted by the roles of the tortuosity for decreasing the effective nanopore diameter, increasing effective nanopore length, and greatly increasing the DNA-pore friction.
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Affiliation(s)
- Junfang Wang
- 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 230026, People's Republic of China
| | - Yilin Wang
- 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 230026, People's Republic of 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 230026, People's Republic of China
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56
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Buyukdagli S, Blossey R, Ala-Nissila T. Ionic current inversion in pressure-driven polymer translocation through nanopores. PHYSICAL REVIEW LETTERS 2015; 114:088303. [PMID: 25768784 DOI: 10.1103/physrevlett.114.088303] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Indexed: 05/24/2023]
Abstract
We predict streaming current inversion with multivalent counterions in hydrodynamically driven polymer translocation events from a correlation-corrected charge transport theory including charge fluctuations around mean-field electrostatics. In the presence of multivalent counterions, electrostatic many-body effects result in the reversal of the DNA charge. The attraction of anions to the charge-inverted DNA molecule reverses the sign of the ionic current through the pore. Our theory allows for a comprehensive understanding of the complex features of the resulting streaming currents. The underlying mechanism is an efficient way to detect DNA charge reversal in pressure-driven translocation experiments with multivalent cations.
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Affiliation(s)
- Sahin Buyukdagli
- Department of Physics, Bilkent University, Ankara 06800, Turkey
- Institut de Recherche Interdisciplinaire USR3078 CNRS and Université Lille I, Parc de la Haute Borne, 52 Avenue de Halley, 59658 Villeneuve d'Ascq, France
| | - Ralf Blossey
- Institut de Recherche Interdisciplinaire USR3078 CNRS and Université Lille I, Parc de la Haute Borne, 52 Avenue de Halley, 59658 Villeneuve d'Ascq, France
| | - T 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 Physics, Brown University, Providence, Box 1843, Rhode Island 02912-1843, USA
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57
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Sean D, de Haan HW, Slater GW. Translocation of a polymer through a nanopore starting from a confining nanotube. Electrophoresis 2015; 36:682-91. [DOI: 10.1002/elps.201400418] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/29/2014] [Accepted: 11/11/2014] [Indexed: 11/12/2022]
Affiliation(s)
- David Sean
- Department of Physics; University of Ottawa; Ottawa Ontario Canada
| | - Hendrick W. de Haan
- Faculty of Science; University of Ontario Institute of Technology; Oshawa Ontario Canada
| | - Gary W. Slater
- Faculty of Science; University of Ontario Institute of Technology; Oshawa Ontario Canada
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58
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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.
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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
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59
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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.
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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
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60
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Sarabadani J, Ikonen T, Ala-Nissila T. Iso-flux tension propagation theory of driven polymer translocation: The role of initial configurations. J Chem Phys 2014; 141:214907. [DOI: 10.1063/1.4903176] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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
- Department of Applied Physics and COMP Center of Excellence, Aalto University School of Science, P.O. Box 11000, FI-00076 Aalto, Espoo, Finland
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, 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 Physics, Brown University, Providence, Rhode Island 02912-1843, USA
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61
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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.
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Affiliation(s)
- Vladimir V Palyulin
- Institute for Physics & Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany.
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62
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Buyukdagli S, Ala-Nissila T. Controlling polymer translocation and ion transport via charge correlations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:12907-15. [PMID: 25310861 DOI: 10.1021/la503327j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We develop a correlation-corrected transport theory in order to predict ionic and polymer transport properties of membrane nanopores under physical conditions where mean-field electrostatics breaks down. The experimentally observed low KCl conductivity of open α-hemolysin pores is quantitatively explained by the presence of surface polarization effects. Upon the penetration of a DNA molecule into the pore, these polarization forces combined with the electroneutrality of DNA sets a lower boundary for the ionic current, explaining the weak salt dependence of blocked pore conductivities at dilute ion concentrations. The addition of multivalent counterions to the solution results in the reversal of the polymer charge and the direction of the electroosmotic flow. With trivalent spermidine or quadrivalent spermine molecules, the charge inversion is strong enough to stop the translocation of the polymer and to reverse its motion. This mechanism can be used efficiently in translocation experiments in order to improve the accuracy of DNA sequencing by minimizing the translocation velocity of the polymer.
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Affiliation(s)
- Sahin Buyukdagli
- Institut de Recherche Interdisciplinaire USR3078 CNRS and Université Lille I , Parc de la Haute Borne, 52 Avenue de Halley, 59658 Villeneuve d'Ascq, France
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63
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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.
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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
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64
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Suhonen PM, Kaski K, Linna RP. Criteria for minimal model of driven polymer translocation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:042702. [PMID: 25375518 DOI: 10.1103/physreve.90.042702] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Indexed: 06/04/2023]
Abstract
While the characteristics of the driven translocation for asymptotically long polymers are well understood, this is not the case for finite-sized polymers, which are relevant for real-world experiments and simulation studies. Most notably, the behavior of the exponent α, which describes the scaling of the translocation time with polymer length, when the driving force fp in the pore is changed, is under debate. By Langevin dynamics simulations of regular and modified translocation models using the freely jointed-chain polymer model we find that a previously reported incomplete model, where the trans side and fluctuations were excluded, gives rise to characteristics that are in stark contradiction with those of the complete model, for which α increases with fp. Our results suggest that contribution due to fluctuations is important. We construct a minimal model where dynamics is completely excluded to show that close alignment with a full translocation model can be achieved. Our findings set very stringent requirements for a minimal model that is supposed to describe the driven polymer translocation correctly.
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Affiliation(s)
- P M Suhonen
- Department of Biomedical Engineering and Computational Science, Aalto University, P.O. Box 12200, FI-00076 Aalto, Finland
| | - K Kaski
- Department of Biomedical Engineering and Computational Science, Aalto University, P.O. Box 12200, FI-00076 Aalto, Finland
| | - R P Linna
- Department of Biomedical Engineering and Computational Science, Aalto University, P.O. Box 12200, FI-00076 Aalto, Finland
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65
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Nikoofard N, Khalilian H, Fazli H. Directed translocation of a flexible polymer through a cone-shaped nano-channel. J Chem Phys 2014; 139:074901. [PMID: 23968109 DOI: 10.1063/1.4818419] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Translocation of a flexible polymer through a cone-shaped channel is studied, theoretically and using computer simulations. Our simulations show that the shape of the channel causes the polymer translocation to be a driven process. The effective driving force of entropic origin acting on the polymer is calculated as a function of the length and the apex-angle of the channel, theoretically. It is found that the translocation time is a non-monotonic function of the apex-angle of the channel. By increasing the apex-angle from zero, the translocation time shows a minimum and then a maximum. Also, it is found that regardless of the value of the apex-angle, the translocation time is a uniformly decreasing function of the channel length. The results of the theory and the simulation are in good qualitative agreement.
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Affiliation(s)
- Narges Nikoofard
- Institute of Nanoscience and Nanotechnology, University of Kashan, Kashan 87317-51167, Iran
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66
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Dubbeldam JLA, Rostiashvili VG, Vilgis TA. Driven translocation of a polymer: Role of pore friction and crowding. J Chem Phys 2014; 141:124112. [DOI: 10.1063/1.4896153] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- J. L. A. Dubbeldam
- Delft Institute of Applied Mathematics (DIAM), Delft University of Technology, 2628CD Delft, The Netherlands
| | - V. G. Rostiashvili
- Max Planck Institute for Polymer Research, 10 Ackermannweg, 55128 Mainz, Germany
| | - T. A. Vilgis
- Max Planck Institute for Polymer Research, 10 Ackermannweg, 55128 Mainz, Germany
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67
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de Haan HW, Slater GW. Biomolecule transport across biomembranes in the presence of crowding: polymer translocation driven by concentration and disorder gradients. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:020601. [PMID: 25215678 DOI: 10.1103/physreve.90.020601] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Indexed: 06/03/2023]
Abstract
The transport of biomolecules across biomembranes occurs in a complex environment where the fluid on both sides of the membrane contains many inclusions. We investigate the translocation of a polymer through a nanopore in such crowded environments via computer simulations. Modeling intracellular and extracellular inclusions as spherical obstacles, the emergence of an entropic driving force is demonstrated for (i) a gradient in the number of obstacles on either side of the pore and (ii) having the obstacles in an ordered arrangement on one side and disordered on the other. With a directional preference of ≈90% of events occurring towards the disordered side and a reduction in the translocation time of ≈30%, the latter case represents a manifestation of entropic trapping. Simple estimates for the magnitude of the driving force are developed for both cases. The effect of allowing the obstacles to move as well as systems containing opposing concentration and disorder gradients are also explored. Demonstrating a robust conclusion that translocation to lower obstacle densities and higher degrees of disorder will be accelerated, these results suggest that accounting for such effects will be critical in developing a realistic model of in vivo translocation.
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Affiliation(s)
- Hendrick W de Haan
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada L1H 7K4
| | - Gary W Slater
- Physics Department, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
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68
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Ikonen T. Driven polymer transport through a periodically patterned channel. J Chem Phys 2014; 140:234906. [PMID: 24952567 DOI: 10.1063/1.4883055] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the driven transport of polymers in a periodically patterned channel using Langevin dynamics simulations in two dimensions. The channel walls are patterned with periodically alternating patches of attractive and non-attractive particles that act as trapping sites for the polymer. We find that the system shows rich dynamical behavior, observing giant diffusion, negative differential mobility, and several different transition mechanisms between the attractive patches. We also show that the channel can act as an efficient high-pass filter for polymers longer than a threshold length Nthr, which can be tuned by adjusting the length of the attractive patches and the driving force. Our findings suggest the possibility of fabricating polymer filtration devices based on patterned nanochannels.
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Affiliation(s)
- Timo Ikonen
- VTT Technical Research Centre of Finland, P.O. Box 1000, FI-02044 VTT, Finland and Department of Applied Physics, Aalto University School of Science, P.O. Box 11000, FI-00076 Aalto, Finland
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69
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Linna RP, Moisio JE, Suhonen PM, Kaski K. Dynamics of polymer ejection from capsid. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:052702. [PMID: 25353824 DOI: 10.1103/physreve.89.052702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Indexed: 06/04/2023]
Abstract
Polymer ejection from a capsid through a nanoscale pore is an important biological process with relevance to modern biotechnology. Here, we study generic capsid ejection using Langevin dynamics. We show that even when the ejection takes place within the drift-dominated region there is a very high probability for the ejection process not to be completed. Introducing a small aligning force at the pore entrance enhances ejection dramatically. Such a pore asymmetry is a candidate for a mechanism by which viral ejection is completed. By detailed high-resolution simulations we show that such capsid ejection is an out-of-equilibrium process that shares many common features with the much studied driven polymer translocation through a pore in a wall or a membrane. We find that the ejection times scale with polymer length, τ ∼ N(α). We show that for the pore without the asymmetry the previous predictions corroborated by Monte Carlo simulations do not hold. For the pore with the asymmetry the scaling exponent varies with the initial monomer density (monomers per capsid volume) ρ inside the capsid. For very low densities ρ ≤ 0.002 the polymer is only weakly confined by the capsid, and we measure α = 1.33, which is close to α=1.4 obtained for polymer translocation. At intermediate densities the scaling exponents α = 1.25 and 1.21 for ρ = 0.01 and 0.02, respectively. These scalings are in accord with a crude derivation for the lower limit α = 1.2. For the asymmetrical pore precise scaling breaks down, when the density exceeds the value for complete confinement by the capsid, ρ ⪆ 0.25. The high-resolution data show that the capsid ejection for both pores, analogously to polymer translocation, can be characterized as a multiplicative stochastic process that is dominated by small-scale transitions.
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Affiliation(s)
- R P Linna
- Department of Biomedical Engineering and Computational Science, Aalto University, P. O. Box 12200, FI-00076 Aalto, Finland
| | - J E Moisio
- Department of Biomedical Engineering and Computational Science, Aalto University, P. O. Box 12200, FI-00076 Aalto, Finland
| | - P M Suhonen
- Department of Biomedical Engineering and Computational Science, Aalto University, P. O. Box 12200, FI-00076 Aalto, Finland
| | - K Kaski
- Department of Biomedical Engineering and Computational Science, Aalto University, P. O. Box 12200, FI-00076 Aalto, Finland
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70
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Adhikari R, Bhattacharya A. Driven translocation of a semi-flexible chain through a nanopore: a Brownian dynamics simulation study in two dimensions. J Chem Phys 2014; 138:204909. [PMID: 23742518 DOI: 10.1063/1.4807002] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study translocation dynamics of a semi-flexible polymer chain through a nanoscopic pore in two dimensions using Langevin dynamics simulation in presence of an external bias F inside the pore. For chain length N and stiffness parameter κb considered in this paper, we observe that the mean first passage time <τ> increases as <τ(κb)>~<τ(κb=0)>lp(aN) , where κb and lp are the stiffness parameter and persistence length, respectively, and aN is a constant that has a weak N dependence. We monitor the time dependence of the last monomer xN(t) at the cis compartment and calculate the tension propagation time (TP) ttp directly from simulation data for <xN(t)> ~ t as alluded in recent nonequlibrium TP theory [T. Sakaue, Phys. Rev. E 76, 021803 (2007)] and its modifications to Brownian dynamics tension propagation theory [T. Ikonen, A. Bhattacharya, T. Ala-Nissila, and W. Sung, Phys. Rev. E 85, 051803 (2012); and J. Chem. Phys. 137, 085101 (2012)] originally developed to study translocation of a fully flexible chain. We also measure ttp from peak position of the waiting time distribution W(s) of the translocation coordinate s (i.e., the monomer inside the pore), and explicitly demonstrate the underlying TP picture along the chain backbone of a translocating chain to be valid for semi-flexible chains as well. From the simulation data, we determine the dependence of ttp on chain persistence length lp and show that the ratio ttp∕<τ> is independent of the bias F.
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Affiliation(s)
- Ramesh Adhikari
- Department of Physics, University of Central Florida, Orlando, Florida 32816-2385, USA
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71
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Polson JM, McCaffrey ACM. Polymer translocation dynamics in the quasi-static limit. J Chem Phys 2013; 138:174902. [PMID: 23656154 DOI: 10.1063/1.4803022] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Monte Carlo (MC) simulations are used to study the dynamics of polymer translocation through a nanopore in the limit where the translocation rate is sufficiently slow that the polymer maintains a state of conformational quasi-equilibrium. The system is modeled as a flexible hard-sphere chain that translocates through a cylindrical hole in a hard flat wall. In some calculations, the nanopore is connected at one end to a spherical cavity. Translocation times are measured directly using MC dynamics simulations. For sufficiently narrow pores, translocation is sufficiently slow that the mean translocation time scales with polymer length N according to <τ> ∝ (N - N(p))(2), where N(p) is the average number of monomers in the nanopore; this scaling is an indication of a quasi-static regime in which polymer-nanopore friction dominates. We use a multiple-histogram method to calculate the variation of the free energy with Q, a coordinate used to quantify the degree of translocation. The free energy functions are used with the Fokker-Planck formalism to calculate translocation time distributions in the quasi-static regime. These calculations also require a friction coefficient, characterized by a quantity N(eff), the effective number of monomers whose dynamics are affected by the confinement of the nanopore. This was determined by fixing the mean of the theoretical distribution to that of the distribution obtained from MC dynamics simulations. The theoretical distributions are in excellent quantitative agreement with the distributions obtained directly by the MC dynamics simulations for physically meaningful values of N(eff). The free energy functions for narrow-pore systems exhibit oscillations with an amplitude that is sensitive to the nanopore length. Generally, larger oscillation amplitudes correspond to longer translocation times.
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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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72
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Edmonds CM, Hesketh PJ, Nair S. Polymer translocation in solid-state nanopores: Dependence on hydrodynamic interactions and polymer configuration. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.07.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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73
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Panja D, Barkema GT, Kolomeisky AB. Through the eye of the needle: recent advances in understanding biopolymer translocation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:413101. [PMID: 24025200 DOI: 10.1088/0953-8984/25/41/413101] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In recent years polymer translocation, i.e., transport of polymeric molecules through nanometer-sized pores and channels embedded in membranes, has witnessed strong advances. It is now possible to observe single-molecule polymer dynamics during the motion through channels with unprecedented spatial and temporal resolution. These striking experimental studies have stimulated many theoretical developments. In this short theory-experiment review, we discuss recent progress in this field with a strong focus on non-equilibrium aspects of polymer dynamics during the translocation process.
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Affiliation(s)
- Debabrata Panja
- Institute for Theoretical Physics, Universiteit Utrecht, Leuvenlaan 4, 3584 CE Utrecht, The Netherlands. Institute for Theoretical Physics, Universiteit van Amsterdam, Science Park 904, Postbus 94485, 1090 GL Amsterdam, The Netherlands
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74
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Saito T, Sakaue T. Cis-trans dynamical asymmetry in driven polymer translocation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:042606. [PMID: 24229205 DOI: 10.1103/physreve.88.042606] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Indexed: 05/24/2023]
Abstract
During polymer translocation driven by, e.g., voltage drop across a nanopore, the segments in the cis side are incessantly pulled into the pore, which are then pushed out of it into the trans side. This pulling and pushing of polymer segments are described in the continuum level by nonlinear transport processes known, respectively, as fast and slow diffusions. By matching solutions of both sides through the mass conservation across the pore, we provide a physical basis for the cis and trans dynamical asymmetry, a feature repeatedly reported in recent numerical simulations. We then predict how the total driving force is dynamically allocated between cis (pulling) and trans (pushing) sides, demonstrating that the trans-side event adds a weak finite-chain length effect to the dynamical scaling.
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Affiliation(s)
- Takuya Saito
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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75
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Bhattacharya A. Translocation dynamics of a semiflexible chain under a bias: Comparison with tension propagation theory. POLYMER SCIENCE SERIES C 2013. [DOI: 10.1134/s1811238213070011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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76
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77
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Chen Y, Luo K. Dynamics of polymer translocation through a nanopore induced by different sizes of crowding agents. J Chem Phys 2013; 138:204903. [DOI: 10.1063/1.4807088] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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78
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Sakaue T. Memory effect and fluctuating anomalous dynamics of a tagged monomer. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:040601. [PMID: 23679360 DOI: 10.1103/physreve.87.040601] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Indexed: 06/02/2023]
Abstract
We analyze the anomalous dynamics of a tagged monomer under external navigation. The memory effect causing the anomaly is elucidated, which depends on the magnitude of the force. In particular, the nonlinear and nonequilibrium memory effect under strong force is characterized by the force-dependent self-affine process for the tension transmission along the connectivity. Utilizing such knowledge, a generalized Langevin equation approach is proposed to quantify the fluctuating dynamics of driven anomalous walkers.
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Affiliation(s)
- Takahiro Sakaue
- Department of Physics, Kyushu University 33, Fukuoka 812-8581, Japan.
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79
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Polson JM, Hassanabad MF, McCaffrey A. Simulation study of the polymer translocation free energy barrier. J Chem Phys 2013; 138:024906. [DOI: 10.1063/1.4774118] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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80
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Ikonen T, Bhattacharya A, Ala-Nissila T, Sung W. Influence of non-universal effects on dynamical scaling in driven polymer translocation. J Chem Phys 2013; 137:085101. [PMID: 22938265 DOI: 10.1063/1.4742188] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the dynamics of driven polymer translocation using both molecular dynamics (MD) simulations and a theoretical model based on the non-equilibrium tension propagation on the cis side subchain. We present theoretical and numerical evidence that the non-universal behavior observed in experiments and simulations are due to finite chain length effects that persist well beyond the relevant experimental and simulation regimes. In particular, we consider the influence of the pore-polymer interactions and show that they give a major contribution to the non-universal effects. In addition, we present comparisons between the theory and MD simulations for several quantities, showing extremely good agreement in the relevant parameter regimes. Finally, we discuss the potential limitations of the present theories.
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Affiliation(s)
- T Ikonen
- Department of Applied Physics and COMP Center of Excellence, Aalto University School of Science, P.O. Box 11000, FI-00076 Aalto, Espoo, Finland
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81
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Ikonen T, Shin J, Sung W, Ala-Nissila T. Polymer translocation under time-dependent driving forces: resonant activation induced by attractive polymer-pore interactions. J Chem Phys 2012; 136:205104. [PMID: 22667592 DOI: 10.1063/1.4722080] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study the driven translocation of polymers under time-dependent driving forces using N-particle Langevin dynamics simulations. We consider the force to be either sinusoidally oscillating in time or dichotomic noise with exponential correlation time, to mimic both plausible experimental setups and naturally occurring biological conditions. In addition, we consider both the case of purely repulsive polymer-pore interactions and the case with additional attractive polymer-pore interactions, typically occurring inside biological pores. We find that the nature of the interaction fundamentally affects the translocation dynamics. For the non-attractive pore, the translocation time crosses over to a fast translocation regime as the frequency of the driving force decreases. In the attractive pore case, because of a free energy well induced inside the pore, the translocation time can be a minimum at the optimal frequency of the force, the so-called resonant activation. In the latter case, we examine the effect of various physical parameters on the resonant activation, and explain our observations using simple theoretical arguments.
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Affiliation(s)
- Timo Ikonen
- Department of Applied Physics, Aalto University School of Science, P.O. Box 11000, FI-00076 Aalto, Espoo, Finland
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82
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Rosa A, Di Ventra M, Micheletti C. Topological jamming of spontaneously knotted polyelectrolyte chains driven through a nanopore. PHYSICAL REVIEW LETTERS 2012; 109:118301. [PMID: 23005684 DOI: 10.1103/physrevlett.109.118301] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Indexed: 06/01/2023]
Abstract
The advent of solid state nanodevices allows for interrogating the physicochemical properties of a polyelectrolyte chain by electrophoretically driving it through a nanopore. Salient dynamical aspects of the translocation process have been recently characterized by theoretical and computational studies of model polymer chains free from self-entanglement. However, sufficiently long equilibrated chains are necessarily knotted. The impact of such topological "defects" on the translocation process is largely unexplored, and is addressed in this Letter. By using Brownian dynamics simulations on a coarse-grained polyelectrolyte model we show that knots, despite being trapped at the pore entrance, do not per se cause the translocation process to jam. Rather, knots introduce an effective friction that increases with the applied force, and practically halts the translocation above a threshold force. The predicted dynamical crossover, which is experimentally verifiable, ought to be relevant in applicative contexts, such as DNA nanopore sequencing.
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Affiliation(s)
- A Rosa
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy.
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83
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Mirigian S, Wang Y, Muthukumar M. Translocation of a heterogeneous polymer. J Chem Phys 2012; 137:064904. [PMID: 22897308 PMCID: PMC3738248 DOI: 10.1063/1.4742970] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 07/25/2012] [Indexed: 12/11/2022] Open
Abstract
We present results on the sequence dependence of translocation kinetics for a partially charged heteropolymer moving through a very thin pore using theoretical tools and Langevin dynamics simulational techniques. The chain is composed of two types of monomers of differing frictional interaction with the pore and charge. We present exact analytical expressions for passage probability, mean first passage time, and mean successful passage times for both reflecting/absorbing and absorbing/absorbing boundary conditions, showing rich and unexpected dependence of translocation behavior on charge fraction, distribution along the chain, and electric field configuration. We find excellent qualitative and good quantitative agreement between theoretical and simulation results. Surprisingly, there emerges a threshold charge fraction of a diblock copolymer beyond which the success rate of translocation is independent of charge fraction. Also, the mean successful translocation time of a diblock copolymer displays non-monotonic behavior with increasing length of the charged block; there is an optimum length of the charged block where the mean translocation rate is the slowest; and there can be a substantial range of higher charge fractions which make the translocation slower than even a minimally charged chain. Additionally, we find for a fixed total charge on the chain, finer distribution along the backbone significantly decreases mean translocation time.
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Affiliation(s)
- Stephen Mirigian
- Department of Polymer Science and Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
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84
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Sakaue T, Saito T, Wada H. Dragging a polymer in a viscous fluid: steady state and transient. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:011804. [PMID: 23005445 DOI: 10.1103/physreve.86.011804] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Indexed: 06/01/2023]
Abstract
We study the conformation and dynamics of a single polymer chain that is pulled by a constant force applied at its one end with the other end free. Such a situation is relevant to the growing technology of manipulating individual macromolecules, which offers a paradigm research for probing far-from-equilibrium responses of long flexible biological polymers. We first analyze the Rouse model for the Gaussian chains for which the exact analytical results can be obtained. More realistic features such as the finite extensibility, the excluded volume, and the hydrodynamic interactions are taken into account with the help of the scaling argument, which leads to various nontrivial predictions such as the force-dependent friction constants. We elucidate (i) generalized dynamical equations of state describing extension and friction laws in steady-state and (ii) the tension propagation laws in the transient process. We point out that the time evolutions of the dynamic friction in the transient process crucially depend on the experimental protocol, i.e., either constant force or constant velocity ensemble. These predictions could be verified in experiments using giant DNAs and chromosomes.
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Affiliation(s)
- Takahiro Sakaue
- Department of Physics, Kyushu University 33, Fukuoka 812-8581, Japan.
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85
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Saito T, Sakaue T. Process time distribution of driven polymer transport. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:061803. [PMID: 23005120 DOI: 10.1103/physreve.85.061803] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Revised: 04/23/2012] [Indexed: 05/24/2023]
Abstract
We discuss the temporal distribution of dynamic processes in driven polymer transport inherent to flexible chains due to stochastic tension propagation. The stochasticity originates from the disordered initial configuration of an equilibrium polymer coil, which results in random paths for tension propagation. We consider the process time for when translocation occurs across a fixed pore and when stretching occurs by pulling the chain end. A scaling argument for the mean and standard deviation of the process time is provided using the two-phase picture for stochastic propagation. The two cases are found to differ remarkably. The process time distribution of the translocation exhibits substantial spreading even in the long-chain limit, unlike that found for the dynamics of polymer stretching. In addition, the process time distribution in the driven translocation is shown to have a characteristic asymmetric shape.
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Affiliation(s)
- Takuya Saito
- Department of Physics, Kyushu University 33, Fukuoka 812-8581, Japan
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