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Polymers
Special Issues
Polymer Translocation
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Polymer Translocation

A special issue of Polymers (ISSN 2073-4360).

Deadline for manuscript submissions: closed (25 November 2018)

Special Issue Editors

Prof. Takahiro Sakaue

E-Mail Website
Guest Editor
Department of Physics and Mathematics, Aoyama Gakuin University, Chuo-ku, Sagamihara 252-5258, Japan
Interests: statistical physics; various nonequilibrium phenomena in nature, in particular those in softmatter and biological systems
Prof. Dr. Tapio Ala-Nissilä

E-Mail Website
Guest Editor
1. Center of Excellence in Quantum Technology, Department of Applied Physics, Aalto University, P.O. Box 11100, 00076 Espoo, Finland
2. Interdisciplinary Centre for Mathematical Modelling, Department of Mathematical Sciences, Loughborough University, Loughborough LE11 3TU, UK
Interests: theoretical and computational statistical and quantum physics: polymers, colloids, nanostructures, functional nanomaterials; polymer translocation; diffusion; stochastic dynamics; surface and interface physics; chemical reactions; fluctuation relations; quantum and classical thermodynamics; open quantum systems; nano and microplasmonics; electromagnetic radiation health issues
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Passage of a biopolymer across a narrow pore is ubiquitous in the cellular biological world. In the mid-1990s, it was recognized that engineering this phenomenon had great potential, most notably to innovate a new generation of DNA sequencers. This discovery opened up an exciting field of research at the border between soft matter and biological sciences. Since then, polymer translocation research has evolved in many directions and has currently become a truly interdisciplinary field that encompasses statistical and computational physics, biological, soft matter and polymer physics, nonlinear and non-equilibrium dynamics, stochastic processes, etc.

The aim of this Special Issue is to provide a platform where relevant researchers from the various disciplines mentioned above can share their approaches, ideas, and opinions to explore this new horizon. We will invite both senior experts and young researchers to contribute. The Special Issue will cover a number of important and open topics related to polymer translocation, including driven and spontaneous translocation, influence of hydrodynamic and electrostatic interactions, alternate translocation schemes for sequencing, and dynamics of polymers under external forcing.

Prof. Takahiro Sakaue
Prof. Tapio Ala-Nissilä
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Polymers is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Polymer translocation
  • Nanopore
  • DNA sequencing
  • Polymer physics
  • Stochastic process
  • Brownian motion
  • Nonequilibrium dynamics
  • Anomalous diffusion

 

Published Papers (6 papers)

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Research

12 pages, 325 KiB  
Article
Polymer Translocation Across a Corrugated Channel: Fick–Jacobs Approximation Extended Beyond the Mean First-Passage Time
by Paolo Malgaretti and Gleb Oshanin
Polymers 2019, 11(2), 251; https://doi.org/10.3390/polym11020251 - 02 Feb 2019
Cited by 13 | Viewed by 2442
Abstract
Polymer translocation across a corrugated channel is a paradigmatic stochastic process encountered in diverse systems. The instance of time when a polymer first arrives to some prescribed location defines an important characteristic time-scale for various phenomena, which are triggered or controlled by such [...] Read more.
Polymer translocation across a corrugated channel is a paradigmatic stochastic process encountered in diverse systems. The instance of time when a polymer first arrives to some prescribed location defines an important characteristic time-scale for various phenomena, which are triggered or controlled by such an event. Here we discuss the translocation dynamics of a Gaussian polymer in a periodically-corrugated channel using an appropriately generalized Fick–Jacobs approach. Our main aim is to probe an effective broadness of the first-passage time distribution (FPTD), by determining the so-called coefficient of variation γ of the FPTD, defined as the ratio of the standard deviation versus the mean first-passage time (MFPT). We present a systematic analysis of γ as a function of a variety of system’s parameters. We show that γ never significantly drops below 1 and, in fact, can attain very large values, implying that the MFPT alone cannot characterize the first-passage statistics of the translocation process exhaustively well. Full article
(This article belongs to the Special Issue Polymer Translocation)
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12 pages, 2128 KiB  
Article
Clog and Release, and Reverse Motions of DNA in a Nanopore
by Tomoya Kubota, Kento Lloyd, Naoto Sakashita, Seiya Minato, Kentaro Ishida and Toshiyuki Mitsui
Polymers 2019, 11(1), 84; https://doi.org/10.3390/polym11010084 - 07 Jan 2019
Cited by 16 | Viewed by 4365
Abstract
Motions of circular and linear DNA molecules of various lengths near a nanopore of 100 or 200 nm diameter were experimentally observed and investigated by fluorescence microscopy. The movement of DNA molecules through nanopores, known as translocation, is mainly driven by electric fields [...] Read more.
Motions of circular and linear DNA molecules of various lengths near a nanopore of 100 or 200 nm diameter were experimentally observed and investigated by fluorescence microscopy. The movement of DNA molecules through nanopores, known as translocation, is mainly driven by electric fields near and inside the pores. We found significant clogging of nanopores by DNA molecules, particularly by circular DNA and linear T4 DNA (165.65 kbp). Here, the probabilities of DNA clogging events, depending on the DNA length and shape—linear or circular—were determined. Furthermore, two distinct DNA motions were observed: clog and release by linear T4 DNA, and a reverse direction motion at the pore entrance by circular DNA, after which both molecules moved away from the pore. Finite element method-based numerical simulations were performed. The results indicated that DNA molecules with pores 100–200 nm in diameter were strongly influenced by opposing hydrodynamic streaming flow, which was further enhanced by bulky DNA configurations. Full article
(This article belongs to the Special Issue Polymer Translocation)
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18 pages, 431 KiB  
Article
Inferring Active Noise Characteristics from the Paired Observations of Anomalous Diffusion
by Takuya Saito and Takahiro Sakaue
Polymers 2019, 11(1), 2; https://doi.org/10.3390/polym11010002 - 20 Dec 2018
Cited by 4 | Viewed by 2617
Abstract
Anomalous diffusion has been most often argued in terms of a position fluctuation of a tracer. We here propose the other fluctuating observable, i.e., momentum transfer defined as the time integral of applied force to hold a tracer’s position. Being a conjugated variable, [...] Read more.
Anomalous diffusion has been most often argued in terms of a position fluctuation of a tracer. We here propose the other fluctuating observable, i.e., momentum transfer defined as the time integral of applied force to hold a tracer’s position. Being a conjugated variable, the momentum transfer is thought of as generating the anomalous diffusion paired with the position’s one. By putting together the paired anomalous diffusions, we aim to extract useful information in complex systems, which can be applied to experiments like tagged monomer observations in chromatin. The polymer being in the equilibrium, the mean square displacement (or variance) of position displacement or momentum transfer exhibits the sub- or superdiffusion, respectively, in which the sum of the anomalous diffusion indices is conserved quite generally, but the nonequilibrium media that generate the active noise may manifest the derivations from the equilibrium relation. We discuss the deviations that reflect the characteristics of the active noise. Full article
(This article belongs to the Special Issue Polymer Translocation)
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20 pages, 1719 KiB  
Article
Dielectric Trapping of Biopolymers Translocating through Insulating Membranes
by Sahin Buyukdagli, Jalal Sarabadani and Tapio Ala-Nissila
Polymers 2018, 10(11), 1242; https://doi.org/10.3390/polym10111242 - 09 Nov 2018
Cited by 8 | Viewed by 2469
Abstract
Sensitive sequencing of biopolymers by nanopore-based translocation techniques requires an extension of the time spent by the molecule in the pore. We develop an electrostatic theory of polymer translocation to show that the translocation time can be extended via the dielectric trapping of [...] Read more.
Sensitive sequencing of biopolymers by nanopore-based translocation techniques requires an extension of the time spent by the molecule in the pore. We develop an electrostatic theory of polymer translocation to show that the translocation time can be extended via the dielectric trapping of the polymer. In dilute salt conditions, the dielectric contrast between the low permittivity membrane and large permittivity solvent gives rise to attractive interactions between the c i s and t r a n s portions of the polymer. This self-attraction acts as a dielectric trap that can enhance the translocation time by orders of magnitude. We also find that electrostatic interactions result in the piecewise scaling of the translocation time τ with the polymer length L. In the short polymer regime L ≲ 10 nm where the external drift force dominates electrostatic polymer interactions, the translocation is characterized by the drift behavior τ ∼ L 2 . In the intermediate length regime 10 nm ≲ L ≲ κ b − 1 where κ b is the Debye–Hückel screening parameter, the dielectric trap takes over the drift force. As a result, increasing polymer length leads to quasi-exponential growth of the translocation time. Finally, in the regime of long polymers L ≳ κ b − 1 where salt screening leads to the saturation of the dielectric trap, the translocation time grows linearly as τ ∼ L . This strong departure from the drift behavior highlights the essential role played by electrostatic interactions in polymer translocation. Full article
(This article belongs to the Special Issue Polymer Translocation)
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25 pages, 2554 KiB  
Article
Translocation of Charged Polymers through a Nanopore in Monovalent and Divalent Salt Solutions: A Scaling Study Exploring over the Entire Driving Force Regimes
by Pai-Yi Hsiao
Polymers 2018, 10(11), 1229; https://doi.org/10.3390/polym10111229 - 06 Nov 2018
Cited by 12 | Viewed by 3255
Abstract
Langevin dynamics simulations are performed to study polyelectrolytes driven through a nanopore in monovalent and divalent salt solutions. The driving electric field E is applied inside the pore, and the strength is varied to cover the four characteristic force regimes depicted by a [...] Read more.
Langevin dynamics simulations are performed to study polyelectrolytes driven through a nanopore in monovalent and divalent salt solutions. The driving electric field E is applied inside the pore, and the strength is varied to cover the four characteristic force regimes depicted by a rederived scaling theory, namely the unbiased (UB) regime, the weakly-driven (WD) regime, the strongly-driven trumpet (SD(T)) regime and the strongly-driven isoflux (SD(I)) regime. By changing the chain length N, the mean translocation time is studied under the scaling form ⟨ τ ⟩ ∼ N α E − δ . The exponents α and δ are calculated in each force regime for the two studied salt cases. Both of them are found to vary with E and N and, hence, are not universal in the parameter’s space. We further investigate the diffusion behavior of translocation. The subdiffusion exponent γ p is extracted. The three essential exponents ν s , q, z p are then obtained from the simulations. Together with γ p , the validness of the scaling theory is verified. Through a comparison with experiments, the location of a usual experimental condition on the scaling plot is pinpointed. Full article
(This article belongs to the Special Issue Polymer Translocation)
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16 pages, 4060 KiB  
Article
Single-Molecule Dynamics and Discrimination between Hydrophilic and Hydrophobic Amino Acids in Peptides, through Controllable, Stepwise Translocation across Nanopores
by Alina Asandei, Isabela S. Dragomir, Giovanni Di Muccio, Mauro Chinappi, Yoonkyung Park and Tudor Luchian
Polymers 2018, 10(8), 885; https://doi.org/10.3390/polym10080885 - 08 Aug 2018
Cited by 13 | Viewed by 4639
Abstract
In this work, we demonstrate the proof-of-concept of real-time discrimination between patches of hydrophilic and hydrophobic monomers in the primary structure of custom-engineered, macro-dipole-like peptides, at uni-molecular level. We employed single-molecule recordings to examine the ionic current through the α-hemolysin (α-HL) nanopore, when [...] Read more.
In this work, we demonstrate the proof-of-concept of real-time discrimination between patches of hydrophilic and hydrophobic monomers in the primary structure of custom-engineered, macro-dipole-like peptides, at uni-molecular level. We employed single-molecule recordings to examine the ionic current through the α-hemolysin (α-HL) nanopore, when serine or isoleucine residues, flanked by segments of oppositely charged arginine and glutamic amino acids functioning as a voltage-dependent “molecular brake” on the peptide, were driven at controllable rates across the nanopore. The observed differences in the ionic currents blockades through the nanopore, visible at time resolutions corresponding to peptide threading through the α-HL’s constriction region, was explained by a simple model of the volumes of electrolyte excluded by either amino acid species, as groups of serine or isoleucine monomers transiently occupy the α-HL. To provide insights into the conditions ensuring optimal throughput of peptide readout through the nanopore, we probed the sidedness-dependence of peptide association to and dissociation from the electrically and geometrically asymmetric α-HL. Full article
(This article belongs to the Special Issue Polymer Translocation)
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