Special Issue "Polymer in Confinement"

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

Deadline for manuscript submissions: closed (31 October 2018).

Special Issue Editor

Dr. Yeng-Long Chen
E-Mail Website
Guest Editor
Institute of Physics Academia Sinica Taiwan, Taipei, Taiwan
Interests: polymer physics; computer simulations of bio-macromolecule physics in confinement; microscopic liquid state theory of colloidal and nano-particles; thermodynamics of nanoparticle-polymer mixtures; dynamics of complex fluids

Special Issue Information

Dear Colleagues,

I would like to invite you to submit a contribution to a Special Issue on the properties of highly-confined polymers. Understanding fundamental changes of polymer conformation and dynamics under strong confinement could have implications in fields ranging from biophysics (gene translation, viral packing, bio-mechanics) to material science (thin film mechanics, filtration/ion-exchange membrane, drug delivery capsules). Strong confinement and surface interactions induce changes to polymer conformation, shifts in the polymer phase transition, enhance polymer knotting, and hinder or facilitate polymer transport in crowded environments. Recent advances in experimental and theoretical modeling have facilitated investigations of microtubules and actin fibers in the cell, DNA in nanopore/nanochannels, dense gels, and the cell nucleus, and large polymers adsorbed on surfaces. This Special Issue aims to provide a forum to discuss key present issues and current obstacles to spur research and solutions in this important area.

Dr. Yeng-Long Chen
Guest Editor

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 papers will be 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 monthly 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 1500 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

  • Confined polymer
  • Glass transition
  • Viral packaging
  • Chromatin physics
  • Nanochannels
  • DNA nanopore
  • DNA knotting
  • Biopolymer
  • Polyelectrolyte

Published Papers (7 papers)

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Research

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Open AccessArticle
Conformation and Dynamics of Long-Chain End-Tethered Polymers in Microchannels
Polymers 2019, 11(3), 488; https://doi.org/10.3390/polym11030488 - 13 Mar 2019
Abstract
Polyelectrolytes constitute an important group of materials, used for such different purposes as the stabilization of emulsions and suspensions or oil recovery. They are also studied and utilized in the field of microfluidics. With respect to the latter, a part of the interest [...] Read more.
Polyelectrolytes constitute an important group of materials, used for such different purposes as the stabilization of emulsions and suspensions or oil recovery. They are also studied and utilized in the field of microfluidics. With respect to the latter, a part of the interest in polyelectrolytes inside microchannels stems from genetic analysis, considering that deoxyribonucleic acid (DNA) molecules are polyelectrolytes. This review summarizes the single-molecule experimental and molecular dynamics simulation-based studies of end-tethered polyelectrolytes, especially addressing their relaxation dynamics and deformation characteristics under various external forces in micro-confined environments. In most of these studies, DNA is considered as a model polyelectrolyte. Apart from summarizing the results obtained in that area, the most important experimental and simulation techniques are explained. Full article
(This article belongs to the Special Issue Polymer in Confinement)
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Open AccessArticle
Statistical Behaviors of Semiflexible Polymer Chains Stretched in Rectangular Tubes
Polymers 2019, 11(2), 260; https://doi.org/10.3390/polym11020260 - 04 Feb 2019
Abstract
We investigated the statistical behaviors of semiflexible polymer chains, which were simultaneously subjected to force stretching and rectangular tube confinement. Based on the wormlike chain model and Odijk deflection theory, we derived a new deflection length, by using which new compact formulas were [...] Read more.
We investigated the statistical behaviors of semiflexible polymer chains, which were simultaneously subjected to force stretching and rectangular tube confinement. Based on the wormlike chain model and Odijk deflection theory, we derived a new deflection length, by using which new compact formulas were obtained for the confinement free energy and force–confinement–extension relations. These newly derived formulas were justified by numerical solutions of the eigenvalue problem associated with the Fokker–Planck governing equation and extensive Brownian dynamics simulations based on the so-called generalized bead-rod (GBR) model. We found that, compared to classical deflection theory, these new formulas were valid for a much more extended range of the confinement size/persistence length ratio and had no adjustable fitting parameters for sufficiently long semiflexible chains in the whole deflection regime. Full article
(This article belongs to the Special Issue Polymer in Confinement)
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Open AccessArticle
Nanochannel-Confined TAMRA-Polypyrrole Stained DNA Stretching by Varying the Ionic Strength from Micromolar to Millimolar Concentrations
Polymers 2019, 11(1), 15; https://doi.org/10.3390/polym11010015 - 22 Dec 2018
Cited by 1
Abstract
Large DNA molecules have been utilized as a model system to investigate polymer physics. However, DNA visualization via intercalating dyes has generated equivocal results due to dye-induced structural deformation, particularly unwanted unwinding of the double helix. Thus, the contour length increases and the [...] Read more.
Large DNA molecules have been utilized as a model system to investigate polymer physics. However, DNA visualization via intercalating dyes has generated equivocal results due to dye-induced structural deformation, particularly unwanted unwinding of the double helix. Thus, the contour length increases and the persistence length changes so unpredictably that there has been a controversy. In this paper, we used TAMRA-polypyrrole to stain single DNA molecules. Since this staining did not change the contour length of B-form DNA, we utilized TAMRA-polypyrrole stained DNA as a tool to measure the persistence length by changing the ionic strength. Then, we investigated DNA stretching in nanochannels by varying the ionic strength from 0.06 mM to 47 mM to evaluate several polymer physics theories proposed by Odijk, de Gennes and recent papers to deal with these regimes. Full article
(This article belongs to the Special Issue Polymer in Confinement)
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Open AccessArticle
Phase-Field Modeling of Freeze Concentration of Protein Solutions
Polymers 2019, 11(1), 10; https://doi.org/10.3390/polym11010010 - 21 Dec 2018
Cited by 1
Abstract
Bulk solutions of therapeutic proteins are often frozen for long-term storage. During the freezing process, proteins in liquid solution redistribute and segregate in the interstitial space between ice crystals. This is due to solute exclusion from ice crystals, higher viscosity of the concentrated [...] Read more.
Bulk solutions of therapeutic proteins are often frozen for long-term storage. During the freezing process, proteins in liquid solution redistribute and segregate in the interstitial space between ice crystals. This is due to solute exclusion from ice crystals, higher viscosity of the concentrated solution, and space confinement between crystals. Such segregation may have a negative impact on the native conformation of protein molecules. To better understand the mechanisms, we developed a phase-field model to describe the growth of ice crystals and the dynamics of freeze concentration at the mesoscale based on mean field approximation of solute concentration and the underlying heat, mass and momentum transport phenomena. The model focuses on evolution of the interfaces between liquid solution and ice crystals, and the degree of solute concentration due to partition, diffusive, and convective effects. The growth of crystals is driven by cooling of the bulk solution, but suppressed by a higher solute concentration due to increase of solution viscosity, decrease of freezing point, and the release of latent heat. The results demonstrate the interplay of solute exclusion, space confinement, heat transfer, coalescence of crystals, and the dynamic formation of narrow gaps between crystals and Plateau border areas along with correlations of thermophysical properties in the supercooled regime. Full article
(This article belongs to the Special Issue Polymer in Confinement)
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Open AccessArticle
Block Copolymer of Flexible and Semi-Flexible Block Confined in Nanopost Array
Polymers 2018, 10(12), 1301; https://doi.org/10.3390/polym10121301 - 23 Nov 2018
Abstract
Coarse-grained molecular dynamics simulations of a diblock copolymer consisting of a flexible and semi-flexible block in a dense array of parallel nanoposts with a square lattice packing were performed. The mutual interactions between the two blocks of the confined diblock chain were investigated [...] Read more.
Coarse-grained molecular dynamics simulations of a diblock copolymer consisting of a flexible and semi-flexible block in a dense array of parallel nanoposts with a square lattice packing were performed. The mutual interactions between the two blocks of the confined diblock chain were investigated through a comparison of their size, structure, and penetration among nanoposts with the corresponding separate chains. The geometry of a nanopost array was varied at constant post separation or at constant width of the passage between nanoposts. The size of a single interstitial volume was comparable to or smaller than the size of the diblock chain. A comparison of the blocks with their separate analogous chains revealed that the mutual interactions between the blocks were shielded by the nanoposts and, thus, the blocks behaved independently. At constant passage width, competitive effects of the axial chain extension in interstitial volumes and the lateral chain expansion among interstitial volumes led to a nonmonotonic behavior of the axial span. The position of the maximum in the span plotted against the filling fraction for a diblock chain was dictated by the semi-flexible block. The semi-flexible block penetrates among the nanoposts more readily and the expansion of the whole diblock copolymer is governed by the semiflexible block. The main findings were explained using the free energy arguments when an interstitial volume was approximated by a channel geometry and a passage aperture by a slit geometry. Detail knowledge of controlled conformational behavior in a compartmentalized environment can contribute to new processes in the storage and retrieval of information. Full article
(This article belongs to the Special Issue Polymer in Confinement)
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Open AccessArticle
Surface-Induced Nanostructures and Phase Diagrams of ABC Linear Triblock Copolymers under Spherical Confinement: A Self-Consistent Field Theory Simulation
Polymers 2018, 10(11), 1276; https://doi.org/10.3390/polym10111276 - 16 Nov 2018
Cited by 1
Abstract
We investigate the nanostructures and phase diagrams of ABC linear triblock copolymers confined in spherical cavities by using real-space self-consistent field theory. Various 3D morphologies, such as spherical concentric lamellae, dumbbell-like cylinder, and rotational structures, are identified in the phase diagrams, which are [...] Read more.
We investigate the nanostructures and phase diagrams of ABC linear triblock copolymers confined in spherical cavities by using real-space self-consistent field theory. Various 3D morphologies, such as spherical concentric lamellae, dumbbell-like cylinder, and rotational structures, are identified in the phase diagrams, which are constructed on the basis of the diameters of spherical cavities and the interaction between the polymers and preferential surfaces. We designate specific monomer-monomer interactions and block compositions, with which the polymers spontaneously form a cylindrical morphology in bulk, and firstly study morphology transformation with a neutral surface when a confining radius progressively increases. We then focus on phase morphologies under the preferential surfaces and consolidate them into phase diagrams. The spherical radius and the degree of preferential interactions can obviously induce the formation of a cylindrical morphology. Theoretical results correspond to an amount of recent experimental observations to a high degree and contribute to synthesising functional materials. Full article
(This article belongs to the Special Issue Polymer in Confinement)
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Review

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Open AccessReview
Theoretical Modeling of Polymer Translocation: From the Electrohydrodynamics of Short Polymers to the Fluctuating Long Polymers
Polymers 2019, 11(1), 118; https://doi.org/10.3390/polym11010118 - 11 Jan 2019
Cited by 1
Abstract
The theoretical formulation of driven polymer translocation through nanopores is complicated by the combination of the pore electrohydrodynamics and the nonequilibrium polymer dynamics originating from the conformational polymer fluctuations. In this review, we discuss the modeling of polymer translocation in the distinct regimes [...] Read more.
The theoretical formulation of driven polymer translocation through nanopores is complicated by the combination of the pore electrohydrodynamics and the nonequilibrium polymer dynamics originating from the conformational polymer fluctuations. In this review, we discuss the modeling of polymer translocation in the distinct regimes of short and long polymers where these two effects decouple. For the case of short polymers where polymer fluctuations are negligible, we present a stiff polymer model including the details of the electrohydrodynamic forces on the translocating molecule. We first show that the electrohydrodynamic theory can accurately characterize the hydrostatic pressure dependence of the polymer translocation velocity and time in pressure-voltage-driven polymer trapping experiments. Then, we discuss the electrostatic correlation mechanisms responsible for the experimentally observed DNA mobility inversion by added multivalent cations in solid-state pores, and the rapid growth of polymer capture rates by added monovalent salt in α -Hemolysin pores. In the opposite regime of long polymers where polymer fluctuations prevail, we review the iso-flux tension propagation (IFTP) theory, which can characterize the translocation dynamics at the level of single segments. The IFTP theory is valid for a variety of polymer translocation and pulling scenarios. We discuss the predictions of the theory for fully flexible and rodlike pore-driven and end-pulled translocation scenarios, where exact analytic results can be derived for the scaling of the translocation time with chain length and driving force. Full article
(This article belongs to the Special Issue Polymer in Confinement)
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