When a flexible polymer is sucked into a localized small hole, the chain can initially respond only locally and the sequential nonequilibrium processes follow in line with the propagation of the tensile force along the chain backbone. We analyze this dynamical process by taking the nonuniform stretching of the polymer into account both with and without hydrodynamics interactions. Earlier conjectures on the absorption time are criticized and new formulae are proposed together with time evolutions of relevant dynamical variables.

We revisit the classical problem of the behavior of an isolated linear polymer chain in confined spaces, introducing the distinction between two different confinement regimes (the weak and the strong confinement regimes, respectively). We then discuss some recent experimental findings concerning the partitioning of individual polymers into protein pores. We also generalize our study to the case of branched polymers, and study the flow-injection properties of such objects into nanoscopic pores, for which the strong confinement regime plays an important role.

Flexible polymers such as long DNA, RNA molecules, and proteins, can pass through a narrow pore whose size is comparable to their molecular thickness. We highlight the richness and complexity involved in the dynamics of this unique mode of molecular transport, called translocation, actively driven by external forces. In particular, the process takes place in the condition far from equilibrium accompanying of large conformational distortion in line with the propagation of the tensile force along the chain backbone. A general framework is proposed, which captures such essential features, whereby can account for reported various experimental data from a unified viewpoint.

We propose a simple mean-field theory for the structure of ring polymer melts. By combining the notion of topological volume fraction and a classical van der Waals theory of fluids, we take into account many body effects of topological origin in dense systems. We predict that although the compact statistics with the Flory exponent ν = 1/3 is realized for very long chains, most practical cases fall into the crossover regime with the apparent exponent ν = 2/5 during which the system evolves toward a topological dense-packed limit.PACS numbers: 61.25. 83.80.Sg Statistics of melts and concentrated solutions of ring polymers is a longstanding problem in polymer physics [1][2][3][4][5][6][7][8][9][10][11][12][13][14]. Unlike linear chain systems, their physical properties crucially depends on the preparation history during which the topology of the system is frozen. Then, the non-crossing requirement creates topological constraints which impose nontrivial restrictions on the phase space of the system, hence, have a strong influence even in statics.In the linear polymer counterpart, a well-known Flory theorem states that the chain conformation is Gaussian characterized by the Flory exponent ν = 1/2 due to the screening of excluded-volume interactions [15][16][17]. This simple (but surprising) result, however, no longer holds for the ring polymer melt. The most basic question arises in the melt of ring polymers free from any mutual-linking and self-knotting. There have been several experimental [6,7] and numerical studies [8][9][10][11][12][13][14] in this direction, but the clear-cut conclusion has not been attained yet.In their seminal paper, Cates and Deutsch (C-D) argued that the unconcatenated rings in the melt may have statistics intermediate between those of collapsed (ν = 1/3) and Gaussian (ν = 1/2) chains [1]. Specifically, they proposed a conjecture on the scaling exponent ν = 2/5 based on Flory-type mean-field theory. While this leading theoretical guide seems to be supported by following numerical simulations [8][9][10][11][12], some of more recent observations claim the collapsed statistics ν = 1/3 for sufficiently long rings [13,14]. The latter result was hypothesized by Khokhlov and Nechaev based on the analogy with lattice animals [2]. Closely related to this is the crumpled globule (CG) model [3,4] It is important to keep in mind that the topological effect manifests itself in the scale larger than some characteristic length ξ 1 . Individual rings in concentrated solutions of small molecular weight N < g 1 ≡ (ξ 1 /a) 2 φ 1/4 (N is the number of monomers in each ring, a is the monomer size and φ is the monomeric volume fraction) thus show Gaussian behaviors with the size R 0 ≃ ξ(N/g) 1/2 ≃ aN 1/2 φ −1/8 where ξ ≃ ag 3/5 ≃ aφ −3/4 is the correlation length of concentration fluctuation. In the present paper, we introduce the notion of the topological volume fraction and construct a mean-filed theory for the concentrated solution of noncatenated long ring polymers. Requiring the theory to be compatible ...

By analyzing the real space non-equilibrium dynamics of polymers, we elucidate the physics of driven translocation and propose its dynamical scaling scenario analogous to that in the surface growth phenomena. We provide a detailed account of the previously proposed tension-propagation formulation and extend it to cover the broader parameter space relevant to real experiments. In addition to a near-equilibrium regime, we identify three distinct non-equilibrium regimes reflecting the steady-state property of a dragged polymer with finite extensibility. Finite-size effects are also pointed out. These elements are shown to be crucial for the appropriate comparison with experiments and simulations.

We analyze static properties of a strongly confined semiflexible polymer, i.e. either trapped in a closed space or compressed by external forces, in an athermal solvent. Like a flexible polymer case, we can resort to an analogy with the semidilute solution, but a complication due to the additional length scale arising from the chain rigidity results in more diverse behaviours depending on system parameters. For each regime, scaling forms of the excess free energy of the confinement are derived. Effects of the confinement geometry and the solvent quality are briefly discussed.

Flexible chains (linear or branched) can be forced to enter into a narrow capillary by using a hydrodynamic flow. Here, we correct our earlier description of this problem by considering the progressive nature of the suction process. We find that the critical current for penetration, Jc, is controlled by the entry of a single blob of the capillary size, and that its scaling structure is the same for branched and linear chains.

We studied the stability and dynamics of a model of a nucleosome, the fundamental unit for the packing of long DNA in eukaryotes, using a Brownian dynamics simulation. For the proper folding of a stiff polymer on a core particle, moderate attractive interaction is shown to be essentially important, which explains the empirical experimental protocol for the reconstitution of nucleosomes. The effect of the chain end on the positioning of the core particle is examined and compared with the experimental data by atomic force microscopy measurement. It is also suggested that the core particle exhibits sliding motion along the chain as a manifestation of Brownian motion.