Related papers: Two-phase stretching of molecular chains
In these lecture notes, which are based on the mini-course given at 2013 Prague School on Mathematical Statistical Physics, we discuss ballistic phase of quenched and annealed stretched polymers in random environment on ${\mathbb Z}^d$ with…
The statistics of randomly branching double-folded ring polymers are relevant to the secondary structure of RNA, the large-scale branching of plectonemic DNA (and thus bacterial chromosomes), the conformations of single-ring polymers…
This paper presents a macroscopic theory, alongside its numerical implementation, aimed at describing, explaining, and predicting the nucleation and propagation of fracture in viscoelastic materials subjected to quasistatic loading…
Entanglement of polymer chains is ubiquitous in elastomers, gels, and biological tissues. While the effects of chain entanglement on elasticity and viscoelasticity of polymer networks have been intensively studied, it remains elusive how…
We introduce a three-state model for a single DNA chain under tension that distinguishes between B-DNA, S-DNA and M (molten or denatured) segments and at the same time correctly accounts for the entropy of molten loops, characterized by the…
We analyze a (1+1)-dimension directed random walk model of a polymer dipped in a medium constituted by two immiscible solvents separated by a flat interface. The polymer chain is heterogeneous in the sense that a single monomer may…
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…
Following Poland and Scheraga, we consider a simplified model for the denaturation transition of DNA. The two strands are modeled as interacting polymer chains. The attractive interactions, which mimic the pairing between the four bases,…
DNA plays a special role in polymer science not just because of the highly selective recognition of complementary single DNA strands but also because bacteria can express DNA chains that are very long yet perfectly monodisperse. The latter…
A simple model of DNA based on two interacting polymers has been used to study the unzipping of a double stranded DNA subjected to a periodic force. We propose a dynamical transition, where without changing the physiological condition, it…
A directed polymer is allowed to branch, with configurations determined by global energy optimization and disorder. A finite size scaling analysis in 2D shows that, if disorder makes branching more and more favorable, a critical transition…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
The dynamic behavior of semi-dilute polymer solutions is governed by an interplay between solvent quality, concentration, molecular weight, and flow type. Semi-dilute solutions are characterized by large fluctuations in concentration,…
In order to interpret recent experimental studies of the dependence of conductance of ds-DNA as the DNA is pulled from the 3'end1-3'end2 ends, which find a sharp conductance jump for a very short (4.5 %) stretching length, we carried out…
DNA unzipping, the separation of its double helix into single strands, is crucial in modulating a host of genetic processes. Although the large-scale separation of double-stranded DNA has been studied with a variety of theoretical and…
We propose a theoretical framework for dealing with a transient polymer network undergoing small deformations, based on the rate of breaking and re-forming of network crosslinks and the evolving elastic reference state. In this framework,…
We present a theoretical description of the dynamics of a semi-flexible polymer being pulled through a nanopore by an external force acting at the pore. Our theory is based on the tensile blob picture of Pincus in which the front of the…
Tracer-diffusion of small molecules through dense systems of chain polymers is studied within an athermal lattice model, where hard core interactions are taken into account by means of the site exclusion principle. An approximate mapping of…
A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination…
The mechanical properties of polymer knots under stretching in a bad or good solvent are investigated by applying a given force $F$ to a point of the knot while keeping another point fixed. The Monte Carlo sampling of the polymer…