Related papers: The evaluation of directionally writhing polymers
The aim of the present paper is the study of the entropic elasticity of the dsDNA molecule, having a cristallographic length L of the order of 10 to 30 persistence lengths A, when it is subject to spatial obstructions. We have not tried to…
The winding number is a concept in complex analysis which has, in the presence of chiral symmetry, a physics interpretation as the topological index belonging to gapped phases of fermions. We study statistical properties of this topological…
We consider an elastic rod model for twisted DNA in the plectonemic regime. The molecule is treated as an impenetrable tube with an effective, adjustable radius. The model is solved analytically and we derive formulas for the contact…
We provide the exact solution of several variants of simple models of the zipping transition of two bound polymers, such as occurs in DNA/RNA, in two and three dimensions using pairs of directed lattice paths. In three dimensions the…
The symmetries of the DNA double helix require a new term in its linear response to stress: the coupling between twist and stretch. Recent experiments with torsionally-constrained single molecules give the first direct measurement of this…
If a semiflexible polymer confined to a narrow channel bends around by 180 degrees, the polymer is said to exhibit a hairpin. The equilibrium extension statistics of the confined polymer are well understood when hairpins are vanishingly…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
We establish a framework for assessing whether the transition state location of a biopolymer, which can be inferred from single molecule pulling experiments, corresponds to the ensemble of structures that have equal probability of reaching…
Entangled polymers are deformed by a strong shear flow. The shape of the polymer, called the form factor, is measured by small angle neutron scattering. However, the real-space molecular structure is not directly available from the…
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…
We discuss the entropy of a circular polymer under a topological constraint. We call it the {\it topological entropy} of the polymer, in short. A ring polymer does not change its topology (knot type) under any thermal fluctuations. Through…
A two-dimensional or quasi-two-dimensional nematic liquid crystal refers to a surface confined system. When such a system is further confined by external line boundaries or excluded from internal line boundaries, the nematic directors form…
In this article we study from a non-perturbative point of view the entanglement of two directed polymers subjected to repulsive interactions given by a Dirac $\delta-$function potential. An exact formula of the so-called second moment of…
We consider a one-dimensional directed polymer in a random potential which is characterized by the Gaussian statistics with the finite size local correlations. It is shown that the well-known Kardar's solution obtained originally for a…
Context: Due to advances in synthesizing lower dimensional materials there is the challenge of finding the wave equation that effectively describes quantum particles moving on 1D and 2D domains. Jensen and Koppe and Da Costa independently…
A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending…
We develop a dynamical approach to infinite volume directed polymer measures in random environments. We define polymer dynamics in 1+1 dimension as a stochastic gradient flow on polymers pinned at the origin, for energy involving quadratic…
The stability of DNA molecule during the encapsulation process is a topic of intense research. We study the thermal stability of the double-stranded DNA molecule of different lengths in a confined space. Using a statistical model we…
We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod like chain, involving two elastic constants, the bending and the twist rigidities. We show that this model is singular and needs a small…
Entangled networks of stiff biopolymers exhibit complex dynamic response, emerging from the topological constraints that neighboring filaments impose upon each other. We propose a class of reference models for entanglement dynamics of stiff…