Related papers: Conserved Linking in Single- and Double-Stranded P…
The presence of knots has been observed in a small fraction of single-domain proteins and related to their thermodynamic and kinetic properties. The exchanging of identical structural elements, typical of domain-swapped proteins, make such…
It is nontrivial whether the average size of a ring polymer should become smaller or larger under a topological constraint. Making use of some knot invariants, we evaluate numerically the mean square radius of gyration for ring polymers…
We report grand canonical Monte Carlo simulations of the critical point properties of homopolymers within the Bond Fluctuation model. By employing Configurational Bias Monte Carlo methods, chain lengths of up to N=60 monomers could be…
The scaling of the bond-bond correlation function $C(s)$ along linear polymer chains is investigated with respect to the curvilinear distance, $s$, along the flexible chain and the monomer density, $\rho$, via Monte Carlo and molecular…
The behavior of mobile linkers connecting two semi-flexible charged polymers, such as polyvalent counterions connecting DNA or F-actin chains, is studied theoretically. The chain bending rigidity induces an effective repulsion between…
We study jamming in model freely rotating polymers as a function of chain length $N$ and bond angle $\theta_0$. The volume fraction at jamming, $\phi_J(\theta_0)$, is minimal for rigid-rod-like chains ($\theta_0 = 0$), and increases…
Molecular dynamics simulations confirm recent extensional flow experiments showing ring polymer melts exhibit strong extension-rate thickening of the viscosity at Weissenberg numbers $Wi<<1$. Thickening coincides with the extreme elongation…
The work in this article is inspired by a classical problem: the statistical physical properties of a closed polymer loop that is wound around a rod. Historically the preserved topology of this system has been addressed through…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
By Monte Carlo simulations of a variant of the bond-fluctuation model without topological constraints we examine the center-of-mass (COM) dynamics of polymer melts in $d=3$ dimensions. Our analysis focuses on the COM displacement…
The conformations of interacting linear polymers on a dynamical planar random lattice are studied using a random two-matrix model. An exact expression for the partition function of self-avoiding chains subject to attractive contact…
We investigate the chain conformation of ring polymers confined to a cylindrical nanochannel using both theoretical analysis and three dimensional Langevin dynamics simulations. We predict that the longitudinal size of a ring polymer scales…
The equilibrium properties of isolated ring molecules were investigated using an off-lattice model with no excluded volume but with dynamics that preserve the topological class. Using an efficient set of long range moves, chains of more…
Our first main result is that correlations between monomers in the dimer model in $\mathbb{Z}^d$ do not decay to zero when $d > 2$. This is the first rigorous result about correlations in the dimer model in dimensions greater than two and…
We use the bond fluctuation model to study the contraction process of two polymer loops with $N$ segments that are connected each to the bottom and top part of a Feringa engine. The change in the size of the molecules as well as the folding…
A novel statistical model for the cooperative binding of monomeric ligands to a linear lattice is developed to study the interaction of ionic surfactant molecules with flexible polyion chain in dilute solution. Electrostatic binding of a…
Polymers are an effective test-bed for studying topological constraints in condensed matter due to a wide array of synthetically-available chain topologies. When linear and ring polymers are blended together, emergent rheological properties…
Brownian motion and viscoelasticity of semiflexible polymers is a subject that has been studied for many years. Still, rigorous analysis has been hindered due to the difficulty in handling the constraint that polymer chains cannot be…
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…
Simulations in which a globular ring polymer with delocalized knots is separated in two interacting loops by a slipping link, or in two non-interacting globuli by a wall with a hole, show how the minimal crossing number of the knots…