Geometry and topology of knotted ring polymers in an array of obstacles

We study knotted polymers in equilibrium with an array of obstacles which models confinement in a gel or immersion in a melt. We find a crossover in both the geometrical and the topological behavior of the polymer. When the polymers' radius of gyration, $R_G$, and that of the region containing the knot, $R_{G,k}$, are small compared to the distance b between the obstacles, the knot is weakly localised and $R_G$ scales as in a good solvent with an amplitude that depends on knot type. In an intermediate regime where $R_G > b > R_{G,k}$, the geometry of the polymer becomes branched. When $R_{G,k}$ exceeds b, the knot delocalises and becomes also branched. In this regime, $R_G$ is independent of knot type. We discuss the implications of this behavior for gel electrophoresis experiments on knotted DNA in weak fields.Comment: 4 pages, 6 figure

Rate dependence of current and fluctuations in jump models with negative differential mobility

Negative differential mobility is the phenomenon in which the velocity of a particle decreases when the force driving it increases. We study this phenomenon in Markov jump models where a particle moves in the presence of walls that act as traps. We consider transition rates that obey local detailed balance but differ in normalisation, the inclusion of a rate to cross a wall and a load factor. We illustrate the full counting statistics for different choices of the jumping rates. We also show examples of thermodynamic uncertainty relations. The variety of behaviours we encounter highlights that negative differential mobility depends crucially on the chosen rates and points out the necessity that such choices should be based on proper coarse-graining studies of a more microscopic description

Validity of the additivity principle in the weakly asymmetric exclusion process with open boundaries

The additivity principle allows a calculation of current fluctuations and associated density profiles in large diffusive systems. In order to test its validity in the weakly asymmetric exclusion process with open boundaries, we use a numerical approach based on the density matrix renormalisation. With this technique, we determine the cumulant generating function of the current and the density profile corresponding to atypical currents in finite systems. We find that these converge to those predicted by the additivity principle. No evidence for dynamical phase transitions is found.Comment: 5 pages, 5 figure