Shocks in the asymmetric exclusion process with internal degree of freedom

We determine all families of Markovian three-states lattice gases with pair interaction and a single local conservation law. One such family of models is an asymmetric exclusion process where particles exist in two different nonconserved states. We derive conditions on the transition rates between the two states such that the shock has a particularly simple structure with minimal intrinsic shock width and random walk dynamics. We calculate the drift velocity and diffusion coefficient of the shock.Comment: 26 pages, 1 figur

Hydrodynamics of the zero-range process in the condensation regime

We argue that the coarse-grained dynamics of the zero-range process in the condensation regime can be described by an extension of the standard hydrodynamic equation obtained from Eulerian scaling even though the system is not locally stationary. Our result is supported by Monte Carlo simulations.Comment: 14 pages, 3 figures. v2: Minor alteration

Why spontaneous symmetry breaking disappears in a bridge system with PDE-friendly boundaries

We consider a driven diffusive system with two types of particles, A and B, coupled at the ends to reservoirs with fixed particle densities. To define stochastic dynamics that correspond to boundary reservoirs we introduce projection measures. The stationary state is shown to be approached dynamically through an infinite reflection of shocks from the boundaries. We argue that spontaneous symmetry breaking observed in similar systems is due to placing effective impurities at the boundaries and therefore does not occur in our system. Monte-Carlo simulations confirm our results.Comment: 24 pages, 7 figure

Increased diversity of egg-associated bacteria on brown trout (Salmo trutta) at elevated temperatures.

The taxonomic composition of egg-associated microbial communities can play a crucial role in the development of fish embryos. In response, hosts increasingly influence the composition of their associated microbial communities during embryogenesis, as concluded from recent field studies and laboratory experiments. However, little is known about the taxonomic composition and the diversity of egg-associated microbial communities within ecosystems; e.g., river networks. We sampled late embryonic stages of naturally spawned brown trout at nine locations within two different river networks and applied 16S rRNA pyrosequencing to describe their bacterial communities. We found no evidence for a significant isolation-by-distance effect on the composition of bacterial communities, and no association between neutral genetic divergence of fish host (based on 11 microsatellites) and phylogenetic distances of the composition of their associated bacterial communities. We characterized core bacterial communities on brown trout eggs and compared them to corresponding water samples with regard to bacterial composition and its presumptive function. Bacterial diversity was positively correlated with water temperature at the spawning locations. We discuss this finding in the context of the increased water temperatures that have been recorded during the last 25 years in the study area

Exact time-dependent correlation functions for the symmetric exclusion process with open boundary

As a simple model for single-file diffusion of hard core particles we investigate the one-dimensional symmetric exclusion process. We consider an open semi-infinite system where one end is coupled to an external reservoir of constant density $\rho^\ast$ and which initially is in an non-equilibrium state with bulk density $\rho_0$. We calculate the exact time-dependent two-point density correlation function $C_{k,l}(t)\equiv -$ and the mean and variance of the integrated average net flux of particles $N(t)-N(0)$ that have entered (or left) the system up to time $t$. We find that the boundary region of the semi-infinite relaxing system is in a state similar to the bulk state of a finite stationary system driven by a boundary gradient. The symmetric exclusion model provides a rare example where such behavior can be proved rigorously on the level of equal-time two-point correlation functions. Some implications for the relaxational dynamics of entangled polymers and for single-file diffusion in colloidal systems are discussed.Comment: 11 pages, uses REVTEX, 2 figures. Minor typos corrected and reference 17 adde

Bethe Ansatz Solution of the Asymmetric Exclusion Process with Open Boundaries

We derive the Bethe ansatz equations describing the complete spectrum of the transition matrix of the partially asymmetric exclusion process with the most general open boundary conditions. For totally asymmetric diffusion we calculate the spectral gap, which characterizes the approach to stationarity at large times. We observe boundary induced crossovers in and between massive, diffusive and KPZ scaling regimes.Comment: 4 pages, 2 figures, published versio

Vimentin intermediate filament rings deform the nucleus during the first steps of adhesion

During cell spreading, cells undergo many changes to their architecture and their mechanical properties. Vimentin, as an integral part of the cell architecture, and its mechanical stability must adapt to the new state of the cell. This study focuses on the structures formed by vimentin during the first steps of cell adhesion. Very early, ball-like structures, or “knots,” are seen and often vimentin filaments emerge in the shape of rings around the nucleus. Although intermediate filaments are not known to be associated to motor proteins to form contractile systems, these rings can nonetheless strongly deform the cell nucleus. In the first 6 to 12 h of adhesion, these vimentin knots and rings disappear, and the intermediate filament network returns to the state seen before detachment of the cells. As these vimentin structures are very transient in the early steps of cell spreading, they have rarely been described in the literature. However, they can also be seen during mitosis, which is an event that involves partial detachment and re-spreading of the cells. Interestingly, the turnover dynamics of vimentin are reduced in both the knots and rings, compared to vimentin in the lamellipodia. It remains to define how the force is transmitted from the ball-like structures to the rings, and to measure the impact of such strong nuclear deformation on gene expression during cell re-spreading and the rearrangement of the vimentin network. Copyright © 2019 Terriac, Schütz and Lautenschläger. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms

Equivalence of a one-dimensional driven-diffusive system and an equilibrium two-dimensional walk model

It is known that a single product shock measure in some of one-dimensional driven-diffusive systems with nearest-neighbor interactions might evolve in time quite similar to a random walker moving on a one-dimensional lattice with reflecting boundaries. The non-equilibrium steady-state of the system in this case can be written in terms of a linear superposition of such uncorrelated shocks. Equivalently, one can write the steady-state of this system using a matrix-product approach with two-dimensional matrices. In this paper we introduce an equilibrium two-dimensional one-transit walk model and find its partition function using a transfer matrix method. We will show that there is a direct connection between the partition functions of these two systems. We will explicitly show that in the steady-state the transfer matrix of the one-transit walk model is related to the matrix representation of the algebra of the driven-diffusive model through a similarity transformation. The physical quantities are also related through the same transformation.Comment: 5 pages, 2 figures, Revte

Spontaneous Symmetry Breaking in a Non-Conserving Two-Species Driven Model

A two species particle model on an open chain with dynamics which is non-conserving in the bulk is introduced. The dynamical rules which define the model obey a symmetry between the two species. The model exhibits a rich behavior which includes spontaneous symmetry breaking and localized shocks. The phase diagram in several regions of parameter space is calculated within mean-field approximation, and compared with Monte-Carlo simulations. In the limit where fluctuations in the number of particles in the system are taken to zero, an exact solution is obtained. We present and analyze a physical picture which serves to explain the different phases of the model