Driven transport on parallel lanes with particle exclusion and obstruction

We investigate a driven two-channel system where particles on different lanes mutually obstruct each other's motion, extending an earlier model by Popkov and Peschel Phys. Rev. E 64, 026126 (2001)]. This obstruction may occur in biological contexts due to steric hinderance where motor proteins carry cargos by "walking" on microtubules. Similarly, the model serves as a description for classical spin transport where charged particles with internal states move unidirectionally on a lattice. Three regimes of qualitatively different behavior are identified, depending on the strength of coupling between the lanes. For small and large coupling strengths the model can be mapped to a one-channel problem, whereas a rich phase behavior emerges for intermediate ones. We derive an approximate but quantitatively accurate theoretical description in terms of a one-site cluster approximation, and obtain insight into the phase behavior through the current-density relations combined with an extremal-current principle. Our results are confirmed by stochastic simulations

Weakly coupled, antiparallel, totally asymmetric simple exclusion processes

We study a system composed of two parallel totally asymmetric simple exclusion processes with open boundaries, where the particles move in the two lanes in opposite directions and are allowed to jump to the other lane with rates inversely proportional to the length of the system. Stationary density profiles are determined and the phase diagram of the model is constructed in the hydrodynamic limit, by solving the differential equations describing the steady state of the system, analytically for vanishing total current and numerically for nonzero total current. The system possesses phases with a localized shock in the density profile in one of the lanes, similarly to exclusion processes endowed with nonconserving kinetics in the bulk. Besides, the system undergoes a discontinuous phase transition, where coherently moving delocalized shocks emerge in both lanes and the fluctuation of the global density is described by an unbiased random walk. This phenomenon is analogous to the phase coexistence observed at the coexistence line of the totally asymmetric simple exclusion process, however, as a consequence of the interaction between lanes, the density profiles are deformed and in the case of asymmetric lane change, the motion of the shocks is confined to a limited domain.Comment: 14 pages, 15 figures, to appear in Phys. Rev.

Direct observation of the tube model in F-actin solutions

Mutual uncrossability of polymers generates topological constraints on their conformations and dynamics, which are generally described using the tube model. We imaged confinement tubes for individual polymers within a F-actin solution by sampling over many successive micrographs of fluorescently labeled probe filaments. The resulting average tube width shows the predicted scaling behavior. Unexpectedly, we found an exponential distribution of tube curvatures which is attributed to transient entropic trapping in network void spaces.Comment: 6 pages, 4 figure

Traffic jams induced by rare switching events in two-lane transport

We investigate a model for driven exclusion processes where internal states are assigned to the particles. The latter account for diverse situations, ranging from spin states in spintronics to parallel lanes in intracellular or vehicular traffic. Introducing a coupling between the internal states by allowing particles to switch from one to another induces an intriguing polarization phenomenon. In a mesoscopic scaling, a rich stationary regime for the density profiles is discovered, with localized domain walls in the density profile of one of the internal states being feasible. We derive the shape of the density profiles as well as resulting phase diagrams analytically by a mean-field approximation and a continuum limit. Continuous as well as discontinuous lines of phase transition emerge, their intersections induce multi-critical behaviour

A diffusive system driven by a battery or by a smoothly varying field

We consider the steady state of a one dimensional diffusive system, such as the symmetric simple exclusion process (SSEP) on a ring, driven by a battery at the origin or by a smoothly varying field along the ring. The battery appears as the limiting case of a smoothly varying field, when the field becomes a delta function at the origin. We find that in the scaling limit, the long range pair correlation functions of the system driven by a battery turn out to be very different from the ones known in the steady state of the SSEP maintained out of equilibrium by contact with two reservoirs, even when the steady state density profiles are identical in both models

Molecular Spiders in One Dimension

Molecular spiders are synthetic bio-molecular systems which have "legs" made of short single-stranded segments of DNA. Spiders move on a surface covered with single-stranded DNA segments complementary to legs. Different mappings are established between various models of spiders and simple exclusion processes. For spiders with simple gait and varying number of legs we compute the diffusion coefficient; when the hopping is biased we also compute their velocity.Comment: 14 pages, 2 figure

Limited Lifespan of Fragile Regions in Mammalian Evolution

An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies supported the existence of fragile regions in mammalian genomes, the most comprehensive phylogenomic study of mammals (Ma et al. (2006) Genome Research 16, 1557-1565) raised some doubts about their existence. We demonstrate that fragile regions are subject to a "birth and death" process, implying that fragility has limited evolutionary lifespan. This finding implies that fragile regions migrate to different locations in different mammals, explaining why there exist only a few chromosomal breakpoints shared between different lineages. The birth and death of fragile regions phenomenon reinforces the hypothesis that rearrangements are promoted by matching segmental duplications and suggests putative locations of the currently active fragile regions in the human genome

Greedy Solution of Ill-Posed Problems: Error Bounds and Exact Inversion

The orthogonal matching pursuit (OMP) is an algorithm to solve sparse approximation problems. Sufficient conditions for exact recovery are known with and without noise. In this paper we investigate the applicability of the OMP for the solution of ill-posed inverse problems in general and in particular for two deconvolution examples from mass spectrometry and digital holography respectively. In sparse approximation problems one often has to deal with the problem of redundancy of a dictionary, i.e. the atoms are not linearly independent. However, one expects them to be approximatively orthogonal and this is quantified by the so-called incoherence. This idea cannot be transfered to ill-posed inverse problems since here the atoms are typically far from orthogonal: The ill-posedness of the operator causes that the correlation of two distinct atoms probably gets huge, i.e. that two atoms can look much alike. Therefore one needs conditions which take the structure of the problem into account and work without the concept of coherence. In this paper we develop results for exact recovery of the support of noisy signals. In the two examples in mass spectrometry and digital holography we show that our results lead to practically relevant estimates such that one may check a priori if the experimental setup guarantees exact deconvolution with OMP. Especially in the example from digital holography our analysis may be regarded as a first step to calculate the resolution power of droplet holography