Intra-cellular transport of single-headed molecular motors KIF1A

Motivated by experiments on single-headed kinesin KIF1A, we develop a model of intra-cellular transport by interacting molecular motors. It captures explicitly not only the effects of ATP hydrolysis, but also the ratchet mechanism which drives individual motors. Our model accounts for the experimentally observed single molecule properties in the low density limit and also predicts a phase diagram that shows the influence of hydrolysis and Langmuir kinetics on the collective spatio-temporal organization of the motors. Finally, we provide experimental evidence for the existence of domain walls in our {\it in-vitro} experiment with fluorescently labeled KIF1A.Comment: 4 pages, REVTEX, 5 EPS figures; Accepted for Publication in Phys. Rev. Let

Disordered driven lattice gases with boundary reservoirs and Langmuir kinetics

The asymmetric simple exclusion process with additional Langmuir kinetics, i.e. attachment and detachment in the bulk, is a paradigmatic model for intracellular transport. Here we study this model in the presence of randomly distributed inhomogeneities ('defects'). Using Monte Carlo simulations, we find a multitude of coexisting high- and low-density domains. The results are generic for one-dimensional driven diffusive systems with short-range interactions and can be understood in terms of a local extremal principle for the current profile. This principle is used to determine current profiles and phase diagrams as well as statistical properties of ensembles of defect samples.Comment: submitted for publishin

Competition of coarsening and shredding of clusters in a driven diffusive lattice gas

We investigate a driven diffusive lattice gas model with two oppositely moving species of particles. The model is motivated by bi-directional traffic of ants on a pre-existing trail. A third species, corresponding to pheromones used by the ants for communication, is not conserved and mediates interactions between the particles. Here we study the spatio-temporal organization of the particles. In the uni-directional variant of this model it is known to be determined by the formation and coarsening of ``loose clusters''. For our bi-directional model, we show that the interaction of oppositely moving clusters is essential. In the late stages of evolution the cluster size oscillates because of a competition between their `shredding' during encounters with oppositely moving counterparts and subsequent "coarsening" during collision-free evolution. We also establish a nontrivial dependence of the spatio-temporal organization on the system size

Functional renormalization group in the broken symmetry phase: momentum dependence and two-parameter scaling of the self-energy

We include spontaneous symmetry breaking into the functional renormalization group (RG) equations for the irreducible vertices of Ginzburg-Landau theories by augmenting these equations by a flow equation for the order parameter, which is determined from the requirement that at each RG step the vertex with one external leg vanishes identically. Using this strategy, we propose a simple truncation of the coupled RG flow equations for the vertices in the broken symmetry phase of the Ising universality class in D dimensions. Our truncation yields the full momentum dependence of the self-energy Sigma (k) and interpolates between lowest order perturbation theory at large momenta k and the critical scaling regime for small k. Close to the critical point, our method yields the self-energy in the scaling form Sigma (k) = k_c^2 sigma^{-} (k | xi, k / k_c), where xi is the order parameter correlation length, k_c is the Ginzburg scale, and sigma^{-} (x, y) is a dimensionless two-parameter scaling function for the broken symmetry phase which we explicitly calculate within our truncation.Comment: 9 pages, 4 figures, puplished versio

Single-Bottleneck Approximation for Driven Lattice Gases with Disorder and Open Boundary Conditions

We investigate the effects of disorder on driven lattice gases with open boundaries using the totally asymmetric simple exclusion process as a paradigmatic example. Disorder is realized by randomly distributed defect sites with reduced hopping rate. In contrast to equilibrium, even macroscopic quantities in disordered non-equilibrium systems depend sensitively on the defect sample. We study the current as function of the entry and exit rates and the realization of disorder and find that it is, in leading order, determined by the longest stretch of consecutive defect sites (single-bottleneck approximation, SBA). Using results from extreme value statistics the SBA allows to study ensembles with fixed defect density which gives accurate results, e.g. for the expectation value of the current. Corrections to SBA come from effective interactions of bottlenecks close to the longest one. Defects close to the boundaries can be described by effective boundary rates and lead to shifts of the phase transitions. Finally it is shown that the SBA also works for more complex models. As an example we discuss a model with internal states that has been proposed to describe transport of the kinesin KIF1A.Comment: submitted to J. Stat. Mec

An empirical test for cellular automaton models of traffic flow

Based on a detailed microscopic test scenario motivated by recent empirical studies of single-vehicle data, several cellular automaton models for traffic flow are compared. We find three levels of agreement with the empirical data: 1) models that do not reproduce even qualitatively the most important empirical observations, 2) models that are on a macroscopic level in reasonable agreement with the empirics, and 3) models that reproduce the empirical data on a microscopic level as well. Our results are not only relevant for applications, but also shed new light on the relevant interactions in traffic flow.Comment: 28 pages, 36 figures, accepted for publication in PR

mer-Bis[3,5-difluoro-2-(2-pyrid­yl)phenyl-κ2 C 1,N]{5-(2-pyridyl-κN)-3-[3-(4-vinyl­benz­yloxy)phen­yl]-1,2,4-triazol-1-ido}iridium(III) methanol solvate

In the title compound, [Ir(C11H6F2N)2(C22H17N4O)]·CH3OH, the coordination at iridium is essentially octa­hedral, but with distortions associated with the bite angles of the ligands [76.25 (9)–80.71 (12)°] and the differing trans influences of C and N ligands [Ir—N = 2.04 Å (average) trans to N but 2.14 Å trans to C]. All three bidentate ligands have coordinating ring systems that are almost coplanar [inter­planar angles = 1.7 (1)–3.8 (2)°]. The vinyl­benzyl group is disordered over two positions with occupations of 0.653 (4) and 0.347 (4). The methanol solvent mol­ecule is involved in a classical O—H⋯N hydrogen bond to a triazole N atom