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The Miles theory of wave amplification by wind is extended to the case of finite depth h and a shear flow with (constant) vorticity {\Omega}. Vorticity is characterised through the non-dimensional parameter {\nu} = {\Omega} U_1 /g, where g the gravitational acceleration, U_1 a characteristic wind velocity and k the wavenumber. The notion of 'wave age' is generalised to account for the effect of vorticity. Several widely used growth rates are derived analytically from the dispersion relation of the wind/water interface, and their dependence on both water depth and vorticity is derived and discussed. Vorticity is seen to shift the maximum wave age, similar to what was previously known to be the effect of water depth. At the same time, a novel effect arises and the growth coefficients, at identical wave age and depth, are shown to experience a net increase or decrease according to the shear gradient in the water flow.

We extend the paradigmatic and versatile TASEP (Totally Asymmetric Simple Exclusion Process) for stochastic 1d transport to allow for two different particle species, each having specific entry and exit rates. We offer a complete mean-field analysis, including a phase diagram, by mapping this model onto an effective one-species TASEP. Stochastic simulations confirm the results, but indicate deviations when the particle species have very different exit rates. We illustrate that this is due to a phenomenon of intermittency, and formulate a refined 'intermittent' mean-field (iMF) theory for this regime. We discuss how non-stationary effects may further enrich the phenomenology.

The cytoskeleton in eukaryotic cells plays several crucial roles. In terms of intracellular transport, motor proteins use the cytoskeletal filaments as a backbone along which they can actively transport biological cargos such as vesicles carrying biochemical reactants. Crossings between such filaments constitute a key element, as they may serve to alter the destination of such payload. Although motor proteins are known to display a rich behaviour at such crossings, the latter have so far only been modelled as simple branching points. Here we explore a model for a crossing between two microtubules which retains the individual tracks consisting of protofilaments, and we construct a schematic representation of the transport paths. We study collective transport exemplified by the Totally Asymmetric Simple Exclusion Process (TASEP), and provide a full analysis of the transport features and the associated phase diagram, by a generic mean-field approach which we confirm through particle-based stochastic simulations. In particular we show that transport through such a compound crossing cannot be approximated from a coarse-grained structure with a simple branching point. Instead, it gives rise to entirely new and counterintuitive features: the fundamental current-density relation for traffic flow is no longer a single-valued function, and it furthermore differs according to whether it is observed upstream or downstream from the crossing. We argue that these novel features may be directly relevant for interpreting experimental measurements.

We raise the question whether a simple model for traffic, generic but based on microscopic rules, can provide an additional angle for interpreting flow through a road system. Using the totally simple exclusion process (TASEP) on a road segment with ramps, we show that measuring the flow directly at the road junctions may be a useful setup. We show that the presence of junctions affects the characterisation of traffic, suggesting that interpretations in terms of a 2-phase or a 3-phase description may be complementary, rather than contradictory. We furthermore argue that hysteresis-like features can appear in a system with junctions, which is intriguing as the TASEP dynamics as such do not lead to hysteresis. We discuss our findings in the light of boundary-driven phase transitions.

ABout our activities on physico-mathematical modelling of intracellularmolecular transport