Self-organized system-size oscillation of a stochastic lattice-gas model

Distributed fixed resources exchanging particles: Phases of an asymmetric exclusion process connected to two reservoirs

We propose and study a conceptual one-dimensional model to explore how the combined interplay between fixed resources with unlimited carrying capacity and particle exchanges between different parts of an extended system can affect the stationary densities in a current-carrying channel connecting different parts of the system. Our model is composed of a totally asymmetric simple exclusion process (TASEP) connecting two particle reservoirs without any internal dynamics, but which can directly exchange particles between each other, ensuring nonvanishing currents in the TASEP lane in the steady states. The total particle number in the system that defines the "resources" available, although held conserved by the model dynamics, can take any value giving unrestricted carrying capacity. We show how the resulting phase diagrams of the model are controlled by relevant parameters, together with the total available resources. These control parameters can be tuned to make the density on the TASEP lane globally uniform or piecewise continuous with localized domain walls, and can also control populations of the two reservoirs. In general, the phase diagrams are quite different from a TASEP with open boundaries. However, in the limit of a large amount of resources, the phase diagrams in the plane of the control parameters become topologically identical to that for an open TASEP along with delocalization of domain walls.

Availability versus carrying capacity: Phases of asymmetric exclusion processes competing for finite pools of resources

We address how the interplay between the finite availability and carrying capacity of particles at different parts of a spatially extended system can control the steady-state currents and density profiles in the one-dimensional current-carrying lanes connecting the different parts of the system. To study this, we set up a minimal model consisting of two particle reservoirs of the same finite carrying capacity connected by two equally sized antiparallel totally asymmetric simple exclusion processes (TASEPs). We focus on the steady-state currents and particle density profiles in the two TASEP lanes. The ensuing phases and the phase diagrams, which can be remarkably complex, are parametrized by the model parameters defining particle exchange between the TASEP lanes and the reservoirs and the filling fraction of the particles that determine the total resources available. These parameters may be tuned to make the densities of the two TASEP lanes globally uniform or piece-wise continuous in the form of a combination of a single localized domain wall and a spatially constant density or a pair of delocalized domain walls. Our model reveals that the two reservoirs can be preferentially populated or depopulated in the steady states.

Availability, storage capacity, and diffusion: Stationary states of an asymmetric exclusion process connected to two reservoirs

We explore how the interplay of finite availability, carrying capacity of particles at different parts of a spatially extended system, and particle diffusion between them control the steady-state currents and density profiles in a one-dimensional current-carrying channel connecting the different parts of the system. To study this, we construct a minimal model consisting of two particle reservoirs of finite carrying capacities connected by a totally asymmetric simple exclusion process (TASEP). In addition to particle transport via TASEP between the reservoirs, the latter can also directly exchange particles via Langmuir kinetics-like processes, modeling particle diffusion between them that can maintain a steady current in the system. We calculate the steady-state density profiles and the associated particle currents in the TASEP lane. The resulting phases and the phase diagrams are quite different from an open TASEP, and are characterized by the model parameters defining particle exchanges between the TASEP and the reservoirs, direct particle exchanges between the reservoirs, and the filling fraction of the particles that determines the total resources available. These parameters can be tuned to make the density on the TASEP lane globally uniform or piecewise continuous, and can make the two reservoirs preferentially populated or depopulated.

Nonequilibrium steady states in coupled asymmetric and symmetric exclusion processes

We propose and study a one-dimensional (1D) model consisting of two lanes with open boundaries. One of the lanes executes diffusive and the other lane driven unidirectional or asymmetric exclusion dynamics, which are mutually coupled through particle exchanges in the bulk. We elucidate the generic nonuniform steady states in this model. We show that in a parameter regime, where hopping along the TASEP lane, diffusion along the SEP lane, and the exchange of particles between the TASEP and SEP lanes compete, the SEP diffusivity D appears as a tuning parameter for both the SEP and TASEP densities for a given exchange rate in the nonequilibrium steady states of this model. Indeed, D can be tuned to achieve phase coexistence in the asymmetric exclusion dynamics together with spatially smoothly varying density in the diffusive dynamics in the steady state. We obtain phase diagrams of the model using mean field theories, and corroborate and complement the results with stochastic Monte Carlo simulations. This model reduces to an isolated open totally asymmetric exclusion process (TASEP) and an open TASEP with bulk particle nonconserving Langmuir kinetics (LK), respectively, in the limits of vanishing and diverging particle diffusivity in the lane executing diffusive dynamics. Thus, this model works as an overarching general model, connecting both pure TASEPs and TASEPs with LK in different asymptotic limits. We further define phases in the SEP and obtain phase diagrams and show their correspondence with the TASEP phases. In addition to its significance as a 1D driven, diffusive model, this model also serves as a simple reduced model for cell biological transport by molecular motors undergoing diffusive and directed motion inside eukaryotic cells.

A closed-loop multi-scale model for intrinsic frequency-dependent regulation of axonal growth

This article develops a closed-loop multi-scale model for axon length regulation based on a frequency-dependent negative feedback mechanism. It builds on earlier models by linking molecular motor dynamics to signaling delays that then determine signal oscillation period. The signal oscillation is treated as a front end for a signaling pathway that modulates axonal length. This model is used to demonstrate the feasibility of such a mechanism and is tested against two previously published reports in which experimental manipulations were performed that resulted in axon growth. The model captures these observations and yields an expression for equilibrium axonal length. One major prediction of the model is that increasing motor density in the body of an axon results in axonal growth-this idea has not yet been explored experimentally.