Exclusion processes on networks as models for cytoskeletal transport

We present a study of exclusion processes on networks as models for complex transport phenomena and in particular for active transport of motor proteins along the cytoskeleton. We argue that active transport processes on networks spontaneously develop density heterogeneities at various scales. These heterogeneities can be regulated through a variety of multi-scale factors, such as the interplay of exclusion interactions, the non-equilibrium nature of the transport process and the network topology. We show how an effective rate approach allows to develop an understanding of the stationary state of transport processes through complex networks from the phase diagram of one single segment. For exclusion processes we rationalize that the stationary state can be classified in three qualitatively different regimes: a homogeneous phase as well as inhomogeneous network and segment phases. In particular, we present here a study of the stationary state on networks of three paradigmatic models from non-equilibrium statistical physics: the totally asymmetric simple exclusion process, the partially asymmetric simple exclusion process and the totally asymmetric simple exclusion process with Langmuir kinetics. With these models we can interpolate between equilibrium (due to bi-directional motion along a network or infinite diffusion) and out-of-equilibrium active directed motion along a network. The study of these models sheds further light on the emergence of density heterogeneities in active phenomena.

Modelling cytoskeletal traffic: an interplay between passive diffusion and active transport

We introduce the totally asymmetric exclusion process with Langmuir kinetics (TASEP-LK) on a network as a microscopic model for active motor protein transport on the cytoskeleton, immersed in the diffusive cytoplasm. We discuss how the interplay between active transport along a network and infinite diffusion in a bulk reservoir leads to a heterogeneous matter distribution on various scales. We find three regimes for steady state transport, corresponding to the scale of the network, of individual segments or local to sites. At low exchange rates strong density heterogeneities develop between different segments in the network. In this regime one has to consider the topological complexity of the whole network to describe transport. In contrast, at moderate exchange rates the transport through the network decouples, and the physics is determined by single segments and the local topology. At last, for very high exchange rates the homogeneous Langmuir process dominates the stationary state. We introduce effective rate diagrams for the network to identify these different regimes. Based on this method we develop an intuitive but generic picture of how the stationary state of excluded volume processes on complex networks can be understood in terms of the single-segment phase diagram.

Aging Dynamics of a Fractal Model Gel

Using molecular dynamics computer simulations we investigate the aging dynamics of a gel. We start from a fractal structure generated by the DLCA-DEF algorithm, onto which we then impose an interaction potential consisting of a short-range attraction as well as a long-range repulsion. After relaxing the system at T=0, we let it evolve at a fixed finite temperature. Depending on the temperature T we find different scenarios for the aging behavior. For T>0.2 the fractal structure is unstable and breaks up into small clusters which relax to equilibrium. For T<0.2 the structure is stable and the dynamics slows down with increasing waiting time. At intermediate and low T the mean squared displacement scales as t^{2/3} and we discuss several mechanisms for this anomalous time dependence. For intermediate T, the self-intermediate scattering function is given by a compressed exponential at small wave-vectors and by a stretched exponential at large wave-vectors. In contrast, for low T it is a stretched exponential for all wave-vectors. This behavior can be traced back to a subtle interplay between elastic rearrangements, fluctuations of chain-like filaments, and heterogeneity.