Cells are strongly out-of-equilibrium systems driven by continuous energy supply. They carry out many vital functions requiring active transport of various ingredients and organelles, some being small, others being large. The cytoskeleton, composed o
f three types of filaments, determines the shape of the cell and plays a role in cell motion. It also serves as a road network for the so-called cytoskeletal motors. These molecules can attach to a cytoskeletal filament, perform directed motion, possibly carrying along some cargo, and then detach. It is a central issue to understand how intracellular transport driven by molecular motors is regulated, in particular because its breakdown is one of the signatures of some neuronal diseases like the Alzheimer. We give a survey of the current knowledge on microtubule based intracellular transport. We first review some biological facts obtained from experiments, and present some modeling attempts based on cellular automata. We start with background knowledge on the original and variants of the TASEP (Totally Asymmetric Simple Exclusion Process), before turning to more application oriented models. After addressing microtubule based transport in general, with a focus on in vitro experiments, and on cooperative effects in the transportation of large cargos by multiple motors, we concentrate on axonal transport, because of its relevance for neuronal diseases. It is a challenge to understand how this transport is organized, given that it takes place in a confined environment and that several types of motors moving in opposite directions are involved. We review several features that could contribute to the efficiency of this transport, including the role of motor-motor interactions and of the dynamics of the underlying microtubule network. Finally, we discuss some still open questions.
In this paper, we explore the two-dimensional behavior of cellular automata with shuffle updates. As a test case, we consider the evacuation of a square room by pedestrians modeled by a cellular automaton model with a static floor field. Shuffle upda
tes are characterized by a variable associated to each particle and called phase, that can be interpreted as the phase in the step cycle in the frame of pedestrian flows. Here we also introduce a dynamics for these phases, in order to modify the properties of the model. We investigate in particular the crossover between low- and high-density regimes that occurs when the density of pedestrians increases, the dependency of the outflow in the strength of the floor field, and the shape of the queue in front of the exit. Eventually we discuss the relevance of these results for pedestrians.
We discuss a theoretical model for bidirectional cargo transport in biological cells, which is driven by teams of molecular motors and subject to thermal fluctuations. The model describes explicitly the directed motion of the molecular motors on the
filament. The motor-cargo coupling is implemented via linear springs. By means of extensive Monte Carlo simulations we show that the model describes the experimentally observed regimes of anomalous diffusion, i.e. subdiffusive behavior at short times followed by superdiffusion at intermediate times. The model results indicate that subdiffuse regime is induced by thermal fluctuations while the superdiffusive motion is generated by correlations of the motors activity. We also tested the efficiency of bidirectional cargo transport in crowded areas by measuring its ability to pass barriers with increased viscosity. Our results show a remarkable gain of efficiency for high viscosities.
Many different types of cellular cargos are transported bidirectionally along microtubules by teams of molecular motors. The motion of this cargo-motors system has been experimentally characterized in vivo as processive with rather persistent directi
onality. Different theoretical approaches have been suggested in order to explore the origin of this kind of motion. An effective theoretical approach, introduced by Muller et al., describes the cargo dynamics as a tug-of-war between different kinds of motors. An alternative approach has been suggested recently by Kunwar et al., who considered the coupling between motor and cargo in more detail. Based on this framework we introduce a model considering single motor positions which we propagate in continuous time. Furthermore, we analyze the possible influence of the discrete time update schemes used in previous publications on the systems dynamic.
Different families of models first developed for fluid mechanics have been extended to road, pedestrian, or intracellular transport. These models allow to describe the systems at different scales and to account for different aspects of dynamics. In t
his paper, we focus on pedestrians and illustrate the various families of models by giving an example of each type. We discuss the specificities of crowds compared to other transport systems.
Inside cells, various cargos are transported by teams of molecular motors. Intriguingly, the motors involved generally have opposite pulling directions, and the resulting cargo dynamics is a biased stochastic motion. It is an open question how the ce
ll can control this bias. Here we develop a model which takes explicitly into account the elastic coupling of the cargo with each motor. We show that bias can be simply controlled or even reversed in a counterintuitive manner via a change in the external force exerted on the cargo or a variation of the ATP binding rate to motors. Furthermore, the superdiffusive behavior found at short time scales indicates the emergence of motor cooperation induced by cargo-mediated coupling.
Driven lattice gases as the ASEP are useful tools for the modeling of various stochastic transport processes carried out by self-driven particles, such as molecular motors or vehicles in road traffic. Often these processes take place in one-dimension
al systems offering several tracks to the particles, and in many cases the particles are able to change track with a given rate. In this work we consider the case of strong coupling where the hopping rate along the tracks and the exchange rates are of the same order, and show how a phenomenological approach based on a domain wall theory can describe the dynamics of the system. In particular, the domain walls on the different tracks form pairs, whose dynamics dominate the behavior of the system.
We calculate exactly the first cumulants of the integrated current and of the activity (which is the total number of changes of configurations) of the symmetric simple exclusion process (SSEP) on a ring with periodic boundary conditions. Our results
indicate that for large system sizes the large deviation functions of the current and of the activity take a universal scaling form, with the same scaling function for both quantities. This scaling function can be understood either by an analysis of Bethe ansatz equations or in terms of a theory based on fluctuating hydrodynamics or on the macroscopic fluctuation theory of Bertini, De Sole, Gabrielli, Jona-Lasinio and Landim.
