2,200 research outputs found
The Asymmetric Exclusion Process revisited: Fluctuations and Dynamics in the Domain Wall Picture
We investigate the total asymmetric exclusion process by analyzing the
dynamics of the shock. Within this approach we are able to calculate the
fluctuations of the number of particles and density profiles not only in the
stationary state but also in the transient regime. We find that the analytical
predictions and the simulation results are in excellent agreement.Comment: 6 figures. Submitted to J. Stat. Phy
Zone clearance in an infinite TASEP with a step initial condition
The TASEP is a paradigmatic model of out-of-equilibrium statistical physics,
for which many quantities have been computed, either exactly or by approximate
methods. In this work we study two new kinds of observables that have some
relevance in biological or traffic models. They represent the probability for a
given clearance zone of the lattice to be empty (for the first time) at a given
time, starting from a step density profile. Exact expressions are obtained for
single-time quantities, while more involved history-dependent observables are
studied by Monte Carlo simulation, and partially predicted by a
phenomenological approach
Environmental control of microtubule-based bidirectional cargo-transport
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 cell 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
Intracellular transport driven by cytoskeletal motors: General mechanisms and defects
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 of 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.Comment: 74 pages, 43 figure
Two dimensional outflows for cellular automata with shuffle updates
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 updates 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.Comment: 20 pages, 5 figures. v2: 16 pages, 5 figures; changed the title,
abstract and structure of the paper. v3: minor change
Motility states in bidirectional cargo transport
Intracellular cargos which are transported by molecular motors move
stochastically along cytoskeleton filaments. In particular for bidirectionally
transported cargos it is an open question whether the characteristics of their
motion can result from pure stochastic fluctuations or whether some
coordination of the motors is needed. The results of a mean-field model of
cargo-motors dynamics, which was proposed by M\"uller et al.[1] suggest the
existence of high motility states which would result from a stochastic
tug-of-war. Here we analyze a non-mean field extension of their model, that
takes explicitly the position of each motor into account. We find that high
motility states then disappear. We consider also a mutual motor-motor
activation, as an explicit mechanism of motor coordination. We show that the
results of the mean-field model are recovered only in case of a strong
motor-motor activation in the limit of a high number of motors.Comment: 6 pages, 10 figure
Fluctuation effects in bidirectional cargo transport
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.Comment: 10 pages, 6 figure
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