623 research outputs found
Traffic of Molecular Motors
Molecular motors perform active movements along cytoskeletal filaments and
drive the traffic of organelles and other cargo particles in cells. In contrast
to the macroscopic traffic of cars, however, the traffic of molecular motors is
characterized by a finite walking distance (or run length) after which a motor
unbinds from the filament along which it moves. Unbound motors perform Brownian
motion in the surrounding aqueous solution until they rebind to a filament. We
use variants of driven lattice gas models to describe the interplay of their
active movements, the unbound diffusion, and the binding/unbinding dynamics. If
the motor concentration is large, motor-motor interactions become important and
lead to a variety of cooperative traffic phenomena such as traffic jams on the
filaments, boundary-induced phase transitions, and spontaneous symmetry
breaking in systems with two species of motors. If the filament is surrounded
by a large reservoir of motors, the jam length, i.e., the extension of the
traffic jams is of the order of the walking distance. Much longer jams can be
found in confined geometries such as tube-like compartments.Comment: 10 pages, latex, uses Springer styles (included), to appear in the
Proceedings of "Traffic and Granular Flow 2005
Walks of molecular motors in two and three dimensions
Molecular motors interacting with cytoskeletal filaments undergo peculiar
random walks consisting of alternating sequences of directed movements along
the filaments and diffusive motion in the surrounding solution. An ensemble of
motors is studied which interacts with a single filament in two and three
dimensions. The time evolution of the probability distribution for the bound
and unbound motors is determined analytically. The diffusion of the motors is
strongly enhanced parallel to the filament. The analytical expressions are in
excellent agreement with the results of Monte Carlo simulations.Comment: 7 pages, 2 figures, to be published in Europhys. Let
A model for bidirectional traffic of cytoskeletal motors
We introduce a stochastic lattice gas model including two particle species
and two parallel lanes. One lane with exclusion interaction and directed motion
and the other lane without exclusion and unbiased diffusion, mimicking a
micotubule filament and the surrounding solution. For a high binding affinity
to the filament, jam-like situations dominate the system's behaviour. The
fundamental process of position exchange of two particles is approximated. In
the case of a many-particle system, we were able to identify a regime in which
the system is rather homogenous presenting only small accumulations of
particles and a regime in which an important fraction of all particles
accumulates in the same cluster. Numerical data proposes that this cluster
formation will occur at all densities for large system sizes. Coupling of
several filaments leads to an enhanced cluster formation compared to the
uncoupled system, suggesting that efficient bidirectional transport on
one-dimensional filaments relies on long-ranged interactions and track
formation.Comment: 20 pages, 9 figure
Spontaneous symmetry breaking in a two-lane model for bidirectional overtaking traffic
First we consider a unidirectional flux \omega_bar of vehicles each of which
is characterized by its `natural' velocity v drawn from a distribution P(v).
The traffic flow is modeled as a collection of straight `world lines' in the
time-space plane, with overtaking events represented by a fixed queuing time
tau imposed on the overtaking vehicle. This geometrical model exhibits platoon
formation and allows, among many other things, for the calculation of the
effective average velocity w=\phi(v) of a vehicle of natural velocity v.
Secondly, we extend the model to two opposite lanes, A and B. We argue that the
queuing time \tau in one lane is determined by the traffic density in the
opposite lane. On the basis of reasonable additional assumptions we establish a
set of equations that couple the two lanes and can be solved numerically. It
appears that above a critical value \omega_bar_c of the control parameter
\omega_bar the symmetry between the lanes is spontaneously broken: there is a
slow lane where long platoons form behind the slowest vehicles, and a fast lane
where overtaking is easy due to the wide spacing between the platoons in the
opposite direction. A variant of the model is studied in which the spatial
vehicle density \rho_bar rather than the flux \omega_bar is the control
parameter. Unequal fluxes \omega_bar_A and \omega_bar_B in the two lanes are
also considered. The symmetry breaking phenomenon exhibited by this model, even
though no doubt hard to observe in pure form in real-life traffic, nevertheless
indicates a tendency of such traffic.Comment: 50 pages, 16 figures; extra references adde
Dynamics of an exclusion process with creation and annihilation
We examine the dynamical properties of an exclusion process with creation and
annihilation of particles in the framework of a phenomenological domain-wall
theory, by scaling arguments and by numerical simulation. We find that the
length- and time scale are finite in the maximum current phase for finite
creation- and annihilation rates as opposed to the algebraically decaying
correlations of the totally asymmetric simple exclusion process (TASEP).
Critical exponents of the transition to the TASEP are determined. The case
where bulk creation- and annihilation rates vanish faster than the inverse of
the system size N is also analyzed. We point out that shock localization is
possible even for rates proportional to 1/N^a, 1<a<2.Comment: 16 pages, 8 figures, typos corrected, references added, section 4
revise
Growth-Rate Dependence Reveals Design Principles of Plasmid Copy Number Control
Genetic circuits in bacteria are intimately coupled to the cellular growth rate as many parameters of gene expression are growth-rate dependent. Growth-rate dependence can be particularly pronounced for genes on plasmids; therefore the native regulatory systems of a plasmid such as its replication control system are characterized by growth-rate dependent parameters and regulator concentrations. This natural growth-rate dependent variation of regulator concentrations can be used for a quantitative analysis of the design of such regulatory systems. Here we analyze the growth-rate dependence of parameters of the copy number control system of ColE1-type plasmids in E. coli. This analysis allows us to infer the form of the control function and suggests that the Rom protein increases the sensitivity of control
Leading-effect vs. Risk-taking in Dynamic Tournaments: Evidence from a Real-life Randomized Experiment
Two 'order effects' may emerge in dynamic tournaments with information feedback. First, participants adjust effort across stages, which could advantage the leading participant who faces a larger 'effective prize' after an initial victory (leading-effect). Second, participants lagging behind may increase risk at the final stage as they have 'nothing to lose' (risk-taking). We use a randomized natural experiment in professional two-game soccer tournaments where the treatment (order of a stage-specific advantage) and team characteristics, e.g. ability, are independent. We develop an identification strategy to test for leading-effects controlling for risk-taking. We find no evidence of leading-effects and negligible risk-taking effects
Effect of promoter architecture on the cell-to-cell variability in gene expression
According to recent experimental evidence, the architecture of a promoter,
defined as the number, strength and regulatory role of the operators that
control the promoter, plays a major role in determining the level of
cell-to-cell variability in gene expression. These quantitative experiments
call for a corresponding modeling effort that addresses the question of how
changes in promoter architecture affect noise in gene expression in a
systematic rather than case-by-case fashion. In this article, we make such a
systematic investigation, based on a simple microscopic model of gene
regulation that incorporates stochastic effects. In particular, we show how
operator strength and operator multiplicity affect this variability. We examine
different modes of transcription factor binding to complex promoters
(cooperative, independent, simultaneous) and how each of these affects the
level of variability in transcription product from cell-to-cell. We propose
that direct comparison between in vivo single-cell experiments and theoretical
predictions for the moments of the probability distribution of mRNA number per
cell can discriminate between different kinetic models of gene regulation.Comment: 35 pages, 6 figures, Submitte
Voxel-based morphometry multi-center mega-analysis of brain structure in social anxiety disorder
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