231 research outputs found
The Advantage of Foraging Myopically
We study the dynamics of a \emph{myopic} forager that randomly wanders on a
lattice in which each site contains one unit of food. Upon encountering a
food-containing site, the forager eats all the food at this site with
probability ; otherwise, the food is left undisturbed. When the forager
eats, it can wander additional steps without food before starving
to death. When the forager does not eat, either by not detecting food on a full
site or by encountering an empty site, the forager goes hungry and comes one
time unit closer to starvation. As the forager wanders, a multiply connected
spatial region where food has been consumed---a desert---is created. The
forager lifetime depends non-monotonically on its degree of myopia , and at
the optimal myopia , the forager lives much longer than a
normal forager that always eats when it encounters food. This optimal lifetime
grows as in one dimension and faster than a
power law in in two and higher dimensions.Comment: 10 pages, 1o figure
Ultra-Slow Vacancy-Mediated Tracer Diffusion in Two Dimensions: The Einstein Relation Verified
We study the dynamics of a charged tracer particle (TP) on a two-dimensional
lattice all sites of which except one (a vacancy) are filled with identical
neutral, hard-core particles. The particles move randomly by exchanging their
positions with the vacancy, subject to the hard-core exclusion. In case when
the charged TP experiences a bias due to external electric field ,
(which favors its jumps in the preferential direction), we determine exactly
the limiting probability distribution of the TP position in terms of
appropriate scaling variables and the leading large-N ( being the discrete
time) behavior of the TP mean displacement ; the latter is
shown to obey an anomalous, logarithmic law . On comparing our results with earlier predictions by Brummelhuis
and Hilhorst (J. Stat. Phys. {\bf 53}, 249 (1988)) for the TP diffusivity
in the unbiased case, we infer that the Einstein relation
between the TP diffusivity and the mobility holds in the leading in order, despite
the fact that both and are not constant but vanish as . We also generalize our approach to the situation with very small but
finite vacancy concentration , in which case we find a ballistic-type law
. We demonstrate that here,
again, both and , calculated in the linear in
approximation, do obey the Einstein relation.Comment: 25 pages, one figure, TeX, submitted to J. Stat. Phy
Averaged residence times of stochastic motions in bounded domains
Two years ago, Blanco and Fournier (Blanco S. and Fournier R., Europhys.
Lett. 2003) calculated the mean first exit time of a domain of a particle
undergoing a randomly reoriented ballistic motion which starts from the
boundary. They showed that it is simply related to the ratio of the volume's
domain over its surface. This work was extended by Mazzolo (Mazzolo A.,
Europhys. Lett. 2004) who studied the case of trajectories which start inside
the volume. In this letter, we propose an alternative formulation of the
problem which allows us to calculate not only the mean exit time, but also the
mean residence time inside a sub-domain. The cases of any combinations of
reflecting and absorbing boundary conditions are considered. Lastly, we
generalize our results for a wide class of stochastic motions.Comment: 7 pages, 3 figure
Mean first-passage time of surface-mediated diffusion in spherical domains
We present an exact calculation of the mean first-passage time to a target on
the surface of a 2D or 3D spherical domain, for a molecule alternating phases
of surface diffusion on the domain boundary and phases of bulk diffusion. The
presented approach is based on an integral equation which can be solved
analytically. Numerically validated approximation schemes, which provide more
tractable expressions of the mean first-passage time are also proposed. In the
framework of this minimal model of surface-mediated reactions, we show
analytically that the mean reaction time can be minimized as a function of the
desorption rate from the surface.Comment: to appear in J. Stat. Phy
Kinetics of active surface-mediated diffusion in spherically symmetric domains
We present an exact calculation of the mean first-passage time to a target on
the surface of a 2D or 3D spherical domain, for a molecule alternating phases
of surface diffusion on the domain boundary and phases of bulk diffusion. We
generalize the results of [J. Stat. Phys. {\bf 142}, 657 (2011)] and consider a
biased diffusion in a general annulus with an arbitrary number of regularly
spaced targets on a partially reflecting surface. The presented approach is
based on an integral equation which can be solved analytically. Numerically
validated approximation schemes, which provide more tractable expressions of
the mean first-passage time are also proposed. In the framework of this minimal
model of surface-mediated reactions, we show analytically that the mean
reaction time can be minimized as a function of the desorption rate from the
surface.Comment: Published online in J. Stat. Phy
Facilitated diffusion of proteins on chromatin
We present a theoretical model of facilitated diffusion of proteins in the
cell nucleus. This model, which takes into account the successive
binding/unbinding events of proteins to DNA, relies on a fractal description of
the chromatin which has been recently evidenced experimentally. Facilitated
diffusion is shown quantitatively to be favorable for a fast localization of a
target locus by a transcription factor, and even to enable the minimization of
the search time by tuning the affinity of the transcription factor with DNA.
This study shows the robustness of the facilitated diffusion mechanism, invoked
so far only for linear conformations of DNA.Comment: 4 pages, 4 figures, accepted versio
Enhanced reaction kinetics in biological cells
The cell cytoskeleton is a striking example of "active" medium driven
out-of-equilibrium by ATP hydrolysis. Such activity has been shown recently to
have a spectacular impact on the mechanical and rheological properties of the
cellular medium, as well as on its transport properties : a generic tracer
particle freely diffuses as in a standard equilibrium medium, but also
intermittently binds with random interaction times to motor proteins, which
perform active ballistic excursions along cytoskeletal filaments. Here, we
propose for the first time an analytical model of transport limited reactions
in active media, and show quantitatively how active transport can enhance
reactivity for large enough tracers like vesicles. We derive analytically the
average interaction time with motor proteins which optimizes the reaction rate,
and reveal remarkable universal features of the optimal configuration. We
discuss why active transport may be beneficial in various biological examples:
cell cytoskeleton, membranes and lamellipodia, and tubular structures like
axons.Comment: 10 pages, 2 figure
First exit times and residence times for discrete random walks on finite lattices
In this paper, we derive explicit formulas for the surface averaged first
exit time of a discrete random walk on a finite lattice. We consider a wide
class of random walks and lattices, including random walks in a non-trivial
potential landscape. We also compute quantities of interest for modelling
surface reactions and other dynamic processes, such as the residence time in a
subvolume, the joint residence time of several particles and the number of hits
on a reflecting surface.Comment: 19 pages, 2 figure
The Advantage of Foraging Myopically
We study the dynamics of a \emph{myopic} forager that randomly wanders on a
lattice in which each site contains one unit of food. Upon encountering a
food-containing site, the forager eats all the food at this site with
probability ; otherwise, the food is left undisturbed. When the forager
eats, it can wander additional steps without food before starving
to death. When the forager does not eat, either by not detecting food on a full
site or by encountering an empty site, the forager goes hungry and comes one
time unit closer to starvation. As the forager wanders, a multiply connected
spatial region where food has been consumed---a desert---is created. The
forager lifetime depends non-monotonically on its degree of myopia , and at
the optimal myopia , the forager lives much longer than a
normal forager that always eats when it encounters food. This optimal lifetime
grows as in one dimension and faster than a
power law in in two and higher dimensions.Comment: 10 pages, 1o figure
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