87 research outputs found
Pseudochemotaxis in inhomogeneous active Brownian systems
We study dynamical properties of confined, self-propelled Brownian particles
in an inhomogeneous activity profile. Using Brownian dynamics simulations, we
calculate the probability to reach a fixed target and the mean first passage
time to the target of an active particle. We show that both these quantities
are strongly influenced by the inhomogeneous activity. When the activity is
distributed such that high-activity zone is located between the target and the
starting location, the target finding probability is increased and the passage
time is decreased in comparison to a uniformly active system. Moreover, for a
continuously distributed profile, the activity gradient results in a drift of
active particle up the gradient bearing resemblance to chemotaxis. Integrating
out the orientational degrees of freedom, we derive an approximate
Fokker-Planck equation and show that the theoretical predictions are in very
good agreement with the Brownian dynamics simulations.Comment: 7 pages, 5 figure
Facilitated diffusion of DNA-binding proteins
The diffusion-controlled limit of reaction times for site-specific
DNA-binding proteins is derived from first principles. We follow the generally
accepted concept that a protein propagates via two competitive modes, a
three-dimensional diffusion in space and a one-dimensional sliding along the
DNA. However, our theoretical treatment of the problem is new. The accuracy of
our analytical model is verified by numerical simulations. The results confirm
that the unspecific binding of protein to DNA, combined with sliding, is
capable to reduce the reaction times significantly.Comment: 4 pages, 2 figures Nov 22 2005 - accepted for PR
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Chain stiffness effect on the properties of topological polymer brushes and the penetration by free chains using MD simulation
Molecular dynamic simulations are carried out to study the static and dynamic properties of topological polymer brushes by taking into account chain stiffness and their topological feature. It is found that chain stiffness plays an important role in topological polymer brushes, and there exists scaling laws for the radius of gyration against chain stiffness and topological feature, indicating that bending interaction is as important as topological constraint. An empirical finitely extensible nonlinear elastic force in terms of chain stiffness and topological features is also obtained by fitting related parameters. A simulation on the invasion of free polymer chains from environment into a ring polymer brush shows that under pressure, such kind of penetration depends largely on chain stiffness, in contrast to the minor influence of topological structure, which seems to be suppressed
Facilitated diffusion of DNA-binding proteins: Simulation of large systems
The recently introduced method of excess collisions (MEC) is modified to
estimate diffusion-controlled reaction times inside systems of arbitrary size.
The resulting MEC-E equations contain a set of empirical parameters, which have
to be calibrated in numerical simulations inside a test system of moderate
size. Once this is done, reaction times of systems of arbitrary dimensions are
derived by extrapolation, with an accuracy of 10 to 15 percent. The achieved
speed up, when compared to explicit simulations of the reaction process, is
increasing proportional to the extrapolated volume of the cell.Comment: 8 pages, 4 figures, submitted to J. Chem. Phy
Modelling diffusional transport in the interphase cell nucleus
In this paper a lattice model for diffusional transport of particles in the
interphase cell nucleus is proposed. Dense networks of chromatin fibers are
created by three different methods: randomly distributed, non-interconnected
obstacles, a random walk chain model, and a self avoiding random walk chain
model with persistence length. By comparing a discrete and a continuous version
of the random walk chain model, we demonstrate that lattice discretization does
not alter particle diffusion. The influence of the 3D geometry of the fiber
network on the particle diffusion is investigated in detail, while varying
occupation volume, chain length, persistence length and walker size. It is
shown that adjacency of the monomers, the excluded volume effect incorporated
in the self avoiding random walk model, and, to a lesser extent, the
persistence length, affect particle diffusion. It is demonstrated how the
introduction of the effective chain occupancy, which is a convolution of the
geometric chain volume with the walker size, eliminates the conformational
effects of the network on the diffusion, i.e., when plotting the diffusion
coefficient as a function of the effective chain volume, the data fall onto a
master curve.Comment: 9 pages, 8 figure
Chemotaxis of cargo-carrying self-propelled particles
Active particles with their characteristic feature of self-propulsion are
regarded as the simplest models for motility in living systems. The
accumulation of active particles in low activity regions has led to the general
belief that chemotaxis requires additional features and at least a minimal
ability to process information and to control motion. We show that
self-propelled particles display chemotaxis and move into regions of higher
activity, if the particles perform work on passive objects, or cargo, to which
they are bound. The origin of this cooperative chemotaxis is the exploration of
the activity gradient by the active particle when bound to a load, resulting in
an average excess force on the load in the direction of higher activity. Using
a minimalistic theoretical model, we capture the most relevant features of
these active-passive dimers and in particular we predict the crossover between
anti-chemotactic and chemotactic behaviour. Moreover we show that merely
connecting active particles to chains is sufficient to obtain the crossover
from anti-chemotaxis to chemotaxis with increasing chain length. Such an active
complex is capable of moving up a gradient of activity such as provided by a
gradient of fuel and to accumulate where the fuel concentration is at its
maximum. The observed transition is of significance to proto-forms of life
enabling them to locate a source of nutrients even in the absence of any
supporting sensomotoric apparatus
Pseudo-chemotaxis of active Brownian particles competing for food
Using Brownian dynamics simulations, the motion of active Brownian particles
(ABPs) in the presence of fuel (or 'food') sources is studied. It is an
established fact that within confined stationary systems, the activity of ABPs
generates density profiles that are enhanced in regions of low activity, which
is generally referred to as 'anti-chemotaxis'. We demonstrate that -- contrary
to common believes -- in non-stationary setups, emerging here as a result of
short fuel bursts, our model ABPs do instead exhibit signatures of chemotactic
behavior. In direct competition with inactive, but otherwise identical Brownian
particles (BPs), the ABPs are shown to fetch a larger amount of food. From a
biological perspective, the ability to turn active would, despite of the
absence of sensoric devices, encompass an evolutionary advantage.Comment: 6 pages, 7 figure
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