1,739 research outputs found
Hydrodynamic mean field solutions of 1D exclusion processes with spatially varying hopping rates
We analyze the open boundary partially asymmetric exclusion process with
smoothly varying internal hopping rates in the infinite-size, mean field limit.
The mean field equations for particle densities are written in terms of Ricatti
equations with the steady-state current as a parameter. These equations are
solved both analytically and numerically. Upon imposing the boundary conditions
set by the injection and extraction rates, the currents are found
self-consistently. We find a number of cases where analytic solutions can be
found exactly or approximated. Results for from asymptotic analyses for
slowly varying hopping rates agree extremely well with those from extensive
Monte Carlo simulations, suggesting that mean field currents asymptotically
approach the exact currents in the hydrodynamic limit, as the hopping rates
vary slowly over the lattice. If the forward hopping rate is greater than or
less than the backward hopping rate throughout the entire chain, the three
standard steady-state phases are preserved. Our analysis reveals the
sensitivity of the current to the relative phase between the forward and
backward hopping rate functions.Comment: 12 pages, 4 figure
The triple-mode pulsating variable V823 Cas
Based on extended multicolour CCD photometry of the triple-mode radial
pulsator V823 Cas we studied the properties of the coupling frequencies invoked
by nonlinear processes. Our results support that a resonance connection as
suggested by Antonello & Aikawa (1998) affects the mode coupling behaviour. The
P1/P0 period ratio of V823 Cas has an "out of range" value if compared with the
period ratios of the known double mode pulsators, while the P2/P1 period ratio
is normal. The periods and period ratios cannot be consistently interpret
without conflict with pulsation and/or evolution models. We attempt to
interpret this failure by the suggestion that at present, the periods of V823
Cas are in a transient, resonance affected state, thus do not reflect the true
parameters of the object. The anomalous period change behaviour of the
fundamental and second overtone modes supports this idea. We have also raised
the possibility that a f0 + f2 = 2f1 resonance may act in triple mode
pulsators.Comment: 10 pages, 7 figures, 5 tables. Accepted for publication in Astronomy
and Astrophysic
Time-Dependent Density Functional Theory for Driven Lattice Gas Systems with Interactions
We present a new method to describe the kinetics of driven lattice gases with
particle-particle interactions beyond hard-core exclusions. The method is based
on the time-dependent density functional theory for lattice systems and allows
one to set up closed evolution equations for mean site occupation numbers in a
systematic manner. Application of the method to a totally asymmetric site
exclusion process with nearest-neighbor interactions yields predictions for the
current-density relation in the bulk, the phase diagram of non-equilibrium
steady states and the time evolution of density profiles that are in good
agreement with results from kinetic Monte Carlo simulations.Comment: 11 pages, 3 figure
Climate Change Effects on Apple and Sour Cherry Phenology in a Gene Bank Plantation of Hungary
The trees observed were grown at Újfehértó, Eastern Hungary in a gene bank with 586 apple and 3 sour cherry cultivars. Each of the cultivars was monitored for its dates of: the beginning of bloom, main bloom and the end of bloom phenophases separately. In the present study, the interactions between the above mentioned phenomena are presented and numerically defined. Results presented proved that the dynamics of weather variables exert measurable effects on the development of fruits. We can find significant correlation between the maximum temperature of March and blooming time of the apple and sour cherry cultivars. If the temperature is increasing in the future the development stages of fruit trees will also shift to an earlier time. It is a serious problem in fruit farming, because the early climatic risk of frost occurrence is generally higher than that of in later times of a year. So, we will need to use more effective protection technologies and new extreme weather tolerant fruit varieties in the future. We should also pay more attention to the time intervals between the blooming and maturity, because the length and appearance of phenological phases have significant influences on quantitative and qualitative parameters of fruits
Two-Channel Totally Asymmetric Simple Exclusion Processes
Totally asymmetric simple exclusion processes, consisting of two coupled
parallel lattice chains with particles interacting with hard-core exclusion and
moving along the channels and between them, are considered. In the limit of
strong coupling between the channels, the particle currents, density profiles
and a phase diagram are calculated exactly by mapping the system into an
effective one-channel totally asymmetric exclusion model. For intermediate
couplings, a simple approximate theory, that describes the particle dynamics in
vertical clusters of two corresponding parallel sites exactly and neglects the
correlations between different vertical clusters, is developed. It is found
that, similarly to the case of one-channel totally asymmetric simple exclusion
processes, there are three stationary state phases, although the phase
boundaries and stationary properties strongly depend on inter-channel coupling.
An extensive computer Monte Carlo simulations fully support the theoretical
predictions.Comment: 13 pages, 10 figure
Local Inhomogeneity in Asymmetric Simple Exclusion Processes with Extended Objects
Totally asymmetric simple exclusion processes (TASEP) with particles which
occupy more than one lattice site and with a local inhomogeneity far away from
the boundaries are investigated. These non-equilibrium processes are relevant
for the understanding of many biological and chemical phenomena. The
steady-state phase diagrams, currents, and bulk densities are calculated using
a simple approximate theory and extensive Monte Carlo computer simulations. It
is found that the phase diagram for TASEP with a local inhomogeneity is
qualitatively similar to homogeneous models, although the phase boundaries are
significantly shifted. The complex dynamics is discussed in terms of
domain-wall theory for driven lattice systems.Comment: 11 pages, 5 figure
Competition for finite resources
The resources in a cell are finite, which implies that the various components
of the cell must compete for resources. One such resource is the ribosomes used
during translation to create proteins. Motivated by this example, we explore
this competition by connecting two totally asymmetric simple exclusion
processes (TASEPs) to a finite pool of particles. Expanding on our previous
work, we focus on the effects on the density and current of having different
entry and exit rates.Comment: 15 pages, 9 figures, v2: minor revisions, v3: additional reference &
minor correction
Power spectra of TASEPs with a localized slow site
The totally asymmetric simple exclusion process (TASEP) with a localized
defect is revisited in this article with attention paid to the power spectra of
the particle occupancy N(t). Intrigued by the oscillatory behaviors in the
power spectra of an ordinary TASEP in high/low density phase(HD/LD) observed by
Adams et al. (2007 Phys. Rev. Lett. 99 020601), we introduce a single slow site
with hopping rate q<1 to the system. As the power spectrum contains
time-correlation information of the particle occupancy of the system, we are
particularly interested in how the defect affects fluctuation in particle
number of the left and right subsystems as well as that of the entire system.
Exploiting Monte Carlo simulations, we observe the disappearance of
oscillations when the defect is located at the center of the system. When the
defect is off center, oscillations are restored. To explore the origin of such
phenomenon, we use a linearized Langevin equation to calculate the power
spectrum for the sublattices and the whole lattice. We provide insights into
the interactions between the sublattices coupled through the defect site for
both simulation and analytical results.Comment: 16 pages, 6 figures; v2: Minor revision
Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding
Ribosome is a molecular machine that polymerizes a protein where the sequence
of the amino acid residues, the monomers of the protein, is dictated by the
sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that
serves as the template. The ribosome is a molecular motor that utilizes the
template mRNA strand also as the track. Thus, in each step the ribosome moves
forward by one codon and, simultaneously, elongates the protein by one amino
acid. We present a theoretical model that captures most of the main steps in
the mechano-chemical cycle of a ribosome. The stochastic movement of the
ribosome consists of an alternating sequence of pause and translocation; the
sum of the durations of a pause and the following translocation is the time of
dwell of the ribosome at the corresponding codon. We derive the analytical
expression for the distribution of the dwell times of a ribosome in our model.
Whereever experimental data are available, our theoretical predictions are
consistent with those results. We suggest appropriate experiments to test the
new predictions of our model, particularly, the effects of the quality control
mechanism of the ribosome and that of their crowding on the mRNA track.Comment: This is an author-created, un-copyedited version of an article
accepted for publication in Physical Biology. IOP Publishing Ltd is not
responsible for any errors or omissions in this version of the manuscript or
any version derived from it. The definitive publisher authenticated version
is available online at DOI:10.1088/1478-3975/8/2/02600
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