571 research outputs found
Connecting protein and mRNA burst distributions for stochastic models of gene expression
The intrinsic stochasticity of gene expression can lead to large variability
in protein levels for genetically identical cells. Such variability in protein
levels can arise from infrequent synthesis of mRNAs which in turn give rise to
bursts of protein expression. Protein expression occurring in bursts has indeed
been observed experimentally and recent studies have also found evidence for
transcriptional bursting, i.e. production of mRNAs in bursts. Given that there
are distinct experimental techniques for quantifying the noise at different
stages of gene expression, it is of interest to derive analytical results
connecting experimental observations at different levels. In this work, we
consider stochastic models of gene expression for which mRNA and protein
production occurs in independent bursts. For such models, we derive analytical
expressions connecting protein and mRNA burst distributions which show how the
functional form of the mRNA burst distribution can be inferred from the protein
burst distribution. Additionally, if gene expression is repressed such that
observed protein bursts arise only from single mRNAs, we show how observations
of protein burst distributions (repressed and unrepressed) can be used to
completely determine the mRNA burst distribution. Assuming independent
contributions from individual bursts, we derive analytical expressions
connecting means and variances for burst and steady-state protein
distributions. Finally, we validate our general analytical results by
considering a specific reaction scheme involving regulation of protein bursts
by small RNAs. For a range of parameters, we derive analytical expressions for
regulated protein distributions that are validated using stochastic
simulations. The analytical results obtained in this work can thus serve as
useful inputs for a broad range of studies focusing on stochasticity in gene
expression
A Persistent Kuroshio in the Glacial East China Sea and Implications for Coral Paleobiogeography
The Kuroshio Current is a major hydrographical feature of the modern East China Sea, but it has been suggested that its flow was diverted to the east of the Ryukyu Arc at the Last Glacial Maximum. Shoaling of the Yonaguni Depression has also been proposed as a cause of Kuroshio Current diversion which, while unlikely to have been significant at the Last Glacial Maximum, may have been an important consideration further back in time. Using an ensemble of highāresolution ocean simulations with climatic boundary conditions emulating those of the Last Glacial Maximum, we present the first regional state estimates of the glacial East China Sea which are both physically consistent and compatible with sea surface temperature proxy compilations. We find that while the Kuroshio Current transport in the East China Sea is slightly reduced at the Last Glacial Maximum, its path is relatively unchanged, with limited sensitivity to glacioeustatic sea level change, glacialāinterglacial changes in climate, and tectonic shoaling of the Yonaguni Depression. Simulations with the best modelāproxy agreement predict only limited contraction of the reef front at the Last Glacial Maximum, and strong surface currents associated with the glacial Kuroshio may have maintained or even improved longādistance coral larval dispersal along the Ryukyu Arc, suggesting that conditions may have enabled coral reefs in this region to remain widespread throughout the last glacial. Further field studies investigating whether this is genuinely the case will provide insights into how the coral reef front responds to longāterm environmental change
Instability of dilute granular flow on rough slope
We study numerically the stability of granular flow on a rough slope in
collisional flow regime in the two-dimension. We examine the density dependence
of the flowing behavior in low density region, and demonstrate that the
particle collisions stabilize the flow above a certain density in the parameter
region where a single particle shows an accelerated behavior. Within this
parameter regime, however, the uniform flow is only metastable and is shown to
be unstable against clustering when the particle density is not high enough.Comment: 4 pages, 6 figures, submitted to J. Phys. Soc. Jpn.; Fig. 2 replaced;
references added; comments added; misprints correcte
Macroscopic traffic models from microscopic car-following models
We present a method to derive macroscopic fluid-dynamic models from
microscopic car-following models via a coarse-graining procedure. The method is
first demonstrated for the optimal velocity model. The derived macroscopic
model consists of a conservation equation and a momentum equation, and the
latter contains a relaxation term, an anticipation term, and a diffusion term.
Properties of the resulting macroscopic model are compared with those of the
optimal velocity model through numerical simulations, and reasonable agreement
is found although there are deviations in the quantitative level. The
derivation is also extended to general car-following models.Comment: 12 pages, 4 figures; to appear in Phys. Rev.
Steady state solutions of hydrodynamic traffic models
We investigate steady state solutions of hydrodynamic traffic models in the
absence of any intrinsic inhomogeneity on roads such as on-ramps. It is shown
that typical hydrodynamic models possess seven different types of inhomogeneous
steady state solutions. The seven solutions include those that have been
reported previously only for microscopic models. The characteristic properties
of wide jam such as moving velocity of its spatiotemporal pattern and/or
out-flux from wide jam are shown to be uniquely determined and thus independent
of initial conditions of dynamic evolution. Topological considerations suggest
that all of the solutions should be common to a wide class of traffic models.
The results are discussed in connection with the universality conjecture for
traffic models. Also the prevalence of the limit-cycle solution in a recent
study of a microscopic model is explained in this approach.Comment: 9 pages, 6 figure
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