666 research outputs found
Exact results for one dimensional stochastic cellular automata for different types of updates
We study two common types of time-noncontinuous updates for one dimensional
stochastic cellular automata with arbitrary nearest neighbor interactions and
arbitrary open boundary conditions. We first construct the stationary states
using the matrix product formalism. This construction then allows to prove a
general connection between the stationary states which are produced by the two
different types of updates. Using this connection, we derive explicit relations
between the densities and correlation functions for these different stationary
states.Comment: 7 pages, Late
A deterministic sandpile automaton revisited
The Bak-Tang-Wiesenfeld (BTW) sandpile model is a cellular automaton which
has been intensively studied during the last years as a paradigm for
self-organized criticality. In this paper, we reconsider a deterministic
version of the BTW model introduced by Wiesenfeld, Theiler and McNamara, where
sand grains are added always to one fixed site on the square lattice. Using the
Abelian sandpile formalism we discuss the static properties of the system. We
present numerical evidence that the deterministic model is only in the BTW
universality class if the initial conditions and the geometric form of the
boundaries do not respect the full symmetry of the square lattice.Comment: 7 pages, 8 figures, EPJ style, accepted for publication in European
Physical Journal
The asymmetric exclusion model with sequential update
We present a solution for the stationary state of an asymmetric exclusion
model with sequential update and open boundary conditions. We solve the model
exactly for random hopping in both directions by applying a matrix-product
formalism which was recently used to solve the model with sublattice-parallel
update[1]. It is shown that the matrix-algebra describing the sequential update
and sublattice-parallel update are identical and can be mapped onto the random
sequential case treated by Derrida et al[2].Comment: 7 pages, Late
The asymmetric exclusion process: Comparison of update procedures
The asymmetric exclusion process (ASEP) has attracted a lot of interest not
only because its many applications, e.g. in the context of the kinetics of
biopolymerization and traffic flow theory, but also because it is a
paradigmatic model for nonequilibrium systems. Here we study the ASEP for
different types of updates, namely random-sequential, sequential,
sublattice-parallel and parallel. In order to compare the effects of the
different update procedures on the properties of the stationary state, we use
large-scale Monte Carlo simulations and analytical methods, especially the
so-called matrix-product Ansatz (MPA). We present in detail the exact solution
for the model with sublattice-parallel and sequential updates using the MPA.
For the case of parallel update, which is important for applications like
traffic flow theory, we determine the phase diagram, the current, and density
profiles based on Monte Carlo simulations. We furthermore suggest a MPA for
that case and derive the corresponding matrix algebra.Comment: 47 pages (11 PostScript figures included), LATEX, Two misprints in
equations correcte
Exact density profiles for fully asymmetric exclusion process with discrete-time dynamics
Exact density profiles in the steady state of the one-dimensional fully
asymmetric simple exclusion process on semi-infinite chains are obtained in the
case of forward-ordered sequential dynamics by taking the thermodynamic limit
in our recent exact results for a finite chain with open boundaries. The
corresponding results for sublattice parallel dynamics follow from the
relationship obtained by Rajewsky and Schreckenberg [Physica A 245, 139 (1997)]
and for parallel dynamics from the mapping found by Evans, Rajewsky and Speer
[J. Stat. Phys. 95, 45 (1999)]. By comparing the asymptotic results appropriate
for parallel update with those published in the latter paper, we correct some
technical errors in the final results given there.Comment: About 10 pages and 3 figures, new references are added and a
comparison is made with the results by de Gier and Nienhuis [Phys. Rev. E 59,
4899(1999)
Mixed messages: re-initiation factors regulate translation of animal mRNAs
When ribosomes encounter upstream open reading frames (uORFs) during scanning of the 5' untranslated region (5' UTR), translation of the downstream ORF requires re-initiation. In a recent paper in Nature, Schleich et al. describe metazoan factors which specifically promote re-initiation
Identification of proteins and miRNAs that specifically bind an mRNA in vivo
Understanding regulation of an mRNA requires knowledge of its regulators. However, methods for reliable de-novo identification of proteins binding to a particular RNA are scarce and were thus far only successfully applied to abundant noncoding RNAs in cell culture. Here, we present vIPR, an RNA-protein crosslink, RNA pulldown, and shotgun proteomics approach to identify proteins bound to selected mRNAs in C. elegans. Applying vIPR to the germline-specific transcript gld-1 led to enrichment of known and novel interactors. By comparing enrichment upon gld-1 and lin-41 pulldown, we demonstrate that vIPR recovers both common and specific RNA-binding proteins, and we validate DAZ-1 as a specific gld-1 regulator. Finally, combining vIPR with small RNA sequencing, we recover known and biologically important transcript-specific miRNA interactions, and we identify miR-84 as a specific interactor of the gld-1 transcript. We envision that vIPR will provide a platform for investigating RNA in vivo regulation in diverse biological systems
circBase: a database for circular RNAs
Recently, several laboratories have reported thousands of circular RNAs (circRNAs) in animals. Numerous circRNAs are highly stable and have specific spatiotemporal expression patterns. Even though a function for circRNAs is unknown, these features make circRNAs an interesting class of RNAs as possible biomarkers and for further research. We developed a database and website, "circBase," where merged and unified data sets of circRNAs and the evidence supporting their expression can be accessed, downloaded, and browsed within the genomic context. circBase also provides scripts to identify known and novel circRNAs in sequencing data. The database is freely accessible through the web server at http://www.circbase.org/
Post-transcriptional regulation by 3' UTRs can be masked by regulatory elements in 5' UTRs
In mRNA sequences, 3' UTRs are thought to contain most elements that specifically regulate localization, turnover, and translation. Although high-throughput experiments indicate that many RNA-binding proteins (RBPs) also bind 5' UTRs, much less is known about specific post-transcriptional control exerted by 5' UTRs. GLD-1 is a conserved RBP and a translational repressor with essential roles in Caenorhabditis elegans germ cell development. Previously, we showed that GLD-1 binds highly conserved sites in both 3' and 5' UTRs. Here, by targeted single-copy insertion of transgenes, we systematically tested in vivo functionality of 5' and 3' UTR binding sites individually and in combination. Our data show that sites in 5' UTRs mediate specific and strong translational repression, independent of exact position. Intriguingly, we found that the functionality of 3' UTR sites can be masked by 5' UTR sites and vice versa. We conclude that it is important to study both UTRs simultaneously
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