Universal scaling behavior of directed percolation around the upper critical dimension

In this work we consider the steady state scaling behavior of directed percolation around the upper critical dimension. In particular we determine numerically the order parameter, its fluctuations as well as the susceptibility as a function of the control parameter and the conjugated field. Additionally to the universal scaling functions, several universal amplitude combinations are considered. We compare our results with those of a renormalization group approach.Comment: 19 pages, 8 figures, accepted for publication in J. Stat. Phy

Phase-separation transition in one-dimensional driven models

A class of models of two-species driven diffusive systems which is shown to exhibit phase separation in d=1 dimensions is introduced. Unlike previously studied models exhibiting similar phenomena, here the relative density of the two species is fluctuating within the macroscopic domain of the phase separtated state. The nature of the phase transition from the homogeneous to the phase-separated state is discussed in view of a recently introduced criterion for phase separation in one-dimensional driven systems

Genome-Wide Mapping of Uncapped and Cleaved Transcripts Reveals a Role for the Nuclear mRNA Cap-Binding Complex in Cotranslational RNA Decay in Arabidopsis

RNA turnover is necessary for controlling proper mRNA levels posttranscriptionally. In general, RNA degradation is via exoribonucleases that degrade RNA either from the 5′ end to the 3′ end, such as XRN4, or in the opposite direction by the multisubunit exosome complex. Here, we use genome-wide mapping of uncapped and cleaved transcripts to reveal the global landscape of cotranslational mRNA decay in the Arabidopsis thaliana transcriptome. We found that this process leaves a clear three nucleotide periodicity in open reading frames. This pattern of cotranslational degradation is especially evident near the ends of open reading frames, where we observe accumulation of cleavage events focused 16 to 17 nucleotides upstream of the stop codon because of ribosomal pausing during translation termination. Following treatment of Arabidopsis plants with the translation inhibitor cycloheximide, cleavage events accumulate 13 to 14 nucleotides upstream of the start codon where initiating ribosomes have been stalled with these sequences in their P site. Further analysis in xrn4 mutant plants indicates that cotranslational RNA decay is XRN4 dependent. Additionally, studies in plants lacking CAP BINDING PROTEIN80/ABA HYPERSENSITIVE1, the largest subunit of the nuclear mRNA cap binding complex, reveal a role for this protein in cotranslational decay. In total, our results demonstrate the global prevalence and features of cotranslational RNA decay in a plant transcriptome

Dynamic correlation functions and Boltzmann Langevin approach for driven one dimensional lattice gas

We study the dynamics of the totally asymmetric exclusion process with open boundaries by phenomenological theories complemented by extensive Monte-Carlo simulations. Upon combining domain wall theory with a kinetic approach known as Boltzmann-Langevin theory we are able to give a complete qualitative picture of the dynamics in the low and high density regime and at the corresponding phase boundary. At the coexistence line between high and low density phases we observe a time scale separation between local density fluctuations and collective domain wall motion, which are well accounted for by the Boltzmann-Langevin and domain wall theory, respectively. We present Monte-Carlo data for the correlation functions and power spectra in the full parameter range of the model.Comment: 10 pages, 9 figure

Spontaneous Symmetry Breaking in a Non-Conserving Two-Species Driven Model

A two species particle model on an open chain with dynamics which is non-conserving in the bulk is introduced. The dynamical rules which define the model obey a symmetry between the two species. The model exhibits a rich behavior which includes spontaneous symmetry breaking and localized shocks. The phase diagram in several regions of parameter space is calculated within mean-field approximation, and compared with Monte-Carlo simulations. In the limit where fluctuations in the number of particles in the system are taken to zero, an exact solution is obtained. We present and analyze a physical picture which serves to explain the different phases of the model

Regulatory Impact of RNA Secondary Structure across the \u3cem\u3eArabidopsis\u3c/em\u3e Transcriptome

The secondary structure of an RNA molecule plays an integral role in its maturation, regulation, and function. However, the global influence of this feature on plant gene expression is still largely unclear. Here, we use a high-throughput, sequencing-based, structure-mapping approach in conjunction with transcriptome-wide sequencing of rRNA-depleted (RNA sequencing), small RNA, and ribosome-bound RNA populations to investigate the impact of RNA secondary structure on gene expression regulation in Arabidopsis thaliana. From this analysis, we find that highly unpaired and paired RNAs are strongly correlated with euchromatic and heterochromatic epigenetic histone modifications, respectively, providing evidence that secondary structure is necessary for these RNA-mediated posttranscriptional regulatory pathways. Additionally, we uncover key structural patterns across protein-coding transcripts that indicate RNA folding demarcates regions of protein translation and likely affects microRNA-mediated regulation of mRNAs in this model plant. We further reveal that RNA folding is significantly anticorrelated with overall transcript abundance, which is often due to the increased propensity of highly structured mRNAs to be degraded and/or processed into small RNAs. Finally, we find that secondary structure affects mRNA translation, suggesting that this feature regulates plant gene expression at multiple levels. These findings provide a global assessment of RNA folding and its significant regulatory effects in a plant transcriptome

Spontaneous Symmetry Breaking in Two-Channel Asymmetric Exclusion Processes with Narrow Entrances

Multi-particle non-equilibrium dynamics in two-channel asymmetric exclusion processes with narrow entrances is investigated theoretically. Particles move on two parallel lattices in opposite directions without changing them, while the channels are coupled only at the boundaries. A particle cannot enter the corresponding lane if the exit site of the other lane is occupied. Stationary phase diagrams, particle currents and densities are calculated in a mean-field approximation. It is shown that there are four stationary phases in the system, with two of them exhibiting spontaneous symmetry breaking phenomena. Extensive Monte Carlo computer simulations confirm qualitatively our predictions, although the phase boundaries and stationary properties deviate from the mean-field results. Computer simulations indicate that several dynamic and phase properties of the system have a strong size dependency, and one of the stationary phases predicted by the mean-field theory disappears in the thermodynamic limit.Comment: 13 page

On-line Excited-State Laser Spectroscopy of Trapped Short-Lived Ra+^+ Ions

As an important step towards an atomic parity violation experiment in one single trapped Ra$^+$ ion, laser spectroscopy experiments were performed with on-line produced short-lived $^{212,213,214}$Ra$^+$ ions. The isotope shift of the 6\,^2D$_{3/2}$\,-\,7\,^2P$_{1/2}$ and 6\,^2D$_{3/2}$\,-\,7\,^2P$_{3/2}$ transitions and the hyperfine structure constant of the 7\,^2S$_{1/2}$ and 6\,^2D$_{3/2}$ states in $^{213}$Ra$^+$ were measured. These values provide a benchmark for the required atomic theory. A lower limit of $232(4)$ ms for the lifetime of the metastable 6\,^2D$_{5/2}$ state was measured by optical shelving.Comment: 4.2 pages, 6 figures, 2 tables

Improving translatability of preclinical studies for neuromuscular disorders: lessons from the TREAT-NMD Advisory Committee for Therapeutics (TACT)

Clinical trials for rare neuromuscular diseases imply, among other investments, a high emotional burden for the whole disease community. Translation of data from preclinical studies to justify any clinical trial must be carefully pondered in order to minimize the risk of clinical trial withdrawal or failure. A rigorous distinction between proof-of-concept and preclinical efficacy studies using animal models is key to support the rationale of a clinical trial involving patients. This Review evaluates the experience accumulated by the TREAT-NMD Advisory Committee for Therapeutics, which provides detailed constructive feedback on clinical proposals for neuromuscular diseases submitted by researchers in both academia and industry, and emphasizes that a timely critical review of preclinical efficacy data from animal models, including biomarkers for specific diseases, combined with adherence to existing guidelines and standard protocols, can significantly help to de-risk clinical programs and prevent disappointments and costly engagement

Measurement of the half-life of the T=12\frac{1}{2} mirror decay of 19^{19}Ne and its implication on physics beyond the standard model

The $\frac{1}{2}^+ \rightarrow \frac{1}{2}^+$ superallowed mixed mirror decay of $^{19}$Ne to $^{19}$F is excellently suited for high precision studies of the weak interaction. However, there is some disagreement on the value of the half-life. In a new measurement we have determined this quantity to be $T_{1/2}$ = $17.2832 \pm 0.0051_{(stat)}$ $\pm 0.0066_{(sys)}$ s, which differs from the previous world average by 3 standard deviations. The impact of this measurement on limits for physics beyond the standard model such as the presence of tensor currents is discussed.Comment: 5 pages, 3 figures, 1 tabl