Ribosome recycling induces optimal translation rate at low ribosomal availability

Funding statement The authors thank BBSRC (BB/F00513/X1, BB/I020926/1 and DTG) and SULSA for funding. Acknowledgement The authors thank R. Allen, L. Ciandrini, B. Gorgoni and P. Greulich for very helpful discussions and careful reading of the manuscript.Peer reviewedPublisher PD

Spatial Autocorrelation Analysis for New FUA Inner Strategic Asset: A Case Study of the Metropolitan City of Milan, Italy

Functional urban areas represent integrated urban contexts whose territories are economically interconnected. They, therefore, include a central city and all the municipalities that make up the commuting area for work reasons. The economic energies and settlement transformations that characterize these territories have been consolidated over time. The current geographic conformation, as defined today, does not provide information on each municipality's rank (role) in the overall functioning. In this perspective, the work presented examines the demographic and urban dynamics that have affected the FUA of Milan in the last 60 years and then evaluates the presence of possible homogeneous geographic clusters (hot and cold spots) through spatial correlation techniques. Statistic validation was performed through the ANOVA and subsequent posthoc analysis (Tukey-Kramer method). Results show a new configurational asset within the FUA of Milan, which could provide a new key to interpreting the territory, aimed at identifying homogeneous areas to adopt new and more effective forms of strategic planning

Robust statistics for deterministic and stochastic gravitational waves in non-Gaussian noise. II. Bayesian analyses

In a previous paper (paper I), we derived a set of near-optimal signal detection techniques for gravitational wave detectors whose noise probability distributions contain non-Gaussian tails. The methods modify standard methods by truncating or clipping sample values which lie in those non-Gaussian tails. The methods were derived, in the frequentist framework, by minimizing false alarm probabilities at fixed false detection probability in the limit of weak signals. For stochastic signals, the resulting statistic consisted of a sum of an autocorrelation term and a cross-correlation term; it was necessary to discard “by hand” the autocorrelation term in order to arrive at the correct, generalized cross-correlation statistic. In the present paper, we present an alternative derivation of the same signal detection techniques from within the Bayesian framework. We compute, for both deterministic and stochastic signals, the probability that a signal is present in the data, in the limit where the signal-to-noise ratio squared per frequency bin is small, where the signal is nevertheless strong enough to be detected (integrated signal-to-noise ratio large compared to 1), and where the total probability in the non-Gaussian tail part of the noise distribution is small. We show that, for each model considered, the resulting probability is to a good approximation a monotonic function of the detection statistic derived in paper I. Moreover, for stochastic signals, the new Bayesian derivation automatically eliminates the problematic autocorrelation term

Sequence-dependent thermodynamics of a coarse-grained DNA model

We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with average sequences. The new parametrization introduces sequence-dependent stacking and base-pairing interaction strengths chosen to reproduce the melting temperatures of short duplexes. By developing a histogram reweighting technique, we are able to fit our parameters to the melting temperatures of thousands of sequences. To demonstrate the flexibility of the model, we study the effects of sequence on: (a) the heterogeneous stacking transition of single strands, (b) the tendency of a duplex to fray at its melting point, (c) the effects of stacking strength in the loop on the melting temperature of hairpins, (d) the force-extension properties of single strands and (e) the structure of a kissing-loop complex. Where possible we compare our results with experimental data and find a good agreement. A simulation code called oxDNA, implementing our model, is available as free software.Comment: 15 page

Searching for supergiant fast X-ray transients with Swift

Supergiant fast X-ray transients (SFXTs) are high mass X-ray binaries (HMXBs) hosting a neutron star and an OB supergiant companion. We examine the available Swift data, as well as other new or archival/serendipitous data, on three sources: IGR J17407-2808, 2XMM J185114.3-000004, and IGR J18175-2419, whose X-ray characteristics qualify them as candidate SFXT, in order to explore their properties and test whether they are consistent with an SFXT nature. As IGR J17407-2808 and 2XMM J185114.3-000004 triggered the Burst Alert Telescope on board Swift, the Swift data allow us to provide their first arcsecond localisations, leading to an unequivocal identification of the source CXOU J174042.0-280724 as the soft X-ray counterpart of IGR J17407-2808, as well as their first broadband spectra, which can be fit with models generally describing accreting neutron stars in HMXBs. While still lacking optical spectroscopy to assess the spectral type of the companion, we propose 2XMM J185114.3-000004 as a very strong SFXT candidate. The nature of IGR J17407-2808 remains, instead, more uncertain. Its broad band properties cannot exclude that the emission originates from either a HMXB (and in that case, a SFXT) or, more likely, a low mass X-ray binary. Finally, based on the deep non-detection in our XRT monitoring campaign and a careful reanalysis of the original Integral data in which the discovery of the source was first reported, we show that IGR J18175-2419 is likely a spurious detection.Comment: Accepted for publication in Astronomy and Astrophysics. 12 pages, 11 figures, 6 table

Impact of positivity and complete positivity on accessibility of Markovian dynamics

We consider a two-dimensional quantum control system evolving under an entropy-increasing irreversible dynamics in the semigroup form. Considering a phenomenological approach to the dynamics, we show that the accessibility property of the system depends on whether its evolution is assumed to be positive or completely positive. In particular, we characterize the family of maps having different accessibility and show the impact of that property on observable quantities by means of a simple physical model.Comment: 11 pages, to appear in J. Phys.

Improved cache performance in Monte Carlo transport calculations using energy banding

We present an energy banding algorithm for Monte Carlo (MC) neutral particle transport simulations which depend on large cross section lookup tables. In MC codes, read-only cross section data tables are accessed frequently, exhibit poor locality, and are typically too much large to fit in fast memory. Thus, performance is often limited by long latencies to RAM, or by off-node communication latencies when the data footprint is very large and must be decomposed on a distributed memory machine. The proposed energy banding algorithm allows maximal temporal reuse of data in band sizes that can flexibly accommodate different architectural features. The energy banding algorithm is general and has a number of benefits compared to the traditional approach. In the present analysis we explore its potential to achieve improvements in time-to-solution on modern cache-based architectures.United States. Department of Energy. Office of Science (Contract DE-AC02-06CH11357

Galactic Cosmic Rays from Superbubbles and the Abundances of Lithium, Beryllium, and Boron

In this article we study the galactic evolution of the LiBeB elements within the framework of a detailed model of the chemical evolution of the Galaxy that includes galactic cosmic ray nucleosynthesis by particles accelerated in superbubbles. The chemical composition of the superbubble consists of varying proportions of ISM and freshly supernova synthesized material. The observational trends of 6 LiBeB evolution are nicely reproduced by models in which GCR come from a mixture of 25% of supernova material with 75% of ISM, except for 6 Li, for which maybe an extra source is required at low metallicities. To account for 7 Li evolution several additional sources have been considered (neutrino-induced nucleosynthesis, nova outbursts, C-stars). The model fulfills the energetic requirements for GCR acceleration.Comment: 25 pages, 9 figures. Accepted for publication in the Astrophysical Journa