Fluctuation-dissipation relations in trap models

Trap models are intuitively appealing and often solvable models of glassy dynamics. In particular, they have been used to study aging and the resulting out-of-equilibrium fluctuation-dissipation relations between correlations and response functions. In this note I show briefly that one such relation, first given by Bouchaud and Dean, is valid for a general class of mean-field trap models: it relies only on the way a perturbation affects the transition rates, but is independent of the distribution of trap depths and the form of the unperturbed transition rates, and holds for all observables that are uncorrelated with the energy. The model with Glauber dynamics and an exponential distribution of trap depths, as considered by Barrat and Mezard, does not fall into this class if the perturbation is introduced in the standard way by shifting all trap energies. I show that a similar relation between response and correlation nevertheless holds for the out-of-equilibrium dynamics at low temperatures. The results point to intriguing parallels between trap models with energetic and entropic barriers.Comment: Extended introduction and discussion of relation to results of cond-mat/0303445. 13 pages, 2 figures, IOP styl

Multiple scaling regimes in simple aging models

We investigate aging in glassy systems based on a simple model, where a point in configuration space performs thermally activated jumps between the minima of a random energy landscape. The model allows us to show explicitly a subaging behavior and multiple scaling regimes for the correlation function. Both the exponents characterizing the scaling of the different relaxation times with the waiting time and those characterizing the asymptotic decay of the scaling functions are obtained analytically by invoking a `partial equilibrium' concept.Comment: 4 pages, 3 figure

Two Physically Distinct Populations of Low-Ionization Nuclear Emission-Line Regions

The nature of Low-ionization Nuclear Emission-line Regions (LINERs) has been an open question for a long time. We study the properties of LINERs from several different aspects. The LINERs are found to consist of two different categories that can be clearly separated in the traditional BPT diagrams, especially in the [OI]/Ha vs. [OIII]/Hb diagram. LINERs with high [O]/Ha ratios (population I) differ from ones with low ratios (population II) in several properties. Broad emission lines are only identified in the spectra of population I LINERs. While only the population II LINERs show luminous infrared emission and occurrence of core-collapse supernovae in the host. Combining these results with the known distribution of stellar populations not only suggests that the two populations have different line excitation mechanisms, but also implies that they are at different evolutionary stages.Comment: 12 pages, 2 figures, accepted by ApJ Lette

Electrical Integrity Tests during Production of the LHC Dipoles

For the LHC dipoles, mandatory electrical integrity tests are performed to qualify the cold mass (CM) at four production stages: individual pole, collared coil, CM before end cover welding and final CM. A description of the measurement equipment and its recent development are presented. After passing the demands set out in the specification, the results of the tests are transmitted to CERN where they are further analyzed. The paper presents the most important results of these measurements. We also report a review of the electrical non-conformities encountered e.g. interturn shorts and quench heater failure, their diagnostic and the cures

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

Long noncoding RNAs (lncRNAs) comprise a diverse class of transcripts that structurally resemble mRNAs but do not encode proteins. Recent genome-wide studies in humans and the mouse have annotated lncRNAs expressed in cell lines and adult tissues, but a systematic analysis of lncRNAs expressed during vertebrate embryogenesis has been elusive. To identify lncRNAs with potential functions in vertebrate embryogenesis, we performed a time-series of RNA-seq experiments at eight stages during early zebrafish development. We reconstructed 56,535 high-confidence transcripts in 28,912 loci, recovering the vast majority of expressed RefSeq transcripts while identifying thousands of novel isoforms and expressed loci. We defined a stringent set of 1133 noncoding multi-exonic transcripts expressed during embryogenesis. These include long intergenic ncRNAs (lincRNAs), intronic overlapping lncRNAs, exonic antisense overlapping lncRNAs, and precursors for small RNAs (sRNAs). Zebrafish lncRNAs share many of the characteristics of their mammalian counterparts: relatively short length, low exon number, low expression, and conservation levels comparable to that of introns. Subsets of lncRNAs carry chromatin signatures characteristic of genes with developmental functions. The temporal expression profile of lncRNAs revealed two novel properties: lncRNAs are expressed in narrower time windows than are protein-coding genes and are specifically enriched in early-stage embryos. In addition, several lncRNAs show tissue-specific expression and distinct subcellular localization patterns. Integrative computational analyses associated individual lncRNAs with specific pathways and functions, ranging from cell cycle regulation to morphogenesis. Our study provides the first systematic identification of lncRNAs in a vertebrate embryo and forms the foundation for future genetic, genomic, and evolutionary studies.National Human Genome Research Institute (U.S.) (Grant 1RO1HG005111-01

Aging, rejuvenation and memory phenomena in spin glasses

In this paper, we review several important features of the out-of-equilibrium dynamics of spin glasses. Starting with the simplest experiments, we discuss the scaling laws used to describe the isothermal aging observed in spin glasses after a quench down to the low temperature phase. We report in particular new results on the sub-aging behaviour of spin glasses. We then discuss the rejuvenation and memory effects observed when a spin glass is submitted to temperature variations during aging, from the point of view of both energy landscape pictures and of real space pictures. We highlight the fact that both approaches point out the necessity of hierarchical processes involved in aging. Finally, we report an investigation of the effect of small temperature variations on aging in spin glass samples with various anisotropies which indicates that this hierarchy depends on the spin anisotropy.Comment: submitted for the Proceedings of Stat Phys 22, Bangalore (India

Wind Energy and the Turbulent Nature of the Atmospheric Boundary Layer

Wind turbines operate in the atmospheric boundary layer, where they are exposed to the turbulent atmospheric flows. As the response time of wind turbine is typically in the range of seconds, they are affected by the small scale intermittent properties of the turbulent wind. Consequently, basic features which are known for small-scale homogeneous isotropic turbulence, and in particular the well-known intermittency problem, have an important impact on the wind energy conversion process. We report on basic research results concerning the small-scale intermittent properties of atmospheric flows and their impact on the wind energy conversion process. The analysis of wind data shows strongly intermittent statistics of wind fluctuations. To achieve numerical modeling a data-driven superposition model is proposed. For the experimental reproduction and adjustment of intermittent flows a so-called active grid setup is presented. Its ability is shown to generate reproducible properties of atmospheric flows on the smaller scales of the laboratory conditions of a wind tunnel. As an application example the response dynamics of different anemometer types are tested. To achieve a proper understanding of the impact of intermittent turbulent inflow properties on wind turbines we present methods of numerical and stochastic modeling, and compare the results to measurement data. As a summarizing result we find that atmospheric turbulence imposes its intermittent features on the complete wind energy conversion process. Intermittent turbulence features are not only present in atmospheric wind, but are also dominant in the loads on the turbine, i.e. rotor torque and thrust, and in the electrical power output signal. We conclude that profound knowledge of turbulent statistics and the application of suitable numerical as well as experimental methods are necessary to grasp these unique features (...)Comment: Accepted by the Journal of Turbulence on May 17, 201

The lncRNA HOTAIR transcription is controlled by HNF4α-induced chromatin topology modulation

The expression of the long noncoding RNA HOTAIR (HOX Transcript Antisense Intergenic RNA) is largely deregulated in epithelial cancers and positively correlates with poor prognosis and progression of hepatocellular carcinoma and gastrointestinal cancers. Furthermore, functional studies revealed a pivotal role for HOTAIR in the epithelial-to-mesenchymal transition, as this RNA is causal for the repressive activity of the master factor SNAIL on epithelial genes. Despite the proven oncogenic role of HOTAIR, its transcriptional regulation is still poorly understood. Here hepatocyte nuclear factor 4-α (HNF4α), as inducer of epithelial differentiation, was demonstrated to directly repress HOTAIR transcription in the mesenchymal-to epithelial transition. Mechanistically, HNF4α was found to cause the release of a chromatin loop on HOTAIR regulatory elements thus exerting an enhancer-blocking activity

Resolving mechanisms of immune-mediated disease in primary CD4 T cells

ABSTRACT Deriving mechanisms of immune-mediated disease from GWAS data remains a formidable challenge, with attempts to identify causal variants being frequently hampered by linkage disequilibrium. To determine whether causal variants could be identified via their functional effects, we adapted a massively-parallel reporter assay for use in primary CD4 T-cells, key effectors of many immune-mediated diseases. Using the results to guide further study, we provide a generalisable framework for resolving disease mechanisms from non-coding associations – illustrated by a locus linked to 6 immune-mediated diseases, where the lead functional variant causally disrupts a super-enhancer within an NF-κB-driven regulatory circuit, triggering unrestrained T-cell activation

The Snail repressor recruits EZH2 to specific genomic sites through the enrollment of the lncRNA HOTAIR in epithelial-to-mesenchymal transition

The transcription factor Snail is a master regulator of cellular identity and epithelial-to-mesenchymal transition (EMT) directly repressing a broad repertoire of epithelial genes. How chromatin modifiers instrumental to its activity are recruited to Snail-specific binding sites is unclear. Here we report that the long non-coding RNA (lncRNA) HOTAIR (for HOX Transcript Antisense Intergenic RNA) mediates a physical interaction between Snail and enhancer of zeste homolog 2 (EZH2), an enzymatic subunit of the polycomb-repressive complex 2 and the main writer of chromatin-repressive marks. The Snail-repressive activity, here monitored on genes with a pivotal function in epithelial and hepatic morphogenesis, differentiation and cell-type identity, depends on the formation of a tripartite Snail/HOTAIR/EZH2 complex. These results demonstrate an lncRNA-mediated mechanism by which a transcriptional factor conveys a general chromatin modifier to specific genes, thereby allowing the execution of hepatocyte transdifferentiation; moreover, they highlight HOTAIR as a crucial player in the Snail-mediated EMT.Oncogene advance online publication, 25 July 2016; doi:10.1038/onc.2016.260