Patterns of the Ferrocyanide-Iodate-Sulfite Reaction Revisited: The Role of Immobilized Carboxylic Functions

4 pagesInternational audienceWe experimentally demonstrate that the standing lamella reaction-diffusion patterns initially observed 17 years ago in a gel-filled open spatial reactor operated with the ferrocyanide-iodate-sulfite bistable reaction requires an upper critical concentration of low-mobility species with weak acid functional groups, a parameter that was overlooked at the time and had made observations difficult to reproduce. The present approach enables the control of the space scale separation between activatory and inhibitory processes. It makes the wealth of exotic pattern dynamics observed earlier easier to reproduce and understand. This contribution should considerably revive the interest in this reaction and boost the search for the control of reaction-diffusion patterns in other bistable systems.Wave and pattern--

Modelling and comparison between lithium-ion energy storage and flywheel energy storage for households

The aim of this project is to model a flywheel that can be used as mechanical energy storage in little volumes to make it able to fit into private homes or gardens. The flywheel technology will be compared to the classic lithium-ion battery. The final objective will be, if possible, to have a theoretical product that could be manufactured and sold to private entities to make each private family or business able to completely be self-sufficient in terms of energy thanks to a solar panels system linked with this energy storage capacit

Dynamical effects induced by long range activation in a nonequilibrium reaction-diffusion system

We both show experimentally and numerically that the time scales separation introduced by long range activation can induce oscillations and excitability in nonequilibrium reaction-diffusion systems that would otherwise only exhibit bistability. Namely, we show that the Chlorite-Tetrathionate reaction, where autocatalytic species diffuses faster than the substrates, the spatial bistability domain in the nonequilibrium phase diagram is extended with oscillatory and excitability domains. A simple model and a more realistic model qualitatively account for the observed behavior. The latter model provides quantitative agreement with the experiments.Comment: 19 pages + 9 figure

MusicDiff: A Diff Tool for MEI

For musicologists, the collation of multiple sources of the same work is a frequent task. By comparing different witnesses, they seek to identify variation, describe dependencies, and ultimately understand the genesis and transmission of (musical) works. Obviously, the need for such comparison is independent from the medium in which a musical work is manifested. In computing, comparing files for difference is a common task, and the well-known Unix utility diff is almost 46 years old. However, diff, like many other such tools, operates on plain text. While many music encoding formats based on plain text exist, formats used in the field of Digital Humanities are typically based on XML. There are dedicated algorithms for comparing XML as well,1 but they only focus on the syntax of XML, but not the semantic structures modelled into such standards as MEI. MEI seeks to describe musical structures, and the XML syntax is just a means to express those structures. A diff tool for music should focus on comparing musical structures, but not the specifics of their serialization into a file format. In Beethovens Werkstatt, a 16-year project focussed on exploring the concepts and requirements of digital genetic editions of music, based on and arguing with examples from Ludwig van Beethoven, a case-bound diff tool for music was developed. The following paper discusses how that specific tool can be generalized, and which use cases such a tool may support

Crafting TabMEI, a Module for Encoding Instrumental Tablatures

In this progress report, we describe the issues encountered during the design and implementation of TabMEI, a new MEI module for encoding instrumental tablatures. We discuss the main challenges faced and lay out our workflow for implementing the TabMEI module. In addition, we present a number of example encodings, and we describe anticipated applications of the module

Turing Instability in a Boundary-fed System

The formation of localized structures in the chlorine dioxide-idodine-malonic acid (CDIMA) reaction-diffusion system is investigated numerically using a realistic model of this system. We analyze the one-dimensional patterns formed along the gradients imposed by boundary feeds, and study their linear stability to symmetry-breaking perturbations (Turing instability) in the plane transverse to these gradients. We establish that an often-invoked simple local linear analysis which neglects longitudinal diffusion is inappropriate for predicting the linear stability of these patterns. Using a fully nonuniform analysis, we investigate the structure of the patterns formed along the gradients and their stability to transverse Turing pattern formation as a function of the values of two control parameters: the malonic acid feed concentration and the size of the reactor in the dimension along the gradients. The results from this investigation are compared with existing experiments.Comment: 41 pages, 18 figures, to be published in Physical Review

Targeted Chromatin Capture (T2C): A novel high resolution high throughput method to detect genomic interactions and regulatory elements.

Background: Significant efforts have recently been put into the investigation of the spatial organization and the chromatin-interaction networks of genomes. Chromosome conformation capture (3C) technology and its derivatives are important tools used in this effort. However, many of these have limitations, such as being limited to one viewpoint, expensive with moderate to low resolution, and/or requiring a large sequencing effort. Techniques like Hi-C provide a genome-wide analysis. However, it requires massive sequencing effort with considerable costs. Here we describe a new technique termed Targeted Chromatin Capture (T2C), to interrogate large selected regions of the genome. T2C provides an unbiased view of the spatial organization of selected loci at superior resolution (single restriction fragment resolution, from 2 to 6 kbp) at much lower costs than Hi-C due to the lower sequencing effort. Results: We applied T2C on well-known model regions, the mouse β-globin locus and the human H19/IGF2 locus. In both cases we identified all known chromatin interactions. Furthermore, we compared the human H19/IGF2 locus data obtained from different chromatin conformation capturing methods with T2C data. We observed the same compartmentalization of the locus, but at a much higher resolution (single restriction fragments vs. the common 40 kbp bins) and higher coverage. Moreover, we compared the β-globin locus in two different biological samples (mouse primary erythroid cells and mouse fetal brain), where it is either actively transcribed or not, to identify possible transcriptional dependent interactions. We identified the known interactions in the β-globin locus and the same topological domains in both mouse primary erythroid cells and in mouse fetal brain with the latter having fewer interactions probably due to the inactivity of the locus. Furthermore, we show that interactions due to the important chromatin proteins, Ldb1 and Ctcf, in both tissues can be analyzed easily to reveal their role on transcriptional interactions and genome folding. Conclusions: T2C is an efficient, easy, and affordable with high (restriction fragment) resolution tool to address both genome compartmentalization and chromatin-interaction networks for specific genomic regions at high resolution for both clinical and non-clinical research

Phase Dynamics of Nearly Stationary Patterns in Activator-Inhibitor Systems

The slow dynamics of nearly stationary patterns in a FitzHugh-Nagumo model are studied using a phase dynamics approach. A Cross-Newell phase equation describing slow and weak modulations of periodic stationary solutions is derived. The derivation applies to the bistable, excitable, and the Turing unstable regimes. In the bistable case stability thresholds are obtained for the Eckhaus and the zigzag instabilities and for the transition to traveling waves. Neutral stability curves demonstrate the destabilization of stationary planar patterns at low wavenumbers to zigzag and traveling modes. Numerical solutions of the model system support the theoretical findings

DNA Sequence Patterns – A Successful Example of Grid Computing in Genome Research and Building Virtual Super-Computers for the Research Commons of e-Societies

The amount of information is growing exponentially with ever-new technologies emerging and is believed to be always at the limit. In contrast, huge resources are obviously available, which are underused in the IT sector, similar as e.g. in the renewable energy sector. Genome research is one of the boosting areas, which needs an extreme amount of IT resources to analyse the sequential organization of genomes, i.e. the relations between distant base pairs and regions within sequences, and its connection to the three-dimensional organization of genomes, which is still a largely unresolved problem. The underusage of resources as those accessible by grid with its fast turnover rates is very astonishing considering the barriers for further development put forward by the inability to satisfy the need for such resources. The phenomenon is a typical example of the Inverse Tragedy of the Commons, i.e. resources are underexploited in contrast to the unsustainable and destructing overexploitation in the Classic Tragedy of the Commons. An analysis of IT and the grid sector which attempts to share resources for better usage efficiency, reveals two challenges, which lead to the heart of the paradox: i) From a macro perspective all grid infrastructures involve not only mere technical solutions but also dominantly all of the autopoietic social sub-systems ranging from religion to policy. ii) On the micro level the individual players and their psychology and risk behaviour are of major importance for acting within the macro autopoietic framework. Consequently, the challenges of grid implementation are similar to those of other pressing global issues as e.g. climate protection. This is well described by extending the Human Ecology triangle to a rectangle: invironment-individual-society-environment. By applying this extension of this classical field of interdisciplinary basic and applied research to the grid sector, i.e. by further extension to an e-Human Grid Ecology rational, the Grid Inverse Tragedy of the Commons can be understood and approached regarding the internalization challenge into e-Society and e-Life, from which then guidelines for the day-to-day management can be derived. This is of general importance for many complex fields and thus with similar paradoxes and challenges. By using grid Long-range power-law correlations were found using correlation analysis on almost the entire observable scale of 132 completely sequenced chromosomes of 0.5x106 to 3.0x107 bp from Archaea, Bacteria, Arabidopsis thaliana, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens. The local correlation coeffi

Nuclear expression of PG-21, SRC-1, and pCREB in regions of the lumbosacral spinal cord involved in pelvic innervation in young adult and aged rats

In rats, ageing results in dysfunctional patterns of micturition and diminished sexual reflexes that may reflect degenerative changes within spinal circuitry. In both sexes the dorsal lateral nucleus and the spinal nucleus of the bulbospongiosus, which lie in the L5-S1 spinal segments, contain motor neurons that innervate perineal muscles, and the external anal and urethral sphincters. Neurons in the sacral parasympathetic nucleus of these segments provide autonomic control of the bladder, cervix and penis and other lower urinary tract structures. Interneurons in the dorsal gray commissure and dorsal horn have also been implicated in lower urinary tract function. This study investigates the cellular localisation of PG-21 androgen receptors, steroid receptor co-activator one (SRC-1) and the phosphorylated form of c-AMP response element binding protein (pCREB) within these spinal nuclei. These are components of signalling pathways that mediate cellular responses to steroid hormones and neurotrophins. Nuclear expression of PG-21 androgen receptors, SRC-1 and pCREB in young and aged rats was quantified using immunohistochemistry. There was a reduction in the number of spinal neurons expressing these molecules in the aged males while in aged females, SRC-1 and pCREB expression was largely unchanged. This suggests that the observed age-related changes may be linked to declining testosterone levels. Acute testosterone therapy restored expression of PG-21 androgen receptor in aged and orchidectomised male rats, however levels of re-expression varied within different nuclei suggesting a more prolonged period of hormone replacement may be required for full restoratio