Communique, 26 January 2004

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Proximity DC squids in the long junction limit

We report the design and measurement of Superconducting/normal/superconducting (SNS) proximity DC squids in the long junction limit, i.e. superconducting loops interrupted by two normal metal wires roughly a micrometer long. Thanks to the clean interface between the metals, at low temperature a large supercurrent flows through the device. The dc squid-like geometry leads to an almost complete periodic modulation of the critical current through the device by a magnetic flux, with a flux periodicity of a flux quantum h/2e through the SNS loop. In addition, we examine the entire field dependence, notably the low and high field dependence of the maximum switching current. In contrast with the well-known Fraunhoffer-type oscillations typical of short wide junctions, we find a monotonous gaussian extinction of the critical current at high field. As shown in [15], this monotonous dependence is typical of long and narrow diffusive junctions. We also find in some cases a puzzling reentrance at low field. In contrast, the temperature dependence of the critical current is well described by the proximity effect theory, as found by Dubos {\it et al.} [16] on SNS wires in the long junction limit. The switching current distributions and hysteretic IV curves also suggest interesting dynamics of long SNS junctions with an important role played by the diffusion time across the junction.Comment: 12 pages, 16 figure

Direct measurement of the phase coherence length in a GaAs/GaAlAs square network

The low temperature magnetoconductance of a large array of quantum coherentloops exhibits Altshuler-Aronov-Spivak oscillations which periodicitycorresponds to 1/2 flux quantum per loop.We show that the measurement of the harmonics content in a square networkprovides an accurate way to determine the electron phase coherence length$L\_{\phi}$ in units of the lattice length without any adjustableparameters.We use this method to determine $L\_{\phi}$ in a network realised from a 2Delectron gas (2DEG) in a GaAS/GaAlAs heterojunction. The temperaturedependence follows a power law $T^{-1/3}$ from 1.3 K to 25 mK with nosaturation, as expected for 1D diffusive electronic motion andelectron-electron scattering as the main decoherence mechanism.Comment: Additional experimental data in version

The MOLDY short-range molecular dynamics package

We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron-carbon alloy

RAPD and microsatellite transferability studies in selected species of Prosopis (section Algarobia) with emphasis on Prosopis juliflora and P. pallida

The genus Prosopis (Leguminosae, Mimosoideae), comprises 44 species widely distributed in arid and semi-arid zones. Prosopis pallida (Humb. & Bonpl. ex Willd.) Kunth and P. juliflora (Sw.) DC. are the two species that are truly tropical apart from P. africana, which is native to tropical Africa (Pasiecznik et al. 2004), and they have been introduced widely beyond their native ranges. However, taxonomic confusion within the genus has hampered exploitation and better management of the species. The present study focusses primarily on evaluating the genetic relationship between Prosopis species from the section Algarobia, containing most species of economic importance, though P. tamarugo from section Strombocarpa is also included for comparison. In total, 12 Prosopis species and a putative P. pallida × P. chilensis hybrid were assessed for their genetic relationships based on RAPD markers and microsatellite transferability. The results show that P. pallida and P. juliflora are not closely related despite some morphological similarity. Evidence also agrees with previous studies which suggest that the grouping of series in section Algarobia is artificial

Overview of EU national legislation on genomics

With the advent of fast, high efficiency and low cost DNA sequencing techniques, the ability to study the human genome by reading the sequence of its DNA is growing exponentially, with a resulting tremendous impact on many fields of scientific research. The application of genomics inside routine healthcare is boosting preventive medicine practices and can lead to personalised treatments that can highly improve the healthcare services and patients' health, and in the same time provide a wealth of data for medical research. In parallel, this has also led to the spread of commercial opportunities to provide consumers with the possibility of sequencing their genomes in a way which is both appealing and affordable. These commercial offers, however, do not always ensure the security of the generated data. In addition, the accuracy and reliability of the offered findings are not homogenous, as there are no standards to guarantee that the quality of the outputs satisfies minimum requirements - in fact, no agreements yet exist on the definition of these requirements. In this frame, a comprehensive knowledge of what is present at the legislative level in the member states of the European Union (plus Switzerland, Iceland and Norway) regarding the regulatory oversight of genomics technologies is of fundamental importance to frame the status of existing European norms, to understand whether possible incompatibilities might arise between frameworks and to highlight eventual gaps

Linking epigenetics and biological conservation: Towards a conservation epigenetics perspective

International audience1. Biodiversity conservation is a global issue where the challenge is to integrate all levels of biodiversity to ensure the long-term evolutionary potential and resilience of biological systems. Genetic approaches have largely contributed to conservation biology by defining "conservation entities" accounting for their evolutionary history and adaptive potential, the so-called evolutionary significant units (ESUs). Yet, these approaches only loosely integrate the short-term ecological history of organisms. 2. Here, we argue that epigenetic variation, and more particularly DNA methylation, represents a molecular component of biodiversity that directly links the genome to the environment. As such, it provides the required information on the ecological background of organisms for an integrative field of conservation biology. 3. We synthesize knowledge about the importance of epigenetic mechanisms in (a) orchestrating fundamental development alternatives in organisms, (b) enabling individuals to respond in real-time to selection pressures and (c) improving ecosystem stability and functioning. 4. Using practical examples in conservation biology, we illustrate the relevance of DNA methylation (a) as biomarkers of past and present environmental stress events as well as biomarkers of physiological conditions of individuals; (b) for documenting the ecological structuring/clustering of wild populations and hence for better integrating ecology into ESUs; (c) for improving conservation transloca-tions; and (d) for studying landscape functional connectivity. 5. We conclude that an epigenetic conservation perspective will provide environmental managers the possibility to refine ESUs, to set conservation plans taking into account the capacity of organisms to rapidly cope with environmental changes, and hence to improve the conservation of wild populations. K E Y W O R D S conservation, DNA methylation, ecological timescales, epigenetic, evolutionary significant unit

A stochastic method for Bayesian estimation of hidden Markov random field models with application to a color model

Abstract—We propose a new stochastic algorithm for computing useful Bayesian estimators of hidden Markov random field (HMRF) models that we call exploration/selection/estimation (ESE) procedure. The algorithm is based on an optimization algorithm of O. François, called the exploration/selection (E/S) algorithm. The novelty consists of using the a posteriori distribution of the HMRF, as exploration distribution in the E/S algorithm. The ESE procedure computes the estimation of the likelihood parameters and the optimal number of region classes, according to global constraints, as well as the segmentation of the image. In our formulation, the total number of region classes is fixed, but classes are allowed or disallowed dynamically. This framework replaces the mechanism of the split-and-merge of regions that can be used in the context of image segmentation. The procedure is applied to the estimation of a HMRF color model for images, whose likelihood is based on multivariate distributions, with each component following a Beta distribution. Meanwhile, a method for computing the maximum likelihood estimators of Beta distributions is presented. Experimental results performed on 100 natural images are reported. We also include a proof of convergence of the E/S algorithm in the case of nonsymmetric exploration graphs. Index Terms—Bayesian estimation of hidden Markov random field (HMRF) models, color model, exploration/selection (E/S) algorithm, image segmentation, maximum likelihood (ML) estimation of Beta distributions. I