Flux-tube geometry and solar wind speed during an activity cycle

The solar wind speed at 1 AU shows variations in latitude and in time which reflect the evolution of the global background magnetic field during the activity cycle. It is commonly accepted that the terminal wind speed in a magnetic flux-tube is anti-correlated with its expansion ratio, which motivated the definition of widely-used semi-empirical scaling laws relating one to the other. In practice, such scaling laws require ad-hoc corrections. A predictive law based solely on physical principles is still missing. We test whether the flux-tube expansion is the controlling factor of the wind speed at all phases of the cycle and at all latitudes using a very large sample of wind-carrying open magnetic flux-tubes. We furthermore search for additional physical parameters based on the geometry of the coronal magnetic field which have an influence on the terminal wind flow speed. We use MHD simulations of the corona and wind coupled to a dynamo model to provide a large statistical ensemble of open flux-tubes which we analyse conjointly in order to identify relations of dependence between the wind speed and geometrical parameters of the flux-tubes which are valid globally (for all latitudes and moments of the cycle). Our study confirms that the terminal speed of the solar wind depends very strongly on the geometry of the open magnetic flux-tubes through which it flows. The total flux-tube expansion is more clearly anti-correlated with the wind speed for fast rather than for slow wind flows, and effectively controls the locations of these flows during solar minima. Overall, the actual asymptotic wind speeds attained are also strongly dependent on field-line inclination and magnetic field amplitude at the foot-points. We suggest ways of including these parameters on future predictive scaling-laws for the solar wind speed.Comment: Accepted for publicaton on Astronomy & Astrophysic

A synoptic view of solar transient evolution in the inner heliosphere using the Heliospheric Imagers on STEREO

By exploiting data from the STEREO/heliospheric imagers (HI) we extend a well-established technique developed for coronal analysis by producing time-elongation plots that reveal the nature of solar transient activity over a far more extensive region of the heliosphere than previously possible from coronagraph images. Despite the simplicity of these plots, their power in demonstrating how the plethora of ascending coronal features observed near the Sun evolve as they move antisunward is obvious. The time-elongation profile of a transient tracked by HI can, moreover, be used to establish its angle out of the plane-of-the-sky; an illustration of such analysis reveals coronal mass ejection material that can be clearly observed propagating out to distances beyond 1AU. This work confirms the value of the time-elongation format in identifying/characterising transient activity in the inner heliosphere, whilst also validating the ability of HI to continuously monitor solar ejecta out to and beyond 1A

GoArrays: highly dynamic and efficient microarray probe design

MOTIVATION: The use of oligonucleotide microarray technology requires a very detailed attention to the design of specific probes spotted on the solid phase. These problems are far from being commonplace since they refer to complex physicochemical constraints. Whereas there are more and more publicly available programs for microarray oligonucleotide design, most of them use the same algorithm or criteria to design oligos, with only little variation. RESULTS: We show that classical approaches used in oligo design software may be inefficient under certain experimental conditions, especially when dealing with complex target mixtures. Indeed, our biological model is a human obligate parasite, the microsporidia Encephalitozoon cuniculi. Targets that are extracted from biological samples are composed of a mixture of pathogen transcripts and host cell transcripts. We propose a new approach to design oligonucleotides which combines good specificity with a potentially high sensitivity. This approach is original in the biological point of view as well as in the algorithmic point of view. We also present an experimental validation of this new strategy by comparing results obtained with standard oligos and with our composite oligos. A specific E.cuniculi microarray will overcome the difficulty to discriminate the parasite mRNAs from the host cell mRNAs demonstrating the power of the microarray approach to elucidate the lifestyle of an intracellular pathogen using mix mRNAs

The Longitudinal Properties of a Solar Energetic Particle Event Investigated Using Modern Solar Imaging

We use combined high-cadence, high-resolution, and multi-point imaging by the Solar-Terrestrial Relations Observatory (STEREO) and the Solar and Heliospheric Observatory to investigate the hour-long eruption of a fast and wide coronal mass ejection (CME) on 2011 March 21 when the twin STEREO spacecraft were located beyond the solar limbs. We analyze the relation between the eruption of the CME, the evolution of an Extreme Ultraviolet (EUV) wave, and the onset of a solar energetic particle (SEP) event measured in situ by the STEREO and near-Earth orbiting spacecraft. Combined ultraviolet and white-light images of the lower corona reveal that in an initial CME lateral "expansion phase," the EUV disturbance tracks the laterally expanding flanks of the CME, both moving parallel to the solar surface with speeds of ~450 km s^(–1). When the lateral expansion of the ejecta ceases, the EUV disturbance carries on propagating parallel to the solar surface but devolves rapidly into a less coherent structure. Multi-point tracking of the CME leading edge and the effects of the launched compression waves (e.g., pushed streamers) give anti-sunward speeds that initially exceed 900 km s^(–1) at all measured position angles. We combine our analysis of ultraviolet and white-light images with a comprehensive study of the velocity dispersion of energetic particles measured in situ by particle detectors located at STEREO-A (STA) and first Lagrange point (L1), to demonstrate that the delayed solar particle release times at STA and L1 are consistent with the time required (30-40 minutes) for the CME to perturb the corona over a wide range of longitudes. This study finds an association between the longitudinal extent of the perturbed corona (in EUV and white light) and the longitudinal extent of the SEP event in the heliosphere

First imaging of corotating interaction regions using the STEREO spacecraft

Plasma parcels are observed propagating from the Sun out to the large coronal heights monitored by the Heliospheric Imagers (HI) instruments onboard the NASA STEREO spacecraft during September 2007. The source region of these out-flowing parcels is found to corotate with the Sun and to be rooted near the western boundary of an equatorial coronal hole. These plasma enhancements evolve during their propagation through the HI cameras’ fields of view and only becoming fully developed in the outer camera field of view. We provide evidence that HI is observing the formation of a Corotating Interaction Region(CIR) where fast solar wind from the equatorial coronal hole is interacting with the slow solar wind of the streamer belt located on the western edge of that coronal hole. A dense plasma parcel is also observed near the footpoint of the observed CIR at a distance less than 0.1AU from the Sun where fast wind would have not had time to catch up slow wind. We suggest that this low-lying plasma enhancement is a plasma parcel which has been disconnected from a helmet streamer and subsequently becomes embedded inside the corotating interaction region

BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts

Abstract Summary: Combinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment. Availability and implementation: BioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilder. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online.</jats:p

Speeds and arrival times of solar transients approximated by self-similar expanding circular fronts

The NASA STEREO mission opened up the possibility to forecast the arrival times, speeds and directions of solar transients from outside the Sun-Earth line. In particular, we are interested in predicting potentially geo-effective Interplanetary Coronal Mass Ejections (ICMEs) from observations of density structures at large observation angles from the Sun (with the STEREO Heliospheric Imager instrument). We contribute to this endeavor by deriving analytical formulas concerning a geometric correction for the ICME speed and arrival time for the technique introduced by Davies et al. (2012, ApJ, in press) called Self-Similar Expansion Fitting (SSEF). This model assumes that a circle propagates outward, along a plane specified by a position angle (e.g. the ecliptic), with constant angular half width (lambda). This is an extension to earlier, more simple models: Fixed-Phi-Fitting (lambda = 0 degree) and Harmonic Mean Fitting (lambda = 90 degree). This approach has the advantage that it is possible to assess clearly, in contrast to previous models, if a particular location in the heliosphere, such as a planet or spacecraft, might be expected to be hit by the ICME front. Our correction formulas are especially significant for glancing hits, where small differences in the direction greatly influence the expected speeds (up to 100-200 km/s) and arrival times (up to two days later than the apex). For very wide ICMEs (2 lambda > 120 degree), the geometric correction becomes very similar to the one derived by M\"ostl et al. (2011, ApJ, 741, id. 34) for the Harmonic Mean model. These analytic expressions can also be used for empirical or analytical models to predict the 1 AU arrival time of an ICME by correcting for effects of hits by the flank rather than the apex, if the width and direction of the ICME in a plane are known and a circular geometry of the ICME front is assumed.Comment: 15 pages, 5 figures, accepted for publication in "Solar Physics

Seeds for effective oligonucleotide design

Background: DNA oligonucleotides are a very useful tool in biology. The best algorithms for designing good DNA oligonucleotides are filtering out unsuitable regions using a seeding approach. Determining the quality of the seeds is crucial for the performance of these algorithms.\ud Results: We present a sound framework for evaluating the quality of seeds for oligonucleotide design. The F-score is used to measure the accuracy of each seed. A number of natural candidates are tested: contiguous (BLAST-like), spaced, transitions-constrained, and multiple spaced seeds. Multiple spaced seeds are the best, with more seeds providing better accuracy. Single spaced and transition seeds are very close whereas, as expected, contiguous seeds come last. Increased accuracy comes at the price of reduced efficiency. An exception is that single spaced and transitions-constrained seeds are both more accurate and more efficient than contiguous ones.\ud Conclusions: Our work confirms another application where multiple spaced seeds perform the best. It will be useful in improving the algorithms for oligonucleotide desig

Natural hazards in Australia : floods

Floods are caused by a number of interacting factors, making it remarkably difficult to explain changes in flood hazard. This paper reviews the current understanding of historical trends and variability in flood hazard across Australia. Links between flood and rainfall trends cannot be made due to the influence of climate processes over a number of spatial and temporal scales as well as landscape changes that affect the catchment response. There are also still considerable uncertainties in future rainfall projections, particularly for sub-daily extreme rainfall events. This is in addition to the inherent uncertainty in hydrological modelling such as antecedent conditions and feedback mechanisms. Research questions are posed based on the current state of knowledge. These include a need for high-resolution climate modelling studies and efforts in compiling and analysing databases of sub-daily rainfall and flood records. Finally there is a need to develop modelling frameworks that can deal with the interaction between climate processes at different spatio-temporal scales, so that historical flood trends can be better explained and future flood behaviour understood