Coronal Loop Expansion Properties Explained Using Separators

One puzzling observed property of coronal loops is that they are of roughly constant thickness along their length. Various studies have found no consistent pattern of width variation along the length of loops observed by TRACE and SOHO. This is at odds with expectations of magnetic flux tube expansion properties, which suggests that loops are widest at their tops, and significantly narrower at their footpoints. Coronal loops correspond to areas of the solar corona which have been preferentially heated by some process, so this observed property might be connected to the mechanisms that heat the corona. One means of energy deposition is magnetic reconnection, which occurs along field lines called separators. These field lines begin and end on magnetic null points, and loops forming near them can therefore be relatively wide at their bases. Thus, coronal energization by magnetic reconnection may replicate the puzzling expansion properties observed in coronal loops. We present results of a Monte Carlo survey of separator field line expansion properties, comparing them to the observed properties of coronal loops.Comment: 16 pages, 9 figures, to be submitted to Ap

The Role of fast magnetosonic waves in the release and conversion via reconnection of energy stored by a current sheet

Using a simple two-dimensional, zero-beta model, we explore the manner by which reconnection at a current sheet releases and dissipates free magnetic energy. We find that only a small fraction (3%-11% depending on current sheet size) of the energy is stored close enough to the current sheet to be dissipated abruptly by the reconnection process. The remaining energy, stored in the larger-scale field, is converted to kinetic energy in a fast magnetosonic disturbance propagating away from the reconnection site, carrying the initial current and generating reconnection-associated flows (inflow and outflow). Some of this reflects from the lower boundary (the photosphere) and refracts back to the X-point reconnection site. Most of this inward wave energy is reflected back again, and continues to bounce between X-point and photosphere until it is gradually dissipated, over many transits. This phase of the energy dissipation process is thus global and lasts far longer than the initial purely local phase. In the process a significant fraction of the energy (25%-60%) remains as undissipated fast magnetosonic waves propagating away from the reconnection site, primarily upward. This flare-generated wave is initiated by unbalanced Lorentz forces in the reconnection-disrupted current sheet, rather than by dissipation-generated pressure, as some previous models have assumed. Depending on the orientation of the initial current sheet the wave front is either a rarefaction, with backward directed flow, or a compression, with forward directed flow

Special features of RAD Sequencing data:implications for genotyping

Restriction site-associated DNA Sequencing (RAD-Seq) is an economical and efficient method for SNP discovery and genotyping. As with other sequencing-by-synthesis methods, RAD-Seq produces stochastic count data and requires sensitive analysis to develop or genotype markers accurately. We show that there are several sources of bias specific to RAD-Seq that are not explicitly addressed by current genotyping tools, namely restriction fragment bias, restriction site heterozygosity and PCR GC content bias. We explore the performance of existing analysis tools given these biases and discuss approaches to limiting or handling biases in RAD-Seq data. While these biases need to be taken seriously, we believe RAD loci affected by them can be excluded or processed with relative ease in most cases and that most RAD loci will be accurately genotyped by existing tools

The glitch activity of neutron stars

We present a statistical study of the glitch population and the behaviour of the glitch activity across the known population of neutron stars. An unbiased glitch database was put together based on systematic searches of radio timing data of 898 rotation-powered pulsars obtained with the Jodrell Bank and Parkes observatories. Glitches identified in similar searches of 5 magnetars were also included. The database contains 384 glitches found in the rotation of 141 of these neutron stars. We confirm that the glitch size distribution is at least bimodal, with one sharp peak at approximately $20\, \rm{\mu\,Hz}$, which we call large glitches, and a broader distribution of smaller glitches. We also explored how the glitch activity $\dot{\nu}_{\rm{g}}$, defined as the mean frequency increment per unit of time due to glitches, correlates with the spin frequency $\nu$, spin-down rate $|\dot{\nu}|$, and various combinations of these, such as energy loss rate, magnetic field, and spin-down age. It is found that the activity is insensitive to the magnetic field and that it correlates strongly with the energy loss rate, though magnetars deviate from the trend defined by the rotation-powered pulsars. However, we find that a constant ratio $\dot\nu_{\rm{g}}/|\dot\nu| = 0.010 \pm 0.001$ is consistent with the behaviour of all rotation-powered pulsars and magnetars. This relation is dominated by large glitches, which occur at a rate directly proportional to $|\dot{\nu}|$. The only exception are the rotation-powered pulsars with the highest values of $|\dot{\nu}|$, such as the Crab pulsar and PSR B0540$-$69, which exhibit a much smaller glitch activity, intrinsically different from each other and from the rest of the population. The activity due to small glitches also shows an increasing trend with $|\dot\nu|$, but this relation is biased by selection effects.Comment: Accepted for publication in A&

Consequences of spontaneous reconnection at a two-dimensional non-force-free current layer

Magnetic neutral points, where the magnitude of the magnetic field vanishes locally, are potential locations for energy conversion in the solar corona. The fact that the magnetic field is identically zero at these points suggests that for the study of current sheet formation and of any subsequent resistive dissipation phase, a finite beta plasma should be considered, rather than neglecting the plasma pressure as has often been the case in the past. The rapid dissipation of a finite current layer in non-force-free equilibrium is investigated numerically, after the sudden onset of an anomalous resistivity. The aim of this study is to determine how the energy is redistributed during the initial diffusion phase, and what is the nature of the outward transmission of information and energy. The resistivity rapidly diffuses the current at the null point. The presence of a plasma pressure allows the vast majority of the free energy to be transferred into internal energy. Most of the converted energy is used in direct heating of the surrounding plasma, and only about 3% is converted into kinetic energy, causing a perturbation in the magnetic field and the plasma which propagates away from the null at the local fast magnetoacoustic speed. The propagating pulses show a complex structure due to the highly non-uniform initial state. It is shown that this perturbation carries no net current as it propagates away from the null. The fact that, under the assumptions taken in this paper, most of the magnetic energy released in the reconnection converts internal energy of the plasma, may be highly important for the chromospheric and coronal heating problem

Dwindling Surface Cooling of a Rotating Jovian Planet Leads to a Convection Zone that Grows to a Finite Depth

Recent measurements of Jupiter's gravitational field (by Juno) and seismology of Saturn's rings (by Cassini) strongly suggest that both planets have a stably-stratified core that still possesses a primordial gradient in the concentration of heavy elements. The existence of such a "diffusely" stratified core has been a surprise as it was long expected that the Jovian planets should be fully convective and hence fully mixed. A vigorous zone of convection, driven by surface cooling, forms at the surface and deepens through entrainment of fluid from underneath. In fact, it was believed that this convection zone should grow so rapidly that the entire planet would be consumed in less than a million years. Here we suggest that two processes, acting in concert, present a solution to this puzzle. All of the giant planets are rapidly rotating and have a cooling rate that declines with time. Both of these effects reduce the rate of fluid entrainment into the convection zone. Through the use of an analytic prescription of entrainment in giant planets, we demonstrate that these two effects, rotation and dwindling surface cooling, result in a convection zone which initially grows but eventually stalls. The depth to which the convective interface asymptotes depends on the rotation rate and on the stratification of the stable interior. Conversely, in a nonrotating planet, or in a planet that maintains a higher level of cooling than current models suggest, the convection zone deepens forever, eventually spanning the entire planet.Comment: 7 pages, 2 figures, accepted for publication by Astrophysical Journal Letter

Magnetohydrodynamics dynamical relaxation of coronal magnetic fields. II. 2D magnetic X-points

We provide a valid magnetohydrostatic equilibrium from the collapse of a 2D X-point in the presence of a finite plasma pressure, in which the current density is not simply concentrated in an infinitesimally thin, one-dimensional current sheet, as found in force-free solutions. In particular, we wish to determine if a finite pressure current sheet will still involve a singular current, and if so, what is the nature of the singularity. We use a full MHD code, with the resistivity set to zero, so that reconnection is not allowed, to run a series of experiments in which an X-point is perturbed and then is allowed to relax towards an equilibrium, via real, viscous damping forces. Changes to the magnitude of the perturbation and the initial plasma pressure are investigated systematically. The final state found in our experiments is a "quasi-static" equilibrium where the viscous relaxation has completely ended, but the peak current density at the null increases very slowly following an asymptotic regime towards an infinite time singularity. Using a high grid resolution allows us to resolve the current structures in this state both in width and length. In comparison with the well known pressureless studies, the system does not evolve towards a thin current sheet, but concentrates the current at the null and the separatrices. The growth rate of the singularity is found to be tD, with 0 < D < 1. This rate depends directly on the initial plasma pressure, and decreases as the pressure is increased. At the end of our study, we present an analytical description of the system in a quasi-static non-singular equilibrium at a given time, in which a finite thick current layer has formed at the null

Quantification of the morphological characteristics of hESC colonies

The maintenance of the undifferentiated state in human embryonic stem cells (hESCs) is critical for further application in regenerative medicine, drug testing and studies of fundamental biology. Currently, the selection of the best quality cells and colonies for propagation is typically performed by eye, in terms of the displayed morphological features, such as prominent/abundant nucleoli and a colony with a tightly packed appearance and a well-defined edge. Using image analysis and computational tools, we precisely quantify these properties using phase-contrast images of hESC colonies of different sizes (0.1–1.1 mm2) during days 2, 3 and 4 after plating. Our analyses reveal noticeable differences in their structure influenced directly by the colony area A. Large colonies (A > 0.6 mm2) have cells with smaller nuclei and a short intercellular distance when compared with small colonies (A  0.6 mm2) due to the proliferation of the cells in the bulk. This increases the colony density and the number of nearest neighbours. We also detect the self-organisation of cells in the colonies where newly divided (smallest) cells cluster together in patches, separated from larger cells at the final stages of the cell cycle. This might influence directly cell-to-cell interactions and the community effects within the colonies since the segregation induced by size differences allows the interchange of neighbours as the cells proliferate and the colony grows. Our findings are relevant to efforts to determine the quality of hESC colonies and establish colony characteristics database

Quantification of the morphological characteristics of hESC colonies

The maintenance of the pluripotent state in human embryonic stem cells (hESCs) is critical for further application in regenerative medicine, drug testing and studies of fundamental biology. Currently, the selection of the best quality cells and colonies for propagation is typically performed by eye, in terms of the displayed morphological features, such as prominent/abundant nucleoli and a colony with a tightly packed appearance and a well-defined edge. Using image analysis and computational tools, we precisely quantify these properties using phase-contrast images of hESC colonies of different sizes (0.1 -- 1.1$\, \text{mm}^2$) during days 2, 3 and 4 after plating. Our analyses reveal noticeable differences in their structure influenced directly by the colony area $A$. Large colonies ($A > 0.6 \, \text{mm}^2$) have cells with smaller nuclei and a short intercellular distance when compared with small colonies ($A < 0.2 \, \text{mm}^2$). The gaps between the cells, which are present in small and medium sized colonies with $A \le 0.6 \, \text{mm}^2$, disappear in large colonies ($A > 0.6 \, \text{mm}^2$) due to the proliferation of the cells in the bulk. This increases the colony density and the number of nearest neighbours. We also detect the self-organisation of cells in the colonies where newly divided (smallest) cells cluster together in patches, separated from larger cells at the final stages of the cell cycle. This might influence directly cell-to-cell interactions and the community effects within the colonies since the segregation induced by size differences allows the interchange of neighbours as the cells proliferate and the colony grows. Our findings are relevant to efforts to determine the quality of hESC colonies and establish colony characteristics database