Abstract:
We investigate simulated turbulent flow within thermally driven stellar convection zones. Different driving sources are studied, including cooling at the top of the convectively unstable region, as occurs in surface convection zones; and heating at the base by nuclear burning. The transport of enthalpy and kinetic energy, and the distribution of turbulent kinetic energy dissipation are studied. We emphasize the importance of global constraints on shaping the quasi-steady flow characteristics, and present an analysis of turbulent convection which is posed as a boundary value problem that can be easily incorporated into standard stellar evolution codes for deep, efficient convection. Direct comparison is made between the theoretical analysis and the simulated flow and very good agreement is found. Some common assumptions traditionally used to treat quasi-steady turbulent flow in stellar models are briefly discussed. The importance and proper treatment of convective boundaries are indicated.

Abstract:
A program is outlined, and first results described, in which fully three-dimensional, time dependent simulations of hydrodynamic turbulence are used as a basis for theoretical investigation of the physics of turbulence in stars. The inadequacy of the treatment of turbulent convection as a diffusive process is discussed. A generalization to rotation and magnetohydrodynamics is indicated, as are connection to simulations of 3D stellar atmospheres.

Abstract:
Simulations of core-collapse supernovae (CCSNe) result in successful explosions once the neutrino luminosity exceeds a critical curve, and recent simulations indicate that turbulence further enables explosion by reducing this critical neutrino luminosity. We propose a theoretical framework to derive this result and take the first steps by deriving the governing mean-field equations. Using Reynolds decomposition, we decompose flow variables into background and turbulent flows and derive self-consistent averaged equations for their evolution. As basic requirements for the CCSN problem, these equations naturally incorporate steady-state accretion, neutrino heating and cooling, non-zero entropy gradients, and turbulence terms associated with buoyant driving, redistribution, and dissipation. Furthermore, analysis of two-dimensional (2D) CCSN simulations validate these Reynolds-averaged equations, and we show that the physics of turbulence entirely accounts for the differences between 1D and 2D CCSN simulations. As a prelude to deriving the reduction in the critical luminosity, we identify the turbulent terms that most influence the conditions for explosion. Generically, turbulence equations require closure models, but these closure models depend upon the macroscopic properties of the flow. To derive a closure model that is appropriate for CCSNe, we cull the literature for relevant closure models and compare each with 2D simulations. These models employ local closure approximations and fail to reproduce the global properties of neutrino-driven turbulence. Motivated by the generic failure of these local models, we propose an original model for turbulence which incorporates global properties of the flow. This global model accurately reproduces the turbulence profiles and evolution of 2D CCSN simulations.

Abstract:
Three-dimensional (3D) hydrodynamic simulations of shell oxygen burning (Meakin and Arnett 2007) exhibit bursty, recurrent fluctuations in turbulent kinetic energy. These are shown to be due to a global instability in the convective region, which has been suppressed in calculations of stellar evolution which use mixing-length theory (MLT). Quantitatively similar behavior occurs in the model of a convective roll (cell) of Lorenz (1963), which is known to have a strange attractor that gives rise to random fluctuations in time.An extension of the Lorenz model, which includes Kolmogorov damping and nuclear burning, is shown to exhibit bursty, recurrent fluctuations like those seen in the 3D simulations. A simple model of a convective layer (composed of multiple Lorenz cells) gives luminosity fluctuations which are suggestive of irregular variables (red giants and supergiants, Schwarzschild 1975). Apparent inconsistencies between Arnett, Meakin, and Young (2009) and Nordlund, Stein, and Asplund (2009) on the nature of convective driving have been resolved, and are discussed.

Abstract:
Three-dimensional (3D) hydrodynamic simulations of shell oxygen burning (Meakin and Arnett, 2007b) exhibit bursty, recurrent fluctuations in turbulent kinetic energy. These are shown to be due to a general instability of the convective cell, requiring only a localized source of heating or cooling. Such fluctuations are shown to be suppressed in simulations of stellar evolution which use mixing-length theory (MLT). Quantitatively similar behavior occurs in the model of a convective roll (cell) of Lorenz (1963), which is known to have a strange attractor that gives rise to chaotic fluctuations in time of velocity and, as we show, luminosity. Study of simulations suggests that the behavior of a Lorenz convective roll may resemble that of a cell in convective flow. We examine some implications of this simplest approximation, and suggest paths for improvement. Using the Lorenz model as representative of a convective cell, a multiple-cell model of a convective layer gives total luminosity fluctuations which are suggestive of irregular variables (red giants and supergiants (Schwarzschild 1975)), and of the long secondary period feature in semi-regular AGB variables (Stothers 2010, Wood, Olivier and Kawaler 2004). This "tau-mechanism" is a new source for stellar variability, which is inherently non-linear (unseen in linear stability analysis), and one closely related to intermittency in turbulence. It was already implicit in the 3D global simulations of Woodward, Porter and Jacobs (2003). This fluctuating behavior is seen in extended 2D simulations of CNeOSi burning shells (Arnett and Meakin 2011b), and may cause instability which leads to eruptions in progenitors of core collapse supernovae PRIOR to collapse.

Abstract:
Two-dimensional (2D) hydrodynamical simulations of progenitor evolution of a 23 solar mass star, close to core collapse (about 1 hour, in 1D), with simultaneously active C, Ne, O, and Si burning shells, are presented and contrasted to existing 1D models (which are forced to be quasi-static). Pronounced asymmetries, and strong dynamical interactions between shells are seen in 2D. Although instigated by turbulence, the dynamic behavior proceeds to sufficiently large amplitudes that it couples to the nuclear burning. Dramatic growth of low order modes is seen, as well as large deviations from spherical symmetry in the burning shells. The vigorous dynamics is more violent than that seen in earlier burning stages in the 3D simulations of a single cell in the oxygen burning shell, or in 2D simulations not including an active Si shell. Linear perturbative analysis does not capture the chaotic behavior of turbulence (e.g., strange attractors such as that discovered by Lorenz), and therefore badly underestimates the vigor of the instability. The limitations of 1D and 2D models are discussed in detail. The 2D models, although flawed geometrically, represent a more realistic treatment of the relevant dynamics than existing 1D models, and present a dramatically different view of the stages of evolution prior to collapse. Implications for interpretation of SN1987A, abundances in young supernova remnants, pre-collapse outbursts, progenitor structure, neutron star kicks, and fallback are outlined. While 2D simulations provide new qualitative insight, fully 3D simulations are needed for a quantitative understanding of this stage of stellar evolution. The necessary properties of such simulations are delineated.

Abstract:
This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. The pairs of plasmids p42f-pRL12, p42e-pRL11 and p42b-pRL9 as well large parts of p42c with pRL10 are shown to be similar, whereas the symbiotic plasmids (p42d and pRL10) are structurally unrelated and seem to follow distinct evolutionary paths. Even though purifying selection is acting on the whole genome, the accessory component is evolving more rapidly. This component is constituted largely for proteins for transport of diverse metabolites and elements of external origin. The present analysis allows us to conclude that a heterogeneous and quickly diversifying group of plasmids co-exists in a common genomic framework.

Abstract:
To demonstrate the principle, we have developed a 2D finite element model of the femur in which body weight, a representation of the pelvis, and ligamentous forces were included. The regions of higher trabecular bone density in the proximal femur (the principal trabecular systems) were assigned a higher modulus than the surrounding trabecular bone. Two-legged and one-legged stances, the latter including an abductor force, were investigated.The inclusion of ligamentous forces in two-legged stance generated compressive stresses in the proximal femur. The increased modulus in areas of greater structural density focuses the stresses through the arch-like internal structure. Including an abductor muscle force in simulated one-legged stance also produced compression, but with a different distribution.This 2D model shows, in principle, that including ligamentous and muscular forces has the effect of generating compressive stresses across most of the proximal femur. The arch-like trabecular structure transmits the compressive loads to the shaft. The greater strength of bone in compression than in tension is then used to advantage. These results support the hypothesis presented. If correct, a better understanding of the stress distribution in the proximal femur may lead to improvements in prosthetic devices and an appreciation of the effects of various surgical procedures affecting load transmission across the hip.Despite recent advances in modelling, and the success of total hip replacements, it is still not clear what stresses are generated within the proximal femur (the head and neck) during physiological loading. The traditional description is based on the work of the nineteenth century engineer, Cullman, who observed the drawings of the anatomist, Meyer, and likened them to the stress pattern of a crane which he was currently analysing [1]. He proposed that a load representing body weight applied to the femoral head, with the lower end of the femoral shaft fixed, would

Abstract:
Issues concerning the structure and evolution of core collapse progenitor stars are discussed with an emphasis on interior evolution. We describe a program designed to investigate the transport and mixing processes associated with stellar turbulence, arguably the greatest source of uncertainty in progenitor structure, besides mass loss, at the time of core collapse. An effort to use precision observations of stellar parameters to constrain theoretical modeling is also described.