Stellar Oscillons

We study the weakly nonlinear evolution of acoustic instability of a plane- parallel polytrope with thermal dissipation in the form of Newton's law of cooling. The most unstable horizontal wavenumbers form a band around zero and this permits the development of a nonlinear pattern theory leading to a complex Ginzburg-Landau equation (CGLE). Numerical solutions for a subcritical, quintic CGLE produce vertically oscillating, localized structures that resemble the oscillons observed in recent experiments of vibrated granular material.Comment: 12 Latex pages using aasms4.sty, 2 postscript figures, submitted to the proceedings of the Florida Workshop in Nonlinear Astrophysics and Physic

Letter from Robert O. Spiegel to B. R. Colson

Letter from Robert O. Spiegel to B. R. Colson. The one-page handwritten note is on Our Florida Friend letterhead and is dated 16 November 1912. There is a transcript of the correspondence included in the item PDF

The tachocline revisited

The solar tachocline is a shear layer located at the base of the solar convection zone. The horizontal shear in the tachocline is likely turbulent, and it is often assumed that this turbulence would be strongly anisotropic as a result of the local stratification. What role this turbulence plays in the tachocline dynamics, however, remains to be determined. In particular, it is not clear whether it would result in a turbulent eddy diffusivity, or anti-diffusivity, or something else entirely. In this paper, we present the first direct numerical simulations of turbulence in horizontal shear flows at low Prandtl number, in an idealized model that ignores rotation and magnetic fields. We find that several regimes exist, depending on the relative importance of the stratification, viscosity and thermal diffusivity. Our results suggest that the tachocline is in the stratified turbulence regime, which has very specific properties controlled by a balance between buoyancy, inertia, and thermal diffusion.Comment: Invited review for the meeting Dynamics of the Sun and Stars: Honoring the Life and Work of Michael J. Thompson (Boulder, Colorado, 24-26 September 2019

Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening

Computational techniques such as structure-based virtual screening require carefully prepared 3D models of potential small-molecule ligands. Though powerful, existing commercial programs for virtual-library preparation have restrictive and/or expensive licenses. Freely available alternatives, though often effective, do not fully account for all possible ionization, tautomeric, and ring-conformational variants. We here present Gypsum-DL, a free, robust open-source program that addresses these challenges. As input, Gypsum-DL accepts virtual compound libraries in SMILES or flat SDF formats. For each molecule in the virtual library, it enumerates appropriate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms. As output, Gypsum-DL produces an SDF file containing each molecular form, with 3D coordinates assigned. To demonstrate its utility, we processed 1558 molecules taken from the NCI Diversity Set VI and 56,608 molecules taken from a Distributed Drug Discovery (D3) combinatorial virtual library. We also used 4463 high-quality protein-ligand complexes from the PDBBind database to show that Gypsum-DL processing can improve virtual-screening pose prediction. Gypsum-DL is available free of charge under the terms of the Apache License, Version 2.0

Operator Bias and the Effect of Training on Visual Assessments of Pasture Yield for Forage Budgets in Northern Australian Savanna

Sustainable management of Australia’s extensive northern grazing lands is challenging given its highly variable interannual rainfall and pasture production. Accordingly, a key management recommendation is to adjust stocking rates to match forage supply (O’Reagain et al., 2014). ‘Stocktake’ is a forage budgeting system (Aisthorpe et al., 2004) widely used and promoted to assist graziers make short-term (\u3c 1 year) adjustments of stocking rate. Budgets are typically calculated at the start of the dry season, to ensure sufficient forage for stock and ground cover levels until the first rains some six to nine months later. The software application ‘Future Beef Stocktake Plus’ has also been developed for use on smart devices (http://www.stocktakeplus.com.au/). A key requirement for forage budgets is an accurate estimate of pasture mass. This is typically done visually with the aid of photo standards of pasture mass, providing a simple, efficient and non-destructive approach. Other key variables of forage budgeting include the percent of the pasture not likely to be consumed by livestock (i.e. percent unpalatable) and pasture wastage that occurs as a result of trampling, decay, leaf drop and consumption by insects. Despite adoption of the Stocktake forage budget system by graziers, key variables do not appear to have been investigated and uncertainty exists on the accuracy of pasture yield estimates. Accordingly, the degree of error, operator variability and the potential impact of factors such as land type and starting yield on yield estimates and hence, calculated stocking rates, are unknown. This study examined operator bias associated with the visual assessment of pasture total standing dry matter (TSDM) using photo standards and the extent to which this bias was affected by operator, land type and starting yield. The effect of training on operator yield assessments was also investigated

Particle Aggregation in a turbulent Keplerian flow

In the problem of planetary formation one seeks a mechanism to gather small solid particles together into larger accumulations of solid matter. Here we describe a scenario in which turbulence mediates this process by aggregating particles into anticyclonic regions. If, as our simulations suggest, anticyclonic vortices form as long-lived coherent structures, the process becomes more powerful because such vortices trap particles effectively. Even if the turbulence is decaying, following the upheaval that formed the disk, there is enough time to make the dust distribution quite lumpy.Comment: 16 pages, 9 figure

Stellar Hydrodynamics in Radiative Regions

We present an analysis of the response of a radiative region to waves generated by a convective region of the star; this wave treatment of the classical problem of ``overshooting'' gives extra mixing relative to the treatment traditionally used in stellar evolutionary codes. The interface between convectively stable and unstable regions is dynamic and nonspherical, so that the nonturbulent material is driven into motion, even in the absence of ``penetrative overshoot.'' These motions may be described by the theory of nonspherical stellar pulsations, and are related to motion measured by helioseismology. Multi-dimensional numerical simulations of convective flow show puzzling features which we explain by this simplified physical model. Gravity waves generated at the interface are dissipated, resulting in slow circulation and mixing seen outside the formal convection zone. The approach may be extended to deal with rotation and composition gradients. Tests of this description in the stellar evolution code TYCHO produce carbon stars on the asymptotic giant branch (AGB), an isochrone age for the Hyades and three young clusters with lithium depletion ages from brown dwarfs, and lithium and beryllium depletion consistent with observations of the Hyades and Pleiades, all without tuning parameters. The insight into the different contributions of rotational and hydrodynamic mixing processes could have important implications for realistic simulation of supernovae and other questions in stellar evolution.Comment: 27 pages, 5 figures, accepted to the Astrophysical Journa

Changes in Solar Dynamics from 1995 to 2002

Data obtained by the GONG and MDI instruments over the last seven years are used to study how solar dynamics -- both rotation and other large scale flows -- have changed with time. In addition to the well known phenomenon of bands of faster and slower rotation moving towards the equator and pole, we find that the zonal flow pattern rises upwards with time. Like the zonal flows, the meridional flows also show distinct solar activity related changes. In particular, the anti-symmetric component of the meridional flow shows a decrease in speed with activity. We do not see any significant temporal variations in the dynamics of the tachocline region where the solar dynamo is believed to be operating.Comment: To appear in ApJ, March 1 200