Holographic turbulence

We construct turbulent black holes in asymptotically AdS_4 spacetime by numerically solving Einstein equations. Both the dual holographic fluid and bulk geometry display signatures of an inverse cascade with the bulk geometry being well approximated by the fluid/gravity gradient expansion. We argue that statistically steady-state black holes dual to d dimensional turbulent flows have horizons which are approximately fractal with fractal dimension D=d+4/3.Comment: 6 pages, 3 figure

Holographic Vortex Liquids and Superfluid Turbulence

Superfluid turbulence, often referred to as quantum turbulence, is a fascinating phenomenon for which a satisfactory theoretical framework is lacking. Holographic duality provides a systematic new approach to studying quantum turbulence by mapping the dynamics of certain quantum theories onto the dynamics of classical gravity. We use this gravitational description to numerically construct turbulent flows in a holographic superfluid in two spatial dimensions. We find that the superfluid kinetic energy spectrum obeys the Kolmogorov -5/3 scaling law, as it does for turbulent flows in normal fluids. We trace this scaling to a direct energy cascade by injecting energy at long wavelengths and watching it flow to a short-distance scale set by the vortex core size, where dissipation by vortex annihilation and vortex drag becomes efficient. This is in sharp contrast with the inverse energy cascade of normal fluid turbulence in two dimensions. We also demonstrate that the microscopic dissipation spectrum has a simple geometric interpretation.Comment: 23 pages, 7 figures. Minor corrections made. Movies and supplementary material available at http://turbulent.lns.mit.edu/Superflui

Formal Definitions of Unbounded Evolution and Innovation Reveal Universal Mechanisms for Open-Ended Evolution in Dynamical Systems

Open-ended evolution (OEE) is relevant to a variety of biological, artificial and technological systems, but has been challenging to reproduce in silico. Most theoretical efforts focus on key aspects of open-ended evolution as it appears in biology. We recast the problem as a more general one in dynamical systems theory, providing simple criteria for open-ended evolution based on two hallmark features: unbounded evolution and innovation. We define unbounded evolution as patterns that are non-repeating within the expected Poincare recurrence time of an equivalent isolated system, and innovation as trajectories not observed in isolated systems. As a case study, we implement novel variants of cellular automata (CA) in which the update rules are allowed to vary with time in three alternative ways. Each is capable of generating conditions for open-ended evolution, but vary in their ability to do so. We find that state-dependent dynamics, widely regarded as a hallmark of life, statistically out-performs other candidate mechanisms, and is the only mechanism to produce open-ended evolution in a scalable manner, essential to the notion of ongoing evolution. This analysis suggests a new framework for unifying mechanisms for generating OEE with features distinctive to life and its artifacts, with broad applicability to biological and artificial systems.Comment: Main document: 17 pages, Supplement: 21 pages Presented at OEE2: The Second Workshop on Open-Ended Evolution, 15th International Conference on the Synthesis and Simulation of Living Systems (ALIFE XV), Canc\'un, Mexico, 4-8 July 2016 (http://www.tim-taylor.com/oee2/

Molecular evidence for ten species and Oligo-Miocene vicariance within a nominal Australian gecko species (Crenadactylus ocellatus, Diplodactylidae)

Extent: 11p.BACKGROUND: Molecular studies have revealed that many putative ‘species’ are actually complexes of multiple morphologically conservative, but genetically divergent ‘cryptic species’. In extreme cases processes such as nonadaptive diversification (speciation without divergent selection) could mask the existence of ancient lineages as divergent as ecologically and morphologically diverse radiations recognised as genera or even families in related groups. The identification of such ancient, but cryptic, lineages has important ramifications for conservation, biogeography and evolutionary biology. Herein, we use an integrated multilocus genetic dataset (allozymes, mtDNA and nuclear DNA) to test whether disjunct populations of the widespread nominal Australian gecko species Crenadactylus ocellatus include distinct evolutionary lineages (species), and to examine the timing of diversification among these populations. RESULTS: We identify at least 10 deeply divergent lineages within the single recognised species Crenadactylus ocellatus, including a radiation of five endemic to the Kimberley region of north-west Australia, and at least four known from areas of less than 100 km2. Lineages restricted to geographically isolated ranges and semi-arid areas across central and western Australia are estimated to have began to diversify in the late Oligocene/early Miocence (~20-30 mya), concurrent with, or even pre-dating, radiations of many iconic, broadly sympatric and much more species-rich Australian vertebrate families (e.g. venomous snakes, dragon lizards and kangaroos). CONCLUSIONS: Instead of a single species, Crenadactylus is a surprisingly speciose and ancient vertebrate radiation. Based on their deep divergence and no evidence of recent gene flow, we recognise each of the 10 main lineages as candidate species. Molecular dating indicates that the genus includes some of the oldest vertebrate lineages confounded within a single species yet identified by molecular assessments of diversity. Highly divergent allopatric lineages are restricted to putative refugia across arid and semi-arid Australia, and provide important evidence towards understanding the history and spread of the Australian arid zone, suggesting at a minimum that semi-arid conditions were present by the early Miocene, and that severe aridity was widespread by the mid to late Miocene. In addition to documenting a remarkable instance of underestimation of vertebrate species diversity in a developed country, these results suggest that increasing integration of molecular dating techniques into cryptic species delimitation will reveal further instances where taxonomic conservatism has led to profound underestimation of not only species numbers, but also highly significant phylogenetic diversity and evolutionary history.Paul M. Oliver, Mark Adams and Paul Dought

Hubble Space Telescope High Resolution Imaging of Kepler Small and Cool Exoplanet Host Stars

High resolution imaging is an important tool for follow-up study of exoplanet candidates found via transit detection with the Kepler Mission. We discuss here HST imaging with the WFC3 of 23 stars that host particularly interesting Kepler planet candidates based on their small size and cool equilibrium temperature estimates. Results include detections, exclusion of background stars that could be a source of false positives for the transits, and detection of physically-associated companions in a number of cases providing dilution measures necessary for planet parameter refinement. For six KOIs, we find that there is ambiguity in which star hosts the transiting planet(s), with potentially strong implications for planetary characteristics. Our sample is evenly distributed in G, K, and M spectral types. Albeit with a small sample size, we find that physically-associated binaries are more common than expected at each spectral type, reaching a factor of 10 frequency excess at M. We document the program detection sensitivities, detections, and deliverables to the Kepler follow-up program archive.Comment: Accepted for the Astronomical Journal; 13 pages with 9 figure

Improved chemistry restraints for crystallographic refinement by integrating the Amber force field into Phenix.

The refinement of biomolecular crystallographic models relies on geometric restraints to help to address the paucity of experimental data typical in these experiments. Limitations in these restraints can degrade the quality of the resulting atomic models. Here, an integration of the full all-atom Amber molecular-dynamics force field into Phenix crystallographic refinement is presented, which enables more complete modeling of biomolecular chemistry. The advantages of the force field include a carefully derived set of torsion-angle potentials, an extensive and flexible set of atom types, Lennard-Jones treatment of nonbonded interactions and a full treatment of crystalline electrostatics. The new combined method was tested against conventional geometry restraints for over 22 000 protein structures. Structures refined with the new method show substantially improved model quality. On average, Ramachandran and rotamer scores are somewhat better, clashscores and MolProbity scores are significantly improved, and the modeling of electrostatics leads to structures that exhibit more, and more correct, hydrogen bonds than those refined using traditional geometry restraints. In general it is found that model improvements are greatest at lower resolutions, prompting plans to add the Amber target function to real-space refinement for use in electron cryo-microscopy. This work opens the door to the future development of more advanced applications such as Amber-based ensemble refinement, quantum-mechanical representation of active sites and improved geometric restraints for simulated annealing

MEASUREMENT OF STRAIN AND LATTICE TILT AT THE MARGINS OF THIN FILM ISLANDS ON SINGLE-CRYSTAL SUBSTRATES BY DOUBLE-CRYSTAL X-RAY TOPOGRAPHY

ABSTRACT Various amounts of strain and lattice deformation were introduced into <111> Si substrates by the deposition of amorphous Si films of different thicknesses. Strain and deformation are concentrated along the film edges and were recorded as contrast in double-crystal X-ray topograph (DXRT) images. The contrast in the DXRT images was measured and was related to lattice deformation by means of the X-ray rocking curve. The technique was able to independently measure deformation from strains and lattice tilts at film edges. These deformations varied linearly with film thickness

An Entomopathogenic Nematode by Any Other Name

Among the diversity of insect-parasitic nematodes, entomopathogenic nematodes (EPNs) are distinct, cooperating with insect-pathogenic bacteria to kill insect hosts. EPNs have adapted specific mechanisms to associate with and transmit bacteria to insect hosts. New discoveries have expanded this guild of nematodes and refine our understanding of the nature and evolution of insect–nematode associations. Here, we clarify the meaning of “entomopathogenic” in nematology and argue that EPNs must rapidly kill their hosts with the aid of bacterial partners and must pass on the associated bacteria to future generations

First Science Results From SOFIA/FORCAST: Super-Resolution Imaging of the S140 Cluster at 37\micron

We present 37\micron\ imaging of the S140 complex of infrared sources centered on IRS1 made with the FORCAST camera on SOFIA. These observations are the longest wavelength imaging to resolve clearly the three main sources seen at shorter wavelengths, IRS 1, 2 and 3, and are nearly at the diffraction limit of the 2.5-m telescope. We also obtained a small number of images at 11 and 31\micron\ that are useful for flux measurement. Our images cover the area of several strong sub-mm sources seen in the area -- SMM 1, 2, and 3 -- that are not coincident with any mid-infrared sources and are not visible in our longer wavelength imaging either. Our new observations confirm previous estimates of the relative dust optical depth and source luminosity for the components in this likely cluster of early B stars. We also investigate the use of super-resolution to go beyond the basic diffraction limit in imaging on SOFIA and find that the van Cittert algorithm, together with the "multi-resolution" technique, provides excellent results