Modelling ripples in Orion with coupled dust dynamics and radiative transfer

In light of the recent detection of direct evidence for the formation of Kelvin-Helmholtz instabilities in the Orion nebula, we expand upon previous modelling efforts by numerically simulating the shear-flow driven gas and dust dynamics in locations where the H$_{II}$ region and the molecular cloud interact. We aim to directly confront the simulation results with the infrared observations. Methods: To numerically model the onset and full nonlinear development of the Kelvin-Helmholtz instability we take the setup proposed to interpret the observations, and adjust it to a full 3D hydrodynamical simulation that includes the dynamics of gas as well as dust. A dust grain distribution with sizes between 5-250 nm is used, exploiting the gas+dust module of the MPI-AMRVAC code, in which the dust species are represented by several pressureless dust fluids. The evolution of the model is followed well into the nonlinear phase. The output of these simulations is then used as input for the SKIRT dust radiative transfer code to obtain infrared images at several stages of the evolution, which can be compared to the observations. Results: We confirm that a 3D Kelvin-Helmholtz instability is able to develop in the proposed setup, and that the formation of the instability is not inhibited by the addition of dust. Kelvin-Helmholtz billows form at the end of the linear phase, and synthetic observations of the billows show striking similarities to the infrared observations. It is pointed out that the high density dust regions preferentially collect on the flanks of the billows. To get agreement with the observed Kelvin-Helmholtz ripples, the assumed geometry between the background radiation, the billows and the observer is seen to be of critical importance.Comment: 8 pages, 10 figure

Genome landscapes and bacteriophage codon usage

Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonmous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of codon usage in prokaryotes and simple eukaryotes. Here we analyze patterns of codon usage across 74 diverse bacteriophages that infect E. coli, P. aeruginosa and L. lactis as their primary host. We introduce the concept of a `genome landscape,' which helps reveal non-trivial, long-range patterns in codon usage across a genome. We develop a series of randomization tests that allow us to interrogate the significance of one aspect of codon usage, such a GC content, while controlling for another aspect, such as adaptation to host-preferred codons. We find that 33 phage genomes exhibit highly non-random patterns in their GC3-content, use of host-preferred codons, or both. We show that the head and tail proteins of these phages exhibit significant bias towards host-preferred codons, relative to the non-structural phage proteins. Our results support the hypothesis of translational selection on viral genes for host-preferred codons, over a broad range of bacteriophages.Comment: 9 Color Figures, 5 Tables, 53 Reference

On parallel Branch and Bound frameworks for Global Optimization

Branch and Bound (B&B) algorithms are known to exhibit an irregularity of the search tree. Therefore, developing a parallel approach for this kind of algorithms is a challenge. The efficiency of a B&B algorithm depends on the chosen Branching, Bounding, Selection, Rejection, and Termination rules. The question we investigate is how the chosen platform consisting of programming language, used libraries, or skeletons influences programming effort and algorithm performance. Selection rule and data management structures are usually hidden to programmers for frameworks with a high level of abstraction, as well as the load balancing strategy, when the algorithm is run in parallel. We investigate the question by implementing a multidimensional Global Optimization B&B algorithm with the help of three frameworks with a different level of abstraction (from more to less): Bobpp, Threading Building Blocks (TBB), and a customized Pthread implementation. The following has been found. The Bobpp implementation is easy to code, but exhibits the poorest scalability. On the contrast, the TBB and Pthread implementations scale almost linearly on the used platform. The TBB approach shows a slightly better productivity

Environmental changes and violent conflict

This letter reviews the scientific literature on whether and how environmental changes affect the risk of violent conflict. The available evidence from qualitative case studies indicates that environmental stress can contribute to violent conflict in some specific cases. Results from quantitative large-N studies, however, strongly suggest that we should be careful in drawing general conclusions. Those large-N studies that we regard as the most sophisticated ones obtain results that are not robust to alternative model specifications and, thus, have been debated. This suggests that environmental changes may, under specific circumstances, increase the risk of violent conflict, but not necessarily in a systematic way and unconditionally. Hence there is, to date, no scientific consensus on the impact of environmental changes on violent conflict. This letter also highlights the most important challenges for further research on the subject. One of the key issues is that the effects of environmental changes on violent conflict are likely to be contingent on a set of economic and political conditions that determine adaptation capacity. In the authors' view, the most important indirect effects are likely to lead from environmental changes via economic performance and migration to violent conflict. © 2012 IOP Publishing Ltd

NASA Planetary Mission Concept Study: Assessing: Dwarf Planet Ceres' past and Present Habitability Potential

The Dawn mission revolutionized our understanding of Ceres during the same decade that has also witnessed the rise of ocean worlds as a research and exploration focus. We will report progress on the Planetary Mission Concept Study (PMCS) on the future exploration of Ceres under the New Frontiers or Flagship program that was selected for NASA funding in October 2019. At the time this writing, the study was just kicked off, hence this abstract reports the study plan as presented in the proposal

Phamerator: a bioinformatic tool for comparative bacteriophage genomics

Background: Bacteriophage genomes have mosaic architectures and are replete with small open reading frames of unknown function, presenting challenges in their annotation, comparative analysis, and representation.Results: We describe here a bioinformatic tool, Phamerator, that assorts protein-coding genes into phamilies of related sequences using pairwise comparisons to generate a database of gene relationships. This database is used to generate genome maps of multiple phages that incorporate nucleotide and amino acid sequence relationships, as well as genes containing conserved domains. Phamerator also generates phamily circle representations of gene phamilies, facilitating analysis of the different evolutionary histories of individual genes that migrate through phage populations by horizontal genetic exchange.Conclusions: Phamerator represents a useful tool for comparative genomic analysis and comparative representations of bacteriophage genomes. © 2011 Cresawn et al; licensee BioMed Central Ltd

External sources of clean technology: evidence from the clean development mechanism

New technology is fundamental to sustainable development. However, inventors from industrialized countries often refuse technology transfer because they worry about reverse-engineering. When can clean technology transfer succeed? We develop a formal model of the political economy of North–South technology transfer. According to the model, technology transfer is possible if (1) the technology in focus has limited global commercial potential or (2) the host developing country does not have the capacity to absorb new technologies for commercial use. If both conditions fail, inventors from industrialized countries worry about the adverse competitiveness effects of reverse-engineering, so technology transfer fails. Data analysis of technology transfer in 4,894 projects implemented under the Kyoto Protocol’s Clean Development Mechanism during the 2004–2010 period provides evidence in support of the model