Microbial Genomic Taxonomy.

This book chapter argues for an open-access catalogue of taxonomic descriptions with prototypes; diagnostic tables; and links to culture collections, to genome and gene sequences, and to other phenotypic and ecological databases. Ideally, the open access taxonomy will be based solely on genome sequences that allow both the phylogenetic allocation of new strains and species in the taxonomic space and the phenotypic/metabolic characterization in open online databases. Careful and thorough annotation of the genome sequences for function and chemotaxonomic data will be required. An alternative Code will be required for the naming strategy of genomes. Current microbial taxonomy is not able to keep up with the pace of development in microbial ecology. Innovative ways of developing microbial taxonomy are, therefore, needed urgently. This novel approach can, for the first time, allow microbial species descriptions using genomes based on ecological and evolutionary theory. One challenge ahead is to leverage the use of genome sequences to obtain insights on the (in silico) phenotypes and ecology of novel taxa.

FASTWIND reloaded: Complete comoving frame transfer for “all” contributing lines

FASTWIND is a unified NLTE atmosphere/spectrum synthesis code originally designed (and frequently used) for the optical/IR spectroscopic analysis of massive stars with winds. Until the previous version (v10), the line transfer for background elements (mostly from the iron-group) was performed in an approximate way, by calculating the individual line-transitions in a single-line Sobolev or comoving frame approach, and by adding up the individual opacities and source functions to quasi-continuum quantities that are used to determine the radiation field for the complete spectrum (see Puls et al. 2005, A&A 435, 669, and updates).We have now updated this approach (v11) and calculate, for all contributing lines (from elements H to Zn), the radiative transfer in the comoving frame, thus also accounting for line-overlap effects in an “exact” way. Related quantities such as temperature, radiative acceleration and formal integral have been improved in parallel. For a typical massive star atmospheric model, the computation times (from scratch, and for a modern desktop computer) are 1.5 h for the atmosphere/NLTE part, and 30 to 45 minutes (when not parallelized) for the formal integral (i.e., SED and normalized flux) in the ranges 900 to 2000 and 3800 to 7000 Å(Δλ = 0.03 Å).We compare our new with analogous results from the alternative code CMFGEN (Hillier & Miller 1998, ApJ 496, 407, and updates), for a grid consisting of 5 O-dwarf and 5 O-supergiant models of different spectral subtype. In most cases, the agreement is very good or even excellent (i.e., for the radiative acceleration), though also certain differences can be spotted. A comparison with results from the previous, approximate method shows equally good agreement, though also here some differences become obvious. Besides the possibility to calculate the (total) radiative acceleration, the new FASTWIND version will allow us to investigate the UV-part of the spectrum in parallel with the optical/IR domain.

Vessel Design for Unintended Detonation: A Comparison of Alternative Code Rules

The Hanford Tank Waste Treatment and Immobilization Plant (WTP) will process waste slurries that have the potential to generate flammable gases and will utilize a number of atmospheric vessels to store these slurries at various stages of the waste treatment process. Throughout the design process, provisions have been made to ensure that these flammable gasses are vented from these vessels and to eliminate potential sources of ignition. However, Bechtel National, Inc. (BNI) would like to be able to demonstrate that these vessels are capable of withstanding a limited number of unintended detonations. It is well known that pressure vessels may be designed for internal detonations. However, these loadings tend to cause very brief transients of high stress that can make traditional stress-based design rules to be difficult to meet. In the past decade, a number of strain-based design methodologies have become available, including ASME Boiler and Pressure Vessel Code (BPVC), Section VIII, Division 2, Part 5; ASME Section VIII, Division 3; ASME Section VIII, Division 3 Code Case 2564; and API 579-1 / ASME FFS-1. Each of these sets of rules permits some degree of plasticity in vessel design, but there are key differences in the specific provisions. In this paper, the use of these different sets of Code rules will be demonstrated in the context of the design of a WTP vessel for a single unintended detonation, and the advantages and disadvantages of these alternative design approaches will be discussed.

Measuring the Consequences of Rules

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism (which measures the expected value of the rule's consequences at a 90 percent acceptance rate), while Michael Ridge advocates variable-rate rule-utilitarianism (which measures the average expected value of the rule's consequences for all different levels of social acceptance). I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal problems that leave us without any viable form of rule-utilitarianism.

Provincialism in Modern India: The Multiple Narratives of Education and their Pain

‘Provincialism’, or the separation of inferior spaces from normative ones, is seen in this essay as a key trope for interpreting modern Indian history. Provincialism, or provinciality, is a space recognizable instantly. It is marked by slowness, by absence of the new and recent, by what is seen on the national level as a brake-effect in an otherwise promising march forwards. Cities, which is what I concentrate on in this essay, are characterizable as provincial by a certain appearance: a topography of narrow streets, by the sloppy merger of the inside and outside, by an absence of discrimination between the jungle and the civilized as animal life proliferates on the roads. Their space is marked by a lack of discipline, and this lack is further exacerbated by an attitude almost aggressive, at any rate stubborn, that seems to embrace every other dimension of life. The provincial citizen is one whose body identifies with the provincial space. It revels in an indifference to the rules of obedience to arbitrary external exercises of power. The provincial space and its citizen are marked in the use of languages by the dominance of regional language over English. Overall, the provincial space is signified in the state as an obstacle, political, economic, and most of all cultural, to what could otherwise be the smooth march forward of unfettered forces of rationality and order. But it signifies itself by an alternative code. That which is indiscipline to the center is freedom to the margins; that which is coarse, is cultured; that which is backward, is rich; that which is alien is intimate; and that which is unable to keep step with a march forward is precisely the intelligent and crafty that refuses to play a non-reflexive, mechanical game.

Turbulence over a compliant surface: numerical simulation and analysis

In this paper we present results from a numerical investigation of turbulent channel flow in the presence of a compliant wall. The compliant wall is modelled as a homogeneous spring-supported plate. The simulation code is validated both by comparison with an alternative code and by reproducing results of linear stability theory. Our results demonstrate that with the wall compliance we used in the simulation there is little change in the very long-time behaviour of the turbulent skin friction drag and little modification to the near-wall turbulent coherent structures. The values of pertinent statistical quantities of the turbulence near the compliant walls converge to those near a rigid wall and the statistical effect of the wall compliance on the turbulent channel flow is small.

An OpenMP Compiler Benchmark

The purpose of this benchmark is to propose several optimization techniques and to test their existence in current OpenMP compilers. Examples are the removal of redundant synchronization constructs, effective constructs for alternative code and orphaned directives. The effectiveness of the compiler generated code is measured by comparing different OpenMP constructs and compilers. If possible, we also compare with the hand coded "equivalent" solution. Six out of seven proposed optimization techniques are already implemented in different compilers. However, most compilers implement only one or two of them.