Magnetic helicity transport in the advective gauge family

Magnetic helicity fluxes are investigated in a family of gauges in which the contribution from ideal magnetohydrodynamics takes the form of a purely advective flux. Numerical simulations of magnetohydrodynamic turbulence in this advective gauge family exhibit instabilities triggered by the build-up of unphysical irrotational contributions to the magnetic vector potential. As a remedy, the vector potential is evolved in a numerically well behaved gauge, from which the advective vector potential is obtained by a gauge transformation. In the kinematic regime, the magnetic helicity density evolves similarly to a passive scalar when resistivity is small and turbulent mixing is mild, i.e. when the fluid Reynolds number is not too large. In the dynamical regime, resistive contributions to the magnetic helicity flux in the advective gauge are found to be significant owing to the development of small length scales in the irrotational part of the magnetic vector potential.Comment: 11 pages, 10 figures, submitted to Physics of Plasma

Evaluation of work experience in construction for young people with cancer: Brief Report

Cancer Care Research Centre, University of Stirling was commissioned by Teenage Cancer Trust to conduct an evaluation of work experience. This is a brief report of the evaluation

Sequence Search Algorithms for Single Pass Sequence Identification: Does One Size Fit All?

Bioinformatic tools have become essential to biologists in their quest to understand the vast quantities of sequence data, and now whole genomes, which are being produced at an ever increasing rate. Much of these sequence data are single-pass sequences, such as sample sequences from organisms closely related to other organisms of interest which have already been sequenced, or cDNAs or expressed sequence tags (ESTs). These single-pass sequences often contain errors, including frameshifts, which complicate the identification of homologues, especially at the protein level. Therefore, sequence searches with this type of data are often performed at the nucleotide level. The most commonly used sequence search algorithms for the identification of homologues are Washington University’s and the National Center for Biotechnology Information's (NCBI) versions of the BLAST suites of tools, which are to be found on websites all over the world. The work reported here examines the use of these tools for comparing sample sequence datasets to a known genome. It shows that care must be taken when choosing the parameters to use with the BLAST algorithms. NCBI’s version of gapped BLASTn gives much shorter, and sometimes different, top alignments to those found using Washington University’s version of BLASTn (which also allows for gaps), when both are used with their default parameters. Most of the differences in performance were found to be due to the choices of default parameters rather than underlying differences between the two algorithms. Washington University’s version, used with defaults, compares very favourably with the results obtained using the accurate but computationally intensive Smith–Waterman algorithm

Analysis of gene expression in operons of Streptomyces coelicolor

BACKGROUND: Recent studies have shown that microarray-derived gene-expression data are useful for operon prediction. However, it is apparent that genes within an operon do not conform to the simple notion that they have equal levels of expression. RESULTS: To investigate the relative transcript levels of intra-operonic genes, we have used a Z-score approach to normalize the expression levels of all genes within an operon to expression of the first gene of that operon. Here we demonstrate that there is a general downward trend in expression from the first to the last gene in Streptomyces coelicolor operons, in contrast to what we observe in Escherichia coli. Combining transcription-factor binding-site prediction with the identification of operonic genes that exhibited higher transcript levels than the first gene of the same operon enabled the discovery of putative internal promoters. The presence of transcription terminators and abundance of putative transcriptional control sequences in S. coelicolor operons are also described. CONCLUSION: Here we have demonstrated a polarity of expression in operons of S. coelicolor not seen in E. coli, bringing caution to those that apply operon prediction strategies based on E. coli 'equal-expression' to divergent species. We speculate that this general difference in transcription behavior could reflect the contrasting lifestyles of the two organisms and, in the case of Streptomyces, might also be influenced by its high G+C content genome. Identification of putative internal promoters, previously thought to cause problems in operon prediction strategies, has also been enabled

Exploring Student Persistence in STEM Programs: A Motivational Model

To address continually decreasing enrollment and rising attrition in post-secondary STEM degree (science, technology, engineering, and mathematics) programs, particularly for women, the present study examines the utility of motivation and emotion variables to account for persistence and achievement in science in male and female students transitioning from high school to junior college. Consistent with self-determination theory (Deci & Ryan, 2012) and achievement-goal theory (Senko, Hulleman, & Harackiewicz, 2011),structural equation modelling based on data from 1,309 students from four English-language CEGEPs showed students’ achievement goals, self-efficacy, and perceived autonomy support to impact intrinsic motivation, emotions, and achievement that, in turn, predicted persistence in the science domain

Magnetorotational turbulence transports angular momentum in stratified disks with low magnetic Prandtl number but magnetic Reynolds number above a critical value

The magnetorotational instability (MRI) may dominate outward transport of angular momentum in accretion disks, allowing material to fall onto the central object. Previous work has established that the MRI can drive a mean-field dynamo, possibly leading to a self-sustaining accretion system. Recently, however, simulations of the scaling of the angular momentum transport parameter \alphaSS with the magnetic Prandtl number \Prandtl have cast doubt on the ability of the MRI to transport astrophysically relevant amounts of angular momentum in real disk systems. Here, we use simulations including explicit physical viscosity and resistivity to show that when vertical stratification is included, mean field dynamo action operates, driving the system to a configuration in which the magnetic field is not fully helical. This relaxes the constraints on the generated field provided by magnetic helicity conservation, allowing the generation of a mean field on timescales independent of the resistivity. Our models demonstrate the existence of a critical magnetic Reynolds number \Rmagc, below which transport becomes strongly \Prandtl-dependent and chaotic, but above which the transport is steady and \Prandtl-independent. Prior simulations showing \Prandtl-dependence had \Rmag < \Rmagc. We conjecture that this steady regime is possible because the mean field dynamo is not helicity-limited and thus does not depend on the details of the helicity ejection process. Scaling to realistic astrophysical parameters suggests that disks around both protostars and stellar mass black holes have \Rmag >> \Rmagc. Thus, we suggest that the strong \Prandtl dependence seen in recent simulations does not occur in real systems.Comment: 17 pages, 9 figures. as accepted to Ap

Momentum-Resolved Inelastic X-ray Scattering as a Novel Tool to Study Charge Gap in Complex Insulators

We report particle-hole pair excitations in a cuprate insulator in the intermediate regimes of momentum-transfers using high energy inelastic x-ray scattering. The excitation spectra show dispersive features near the Mott edge which shed light on the momentum structure of the upper Hubbard band in cuprates. We briefly discuss the potential use of such a technique to study the momentum dependence of unoccupied bands and q-dependent charge fluctuations in complex insulators.Comment: 3 pages, 2 figures, Revise