The relaxation of two-dimensional rolls in Rayleigh–Bénard convection

Large aspect ratio, two-dimensional, periodic convection layers containing a Boussinesq fluid of finite Prandtl number bounded by rigid or free horizontal surfaces are investigated numerically. The fluid equations are solved using both a standard pseudospectral and a Fourier integral method for the time evolution of finite initial perturbations, both random thermal perturbations and localized roll disturbances, into a final equilibrium state. The suggestion that a Fourier integral solution method is required to yield roll relaxation, the two-dimensional process increasing the convection wavelength to values larger than critical, is investigated. Roll relaxation is found for both free-slip and no-slip surfaces using either solution method as long as the initial state is chosen to be of the form of a localized roll disturbance. A wide variety of simulations are performed and roll relaxation is found to be independent of the periodic domain length, weakly dependent on the Rayleigh number and dependent upon the magnitude of the initial localized roll disturbances

Antimicrobial antagonists against food pathogens; a bacteriocin perspective

peer-reviewedEfforts are continuing to find novel bacteriocins with enhanced specificity and potency. Traditional plating techniques are still being used for bacteriocin screening studies, however, the availability of ever more bacterial genome sequences and the use of in silico gene mining tools have revealed novel bacteriocin gene clusters that would otherwise have been overlooked. Furthermore, synthetic biology and bioengineering-based approaches are allowing scientists to harness existing and novel bacteriocin gene clusters through expression in different hosts and by enhancing functionalities. The same principles apply to bacteriocin producing probiotic cultures and their application to control pathogens in the gut. We can expect that the recent developments on bacteriocins from Lactic Acid Bacteria (LAB) described here will contribute greatly to increased commercialisation of bacteriocins in food systems.This work was funded by the Alimentary Pharmabiotic Centre, a research centre funded by Science Foundation Ireland (SFI), through the Irish Government’s National Development Plan. The authors and their work were supported by SFI (grant no. 12/RC/2273

Microbial Effects on Repository Performance

This report presents a critical review of the international literature on microbial effects in and around a deep geological repository for higher activity wastes. It is aimed at those who are familiar with the nuclear industry and radioactive waste disposal, but who are not experts in microbiology; they may have a limited knowledge of how microbiology may be integrated into and impact upon radioactive waste disposal safety cases and associated performance assessments (PA)

Towers of recollement and bases for diagram algebras: planar diagrams and a little beyond

The recollement approach to the representation theory of sequences of algebras is extended to pass basis information directly through the globalisation functor. The method is hence adapted to treat sequences that are not necessarily towers by inclusion, such as symplectic blob algebras (diagram algebra quotients of the type-\hati{C} Hecke algebras). By carefully reviewing the diagram algebra construction, we find a new set of functors interrelating module categories of ordinary blob algebras (diagram algebra quotients of the type-${B}$ Hecke algebras) at {\em different} values of the algebra parameters. We show that these functors generalise to determine the structure of symplectic blob algebras, and hence of certain two-boundary Temperley-Lieb algebras arising in Statistical Mechanics. We identify the diagram basis with a cellular basis for each symplectic blob algebra, and prove that these algebras are quasihereditary over a field for almost all parameter choices, and generically semisimple. (That is, we give bases for all cell and standard modules.)Comment: 61 page

Rayleigh-Benard Convection with a Radial Ramp in Plate Separation

Pattern formation in Rayleigh-Benard convection in a large-aspect-ratio cylinder with a radial ramp in the plate separation is studied analytically and numerically by performing numerical simulations of the Boussinesq equations. A horizontal mean flow and a vertical large scale counterflow are quantified and used to understand the pattern wavenumber. Our results suggest that the mean flow, generated by amplitude gradients, plays an important role in the roll compression observed as the control parameter is increased. Near threshold the mean flow has a quadrupole dependence with a single vortex in each quadrant while away from threshold the mean flow exhibits an octupole dependence with a counter-rotating pair of vortices in each quadrant. This is confirmed analytically using the amplitude equation and Cross-Newell mean flow equation. By performing numerical experiments the large scale counterflow is also found to aid in the roll compression away from threshold but to a much lesser degree. Our results yield an understanding of the pattern wavenumbers observed in experiment away from threshold and suggest that near threshold the mean flow and large scale counterflow are not responsible for the observed shift to smaller than critical wavenumbers.Comment: 10 pages, 13 figure

Atypical Listeria innocua strains possess an intact LIPI-3

peer-reviewedBackground: Listeria monocytogenes is a food-borne pathogen which is the causative agent of listeriosis and can be divided into three evolutionary lineages I, II and III. While all strains possess the well established virulence factors associated with the Listeria pathogenicity island I (LIPI-1), lineage I strains also possess an additional pathogenicity island designated LIPI-3 which encodes listeriolysin S (LLS), a post-translationally modified cytolytic peptide. Up until now, this pathogenicity island has been identified exclusively in a subset of lineage I isolates of the pathogen Listeria monocytogenes. Results: In total 64 L. innocua strains were screened for the presence of LIPI-3. Here we report the identification of an intact LIPI-3 in 11 isolates of L. innocua and the remnants of the cluster in several others. Significantly, we can reveal that placing the L. innocua lls genes under the control of a constitutive promoter results in a haemolytic phenotype, confirming that the cluster is capable of encoding a functional haemolysin. Conclusions: Although the presence of the LIPI-3 gene cluster is confined to lineage I isolates of L. monocytogenes, a corresponding gene cluster or its remnants have been identified in many L. innocua strains.This work was funded by the Enterprise Ireland Commercialisation fund, a programme which is co-financed by the EU through the ERDF. This work was also supported by the Irish Government under the National Development Plan, through Science Foundation Ireland Investigator awards; (06/IN.1/B98) and (10/IN.1/B3027)

The stochastic dynamics of nanoscale mechanical oscillators immersed in a viscous fluid

The stochastic response of nanoscale oscillators of arbitrary geometry immersed in a viscous fluid is studied. Using the fluctuation-dissipation theorem it is shown that deterministic calculations of the governing fluid and solid equations can be used in a straightforward manner to directly calculate the stochastic response that would be measured in experiment. We use this approach to investigate the fluid coupled motion of single and multiple cantilevers with experimentally motivated geometries.Comment: 5 pages, 5 figure