Steady-state, effective-temperature dynamics in a glassy material

We present an STZ-based analysis of numerical simulations by Haxton and Liu (HL). The extensive HL data sharply test the basic assumptions of the STZ theory, especially the central role played by the effective disorder temperature as a dynamical state variable. We find that the theory survives these tests, and that the HL data provide important and interesting constraints on some of its specific ingredients. Our most surprising conclusion is that, when driven at various constant shear rates in the low-temperature glassy state, the HL system exhibits a classic glass transition, including super-Arrhenius behavior, as a function of the effective temperature.Comment: 9 pages, 6 figure

Inter- and Intra-Chain Attractions in Solutions of Flexible Polyelectrolytes at Nonzero Concentration

Constant temperature molecular dynamics simulations were used to study solutions of flexible polyelectrolyte chains at nonzero concentrations with explicit counterions and unscreened coulombic interactions. Counterion condensation, measured via the self-diffusion coefficient of the counterions, is found to increase with polymer concentration, but contrary to the prediction of Manning theory, the renormalized charge fraction on the chains decreases with increasing Bjerrum length without showing any saturation. Scaling analysis of the radius of gyration shows that the chains are extended at low polymer concentrations and small Bjerrum lengths, while at sufficiently large Bjerrum lengths, the chains shrink to produce compact structures with exponents smaller than a gaussian chain, suggesting the presence of attractive intrachain interactions. A careful study of the radial distribution function of the center-of-mass of the polyelectrolyte chains shows clear evidence that effective interchain attractive interactions also exist in solutions of flexible polyelectrolytes, similar to what has been found for rodlike polyelectrolytes. Our results suggest that the broad maximum observed in scattering experiments is due to clustering of chains.Comment: 12 pages, REVTeX, 15 eps figure

Gene loss and lineage specific restriction-modification systems associated with niche differentiation in the Campylobacter jejuni Sequence Type 403 clonal complex

Campylobacter jejuni is a highly diverse species of bacteria commonly associated with infectious intestinal disease of humans and zoonotic carriage in poultry, cattle, pigs, and other animals. The species contains a large number of distinct clonal complexes that vary from host generalist lineages commonly found in poultry, livestock, and human disease cases to host-adapted specialized lineages primarily associated with livestock or poultry. Here, we present novel data on the ST403 clonal complex of C. jejuni, a lineage that has not been reported in avian hosts. Our data show that the lineage exhibits a distinctive pattern of intralineage recombination that is accompanied by the presence of lineage-specific restriction-modification systems. Furthermore, we show that the ST403 complex has undergone gene decay at a number of loci. Our data provide a putative link between the lack of association with avian hosts of C. jejuni ST403 and both gene gain and gene loss through nonsense mutations in coding sequences of genes, resulting in pseudogene formation

Research into Western Australian honeys

On the 26 February 2002, the then Department of Agriculture released a media statement about the results of research conducted by Rob Manning and Nola Mercer about WA honeys’ antimicrobial activity using an assay developed in New Zealand. The research showed that Western Australian honey had some of the highest activity levels in the world due to a naturally occurring enzyme in the honey. Upon dilution of honey, the enzyme glucose oxidase produces low concentrations of hydrogen peroxide which is the source of its antimicrobial activity. It is different to Manuka (Leptospermum scoparium) honey from New Zealand which is termed a ‘non-peroxide’ (Molan and Russell 1988) honey because it’s activity is derived from a chemical called methylglyoxal. The chemical, the “Unique Manuka Factor (UMF)” in Manuka is unique and so far it has only been discovered in honey from Leptospermum species (Allen et al. 1991; Anon 1998; Davis 2005) which includes a species found in Western Australia (Beeinformed 2008). Since 2002

Counterions at Charged Cylinders: Criticality and universality beyond mean-field

The counterion-condensation transition at charged cylinders is studied using Monte-Carlo simulation methods. Employing logarithmically rescaled radial coordinates, large system sizes are tractable and the critical behavior is determined by a combined finite-size and finite-ion-number analysis. Critical counterion localization exponents are introduced and found to be in accord with mean-field theory both in 2 and 3 dimensions. In 3D the heat capacity shows a universal jump at the transition, while in 2D, it consists of discrete peaks where single counterions successively condense.Comment: 4 pages, 3 figures; submitted to Phys. Rev. Lett. (2005

Measurement of correlations between low-frequency vibrational modes and particle rearrangements in quasi-two-dimensional colloidal glasses

We investigate correlations between low-frequency vibrational modes and rearrangements in two-dimensional colloidal glasses composed of thermosensitive microgel particles which readily permit variation of sample packing fraction. At each packing fraction, the particle displacement covariance matrix is measured and used to extract the vibrational spectrum of the "shadow" colloidal glass (i.e., the particle network with the same geometry and interactions as the sample colloid but absent damping). Rearrangements are induced by successive, small reductions in packing fraction. The experimental results suggest that low-frequency quasi-localized phonon modes in colloidal glasses, i.e., modes that present low energy barriers for system rearrangements, are spatially correlated with rearrangements in this thermal system

Honeybee pollination, technical data for potential honey-bee pollinated crops and orchards in Western Australia

The future of pollination of crops by beekeepers in Western Australia is encouraging. The number of crops that can be pollinated are on the increase and in the fruit sector, new varieties are being planted and established crops are being expanded.The use of honeybees in pollination will become very important as cropping areas enlarge and as export markets expand, with premium prices for quality. This bulletin covers general guidance on developing a bee pollination services with specific advice for managing pollination services for vegetable, broadacre grain, fruit, nuts crops.https://researchlibrary.agric.wa.gov.au/bulletins/1232/thumbnail.jp

Rate dependent shear bands in a shear transformation zone model of amorphous solids

We use Shear Transformation Zone (STZ) theory to develop a deformation map for amorphous solids as a function of the imposed shear rate and initial material preparation. The STZ formulation incorporates recent simulation results [Haxton and Liu, PRL 99 195701 (2007)] showing that the steady state effective temperature is rate dependent. The resulting model predicts a wide range of deformation behavior as a function of the initial conditions, including homogeneous deformation, broad shear bands, extremely thin shear bands, and the onset of material failure. In particular, the STZ model predicts homogeneous deformation for shorter quench times and lower strain rates, and inhomogeneous deformation for longer quench times and higher strain rates. The location of the transition between homogeneous and inhomogeneous flow on the deformation map is determined in part by the steady state effective temperature, which is likely material dependent. This model also suggests that material failure occurs due to a runaway feedback between shear heating and the local disorder, and provides an explanation for the thickness of shear bands near the onset of material failure. We find that this model, which resolves dynamics within a sheared material interface, predicts that the stress weakens with strain much more rapidly than a similar model which uses a single state variable to specify internal dynamics on the interface.Comment: 10 pages, 13 figures, corrected typos, added section on rate strengthening vs. rate weakening material

Scaling and Universality in the Counterion-Condensation Transition at Charged Cylinders

We address the critical and universal aspects of counterion-condensation transition at a single charged cylinder in both two and three spatial dimensions using numerical and analytical methods. By introducing a novel Monte-Carlo sampling method in logarithmic radial scale, we are able to numerically simulate the critical limit of infinite system size (corresponding to infinite-dilution limit) within tractable equilibration times. The critical exponents are determined for the inverse moments of the counterionic density profile (which play the role of the order parameters and represent the inverse localization length of counterions) both within mean-field theory and within Monte-Carlo simulations. In three dimensions (3D), correlation effects (neglected within mean-field theory) lead to an excessive accumulation of counterions near the charged cylinder below the critical temperature (condensation phase), while surprisingly, the critical region exhibits universal critical exponents in accord with the mean-field theory. In two dimensions (2D), we demonstrate, using both numerical and analytical approaches, that the mean-field theory becomes exact at all temperatures (Manning parameters), when number of counterions tends to infinity. For finite particle number, however, the 2D problem displays a series of peculiar singular points (with diverging heat capacity), which reflect successive de-localization events of individual counterions from the central cylinder. In both 2D and 3D, the heat capacity shows a universal jump at the critical point, and the energy develops a pronounced peak. The asymptotic behavior of the energy peak location is used to locate the critical temperature, which is also found to be universal and in accordance with the mean-field prediction.Comment: 31 pages, 16 figure

Superintegrability on the two-dimensional hyperboloid

In this work we examine the basis functions for classical and quantum mechanical systems on the two-dimensional hyperboloid that admit separation of variables in at least two coordinate systems. We present all of these cases from a unified point of view. In particular, all of the special functions that arise via variable separation have their essential features expressed in terms of their zeros. The principal new results are the details of the polynomial bases for each of the nonsubgroup bases, not just the subgroup spherical coordinate cases, and the details of the structure of the quadratic symmetry algebras