Laboratory Growth Systems in Biofilm Research

The huge variety of ecosystems that we collectively refer to as biofilm is reflected by the numerous different systems available to grow them in the laboratory. The relationship between in situ systems, microcosms and laboratory models is defined and discussed. The first two represent holistic approaches designed to assess the structure and function of particular biofilms: the last is analytical and reductionist, aiming to isolate specific functions of biofilms in order to understand properties that can apply to biofilm in general. Properties of a model can be completely understood whilst this is unlikely with natural ecosystems because of the possibility of unculturable species which could play an unrecognised but important part in its structure and function. A range of systems is reviewed. These include simple surfaces exposed to nutrient in different ways, flow systems such as the Robbins device and constant shear devices such as the Rototorque and the Fowler cell adhesion measurement module. The constant depth film fermenter (CDFF) is described as are membrane based models including the membrane biofilm and the perfused biofilm reactors. Some examples of microcosms are described. The concept and value of steady state biofilm is introduced in terms of the CDFF and of fluidised bed reactors. A number of commercially available film fermenters are listed in the appendix

Defect Production in Slow First Order Phase Transitions

We study the formation of vortices in a U(1) gauge theory following a first-order transition proceeding by bubble nucleation, in particular the effect of a low velocity of expansion of the bubble walls. To do this, we use a two-dimensional model in which bubbles are nucleated at random points in a plane and at random times and then expand at some velocity $v_{\rm b}<c$. Within each bubble, the phase angle is assigned one of three discrete values. When bubbles collide, magnetic `fluxons' appear: if the phases are different, a fluxon--anti-fluxon pair is formed. These fluxons are eventually trapped in three-bubble collisions when they may annihilate or form quantized vortices. We study in particular the effect of changing the bubble expansion speed on the vortex density and the extent of vortex--anti-vortex correlation.Comment: 13 pages, RevTeX, 15 uuencoded postscript figure

Structural origin of the anomalous temperature dependence of the local magnetic moments in the CaFe2_{2}As2_{2} family of materials

We report a combination of Fe K$\beta$ x-ray emission spectroscopy and $ab$-intio calculations to investigate the correlation between structural and magnetic degrees of freedom in CaFe$_{2}$(As$_{1-x}$P$_{x}$)$_{2}$. The puzzling temperature behavior of the local moment found in rare earth-doped CaFe$_{2}$As$_{2}$ [\textit{H. Gretarsson, et al., Phys. Rev. Lett. {\bf 110}, 047003 (2013)}] is also observed in CaFe$_{2}$(As$_{1-x}$P$_{x}$)$_{2}$. We explain this phenomenon based on first-principles calculations with scaled magnetic interaction. One scaling parameter is sufficient to describe quantitatively the magnetic moments in both CaFe$_{2}$(As$_{1-x}$P$_{x}$)$_{2}$ ($x=0.055$) and Ca$_{0.78}$La$_{0.22}$Fe$_{2}$As$_{2}$ at all temperatures. The anomalous growth of the local moments with increasing temperature can be understood from the observed large thermal expansion of the $c$-axis lattice parameter combined with strong magnetoelastic coupling. These effects originate from the strong tendency to form As-As dimers across the Ca layer in the CaFe$_{2}$As$_{2}$ family of materials. Our results emphasize the dual local-itinerant character of magnetism in Fe pnictides

Bacteria classification using Cyranose 320 electronic nose

Background An electronic nose (e-nose), the Cyrano Sciences' Cyranose 320, comprising an array of thirty-two polymer carbon black composite sensors has been used to identify six species of bacteria responsible for eye infections when present at a range of concentrations in saline solutions. Readings were taken from the headspace of the samples by manually introducing the portable e-nose system into a sterile glass containing a fixed volume of bacteria in suspension. Gathered data were a very complex mixture of different chemical compounds. Method Linear Principal Component Analysis (PCA) method was able to classify four classes of bacteria out of six classes though in reality other two classes were not better evident from PCA analysis and we got 74% classification accuracy from PCA. An innovative data clustering approach was investigated for these bacteria data by combining the 3-dimensional scatter plot, Fuzzy C Means (FCM) and Self Organizing Map (SOM) network. Using these three data clustering algorithms simultaneously better 'classification' of six eye bacteria classes were represented. Then three supervised classifiers, namely Multi Layer Perceptron (MLP), Probabilistic Neural network (PNN) and Radial basis function network (RBF), were used to classify the six bacteria classes. Results A [6 × 1] SOM network gave 96% accuracy for bacteria classification which was best accuracy. A comparative evaluation of the classifiers was conducted for this application. The best results suggest that we are able to predict six classes of bacteria with up to 98% accuracy with the application of the RBF network. Conclusion This type of bacteria data analysis and feature extraction is very difficult. But we can conclude that this combined use of three nonlinear methods can solve the feature extraction problem with very complex data and enhance the performance of Cyranose 320

Spin reorientation in FeCrAs revealed by single-crystal neutron diffraction

The magnetic structure of the "nonmetallic metal" FeCrAs, a compound with the characters of both metals and insulators, was examined as a function of temperature using single-crystal neutron diffraction. The magnetic propagation vector was found to be $\mathit{k}$ = (1/3, 1/3, 0), and the magnetic reflections disppeared above $\mathit{T_{N}}$ = 116(1) K. In the ground state, the Cr sublattice shows an in-plane spiral antiferromagnetic order. The moment sizes of the Cr ions were found to be small, due to strong magnetic frustration in the distorted Kagome lattice or the itinerant nature of the Cr magnetism, and vary between 0.8 and 1.4 $\mu_{B}$ on different sites as expected for a spin-density-wave (SDW) type order. The upper limit of the moment on the Fe sublattice is estimated to be less than 0.1 $\mu_{B}$. With increasing temperature up to 95 K, the Cr moments cant out of the $\mathit{ab}$ plane gradually, with the in-plane components being suppressed and the out-of-plane components increasing in contrast. This spin-reorientation of Cr moments can explain the dip in the $\mathit{c}$-direction magnetic susceptibility and the kink in the magnetic order parameter at $\mathit{T_{O}}$ ~ 100 K, a second magnetic transition which was unexplained before. We have also discussed the similarity between FeCrAs and the model itinerant magnet Cr, which exhibits spin-flip transitions and SDW-type antiferromagnetism.Comment: 8 pages, 7 figures, Accepted by Phys. Rev.