Metabolite and transcriptome analysis of Campylobacter jejuni in vitro growth reveals a stationary-phase physiological switch.

Campylobacter jejuni is a prevalent cause of food-borne diarrhoeal illness in humans. Understanding of the physiological and metabolic capabilities of the organism is limited. We report a detailed analysis of the C. jejuni growth cycle in batch culture. Combined transcriptomic, phenotypic and metabolic analysis demonstrates a highly dynamic 'stationary phase', characterized by a peak in motility, numerous gene expression changes and substrate switching, despite transcript changes that indicate a metabolic downshift upon the onset of stationary phase. Video tracking of bacterial motility identifies peak activity during stationary phase. Amino acid analysis of culture supernatants shows a preferential order of amino acid utilization. Proton NMR (1H-NMR) highlights an acetate switch mechanism whereby bacteria change from acetate excretion to acetate uptake, most probably in response to depletion of other substrates. Acetate production requires pta (Cj0688) and ackA (Cj0689), although the acs homologue (Cj1537c) is not required. Insertion mutants in Cj0688 and Cj0689 maintain viability less well during the stationary and decline phases of the growth cycle than wild-type C. jejuni, suggesting that these genes, and the acetate pathway, are important for survival.

Influence of ion energy and substrate temperature on the optical and electronic properties of tetrahedral amorphous carbon (ta-C) films

The properties of amorphous carbon (a-C) deposited using a filtered cathodic vacuum arc as a function of the ion energy and substrate temperature are reported. The sp3 fraction was found to strongly depend on the ion energy, giving a highly sp3 bonded a-C denoted as tetrahedral amorphous carbon (ta-C) at ion energies around 100 eV. The optical band gap was found to follow similar trends to other diamondlike carbon films, varying almost linearly with sp2 fraction. The dependence of the electronic properties are discussed in terms of models of the electronic structure of a-C. The structure of ta-C was also strongly dependent on the deposition temperature, changing sharply to sp2 above a transition temperature, T1, of ≈200°C. Furthermore, T1 was found to decrease with increasing ion energy. Most film properties, such as compressive stress and plasmon energy, were correlated to the sp3 fraction. However, the optical and electrical properties were found to undergo a more gradual transition with the deposition temperature which we attribute to the medium range order of sp2 sites. We attribute the variation in film properties with the deposition temperature to diffusion of interstitials to the surface above T1 due to thermal activation, leading to the relaxation of density in context of a growth model. © 1997 American Institute of Physics.

Growth of ultrahigh density vertically aligned carbon nanotube forests for interconnects.

We present a general catalyst design to synthesize ultrahigh density, aligned forests of carbon nanotubes by cyclic deposition and annealing of catalyst thin films. This leads to nanotube forests with an area density of at least 10(13) cm(-2), over 1 order of magnitude higher than existing values, and close to the limit of a fully dense forest. The technique consists of cycles of ultrathin metal film deposition, annealing, and immobilization. These ultradense forests are needed to use carbon nanotubes as vias and interconnects in integrated circuits and thermal interface materials. Further density increase to 10(14) cm(-2) by reducing nanotube diameter is possible, and it is also applicable to nanowires.

The fracture energy of metal fibre reinforced ceramic composites (MFCs)

A model is presented for prediction of the fracture energy of ceramic-matrix composites containing dispersed metallic fibres. It is assumed that the work of fracture comes entirely from pull-out and/or plastic deformation of fibres bridging the crack plane. Comparisons are presented between these predictions and experimental measurements made on a commercially-available composite material of this type, containing stainless steel (304) fibres in a matrix predominantly comprising alumina and alumino-silicate phases. Good agreement is observed, and it's noted that there is scope for the fracture energy levels to be high (~20kJm-2). Higher toughness levels are both predicted and observed for coarser fibres, up to a practical limit for the fibre diameter of the order of 0.5mm. Other deductions are also made concerning strategies for optimisation of the toughness of this type of material. © 2010 Elsevier Ltd.

Material properties and tribological performance of rf-PECVD deposited DLC coatings

Diamond-like carbon (DLC) coatings were deposited on to silicon, glass and metal substrates, using an rf-plasma enhanced chemical vapour deposition (rf-PECVD) process. The resultant film properties were evaluated in respect of material and interfacial property control, based on bias voltage variation and the introduction of inert (He and Ar) and reactive (N2) diluting gases in a CH4 plasma. The analysis techniques used to assess the material properties of the films included AFM, EELS, RBS/ERDA, spectroscopic, electrical, stress, microhardness, and adhesion. These were correlated to the tribological performance of the coatings using wear measurements. The most important observation is that He dilution (>90%) promotes enhanced adhesion with respect to all substrate material studies. Coatings typically exhibit a microhardness of the order of 10-20 GPa in films 0.1of fricton <0.1 and surface RMS roughness as low as 2Å. The results are discussed with respect to surface pre-treatment, ion surface bombardment, interfacial reactivity and changes in plasma gas breakdown processes. | Diamond-like carbon (DLC) coatings were deposited on to silicon, glass and metal substrates, using an rf-plasma enhanced chemical vapour deposition (rf-PECVD) process. The resultant film properties were evaluated in respect of material and interfacial property control, based on bias voltage variation and the introduction of inert (He and Ar) and reactive (N2) diluting gases in a CH4 plasma. The analysis techniques used to assess the material properties of the films included AFM, EELS, RBS/ERDA, spectroscopic, electrical, stress, microhardness, and adhesion. These were correlated to the tribological performance of the coatings using wear measurements. The most important observation is that He dilution (>90%) promotes enhanced adhesion with respect to all substrate materials studied. Coatings typically exhibit a microhardness of the order of 10-20 GPa in films 0.1 < d < 2 μm thick, with associated electrical resistivity in the range 108 < ρ < 1012 Ω·cm, coefficient of friction <0.1 and surface RMS roughness as low as 2 A. The results are discussed with respect to surface pre-treatment, ion surface bombardment, interfacial reactivity and changes in plasma gas breakdown processes.

A Bayesian approach to tracking in single molecule fluorescence microscopy

Using fluorescence microscopy with single molecule sensitivity it is now possible to follow the movement of individual fluorophore tagged molecules such as proteins and lipids in the cell membrane with nanometer precision. These experiments are important as they allow many key biological processes on the cell membrane and in the cell, such as transcription, translation and DNA replication, to be studied at new levels of detail. Computerized microscopes generate sequences of images (in the order of tens to hundreds) of the molecules diffusing and one of the challenges is to track these molecules to obtain reliable statistics such as speed distributions, diffusion patterns, intracellular positioning, etc. The data set is challenging because the molecules are tagged with a single or small number of fluorophores, which makes it difficult to distinguish them from the background, the fluorophore bleaches irreversibly over time, the number of tagged molecules are unknown and there is occasional loss of signal from the tagged molecules. All these factors make accurate tracking over long trajectories difficult. Also the experiments are technically difficulty to conduct and thus there is a pressing need to develop better algorithms to extract the maximum information from the data. For this purpose we propose a Bayesian approach and apply our technique to synthetic and a real experimental data set.

Torsional Behaviour of Cello Strings

The behaviour of a bowed string depends, among other things, on the frequency, impedance and internal damping of torsional waves on the string. Very little published information is available about these quantities, especially the torsional damping. Measurements of all relevant torsional properties have been made on cello strings of three different constructions. These show that the torsional modes are harmonically spaced to reasonable accuracy, and that the Q factors are approximately equal for all modes of a given string. These torsional Q factors are roughly an order of magnitude smaller than those of the transverse modes of the same string. The torsional wave speed varies somewhat with the tension in the string, decreasing with higher tension. The damping factors are not significantly influenced by tension. These results have been expressed in terms of a novel "reflection function" [1] suitable for direct incorporation into simulations of the bowing process.

Optical waveguides and switches based on periodic arrays of carbon nanotubes

This document presents the modeling and characterization of novel optical devices based on periodic arrays of multiwalled carbon nanotubes. Vertically aligned carbon nanotubes can be grown in the arrangement of two-dimensional arrays of precisely determined dimensions. Having their dimensions comparable to the wavelength of light makes carbon nanotubes good candidates for utilization in nano-scale optical devices. We report that highly dense periodic arrays of multiwalled carbon nanotubes can be utilized as sub-wavelength structures for establishing advanced optical materials, such as metamaterials and photonic crystals. We demonstrate that when carbon nanotubes are grown close together at spacing of the order of few hundred nanometers, they display artificial optical properties towards the incident light, acting as metamaterials. By utilizing these properties we have established micro-scaled plasmonic high pass filter which operates in the optical domain. Highly dense arrays of multiwalled also offer a periodic dielectric constant to the incident light and display interesting photonic band gaps, which are frequency domains within which on wave propagation can take place. We have utilized these band gaps displayed by a periodic nanotube array, having 400 nm spacing, to construct photonic crystals based optical waveguides and switches. © 2011 IEEE.

Efficient sampling of atomic configurational spaces.

We describe a method to explore the configurational phase space of chemical systems. It is based on the nested sampling algorithm recently proposed by Skilling (AIP Conf. Proc. 2004, 395; J. Bayesian Anal. 2006, 1, 833) and allows us to explore the entire potential energy surface (PES) efficiently in an unbiased way. The algorithm has two parameters which directly control the trade-off between the resolution with which the space is explored and the computational cost. We demonstrate the use of nested sampling on Lennard-Jones (LJ) clusters. Nested sampling provides a straightforward approximation for the partition function; thus, evaluating expectation values of arbitrary smooth operators at arbitrary temperatures becomes a simple postprocessing step. Access to absolute free energies allows us to determine the temperature-density phase diagram for LJ cluster stability. Even for relatively small clusters, the efficiency gain over parallel tempering in calculating the heat capacity is an order of magnitude or more. Furthermore, by analyzing the topology of the resulting samples, we are able to visualize the PES in a new and illuminating way. We identify a discretely valued order parameter with basins and suprabasins of the PES, allowing a straightforward and unambiguous definition of macroscopic states of an atomistic system and the evaluation of the associated free energies.