Focused ion beam milling and ultramicrotomy of mineralised ivory dentine for analytical transmission electron microscopy

The use of focused ion beam (FIB) milling for preparation of sections of mineralised ivory dentine for transmission electron microscopy (TEM) is investigated. Ivory dentine is essentially composed of fibrillar type-I collagen and apatite crystals. The aim of this project is to gain a clearer understanding of the relationship between the organic and inorganic components of ivory dentine using analytical TEM, in order to utilise these analytical techniques in the context of common skeletal diseases such as osteoporosis and arthritis. TEM sections were prepared in both single and dual beam FIB instruments, using two standard lift-out techniques, in situ and ex situ. The FIB sections were systematically compared with sections prepared by ultramicrotomy, the traditional preparation route in biological systems, in terms of structural and chemical differences. A clear advantage of FIB milling over ultramicrotomy is that dehydration, embedding and section flotation can be eliminated, so that partial mineral loss due to dissolution is avoided. The characteristic banding of collagen fibrils was clearly seen in FIB milled sections without the need for any chemical staining, as is commonly employed in ultramicrotomy. The FIB milling technique was able to produce high-quality TEM sections of ivory dentine, which are suitable for further investigation using electron energy-loss spectroscopy (EELS) and energy-filtering TEM (EFTEM) to probe the collagen/apatite interface.     

Investigating the role of microbes in mineral weathering: Nanometre-scale characterisation of the cell–mineral interface using FIB and TEM

Focused ion beam (FIB) sample preparation in combination with subsequent transmission electron microscopy (TEM) analysis are powerful tools for nanometre-scale examination of the cell–mineral interface in bio-geological samples. In this study, we used FIB-TEM to investigate the interaction between a cyanobacterium (Hassallia byssoidea) and a common sheet silicate mineral (biotite) following a laboratory-based bioweathering, incubation experiment. We discuss the FIB preparation of cross-sections of the cell mineral interface for TEM investigation. We also establish an electron fluence threshold (at 200 keV) in biotite for the transition from scanning (S)TEM electron beam induced contamination build up on the surface of biotite thin sections to mass loss, or hole-drilling within the sections. Working below this threshold fluence nanometre-scale structural and elemental information has been obtained from biotite directly underneath cyanobacterial cells incubated on the biotite for 3 months. No physical alteration of the biotite was detected by TEM imaging and diffraction with little or no elemental alteration detected by STEM–energy dispersive X-ray (EDX) elemental line-scanning or by energy filtered TEM (EF-TEM) jump ratio elemental mapping. As such we present evidence that the cyanobacterial strain of H. byssoidea did not cause any measurable alteration of biotite, within the resolution limits of the analysis techniques used, after 3 months of incubation on its surface.     

Measurement of apex angle of the prism using total internal reflection

Total internal reflection technique is examined critically for the measurement of apex angle of the prism. Recognition of the critical boundary completely specifies the apex angle ‘A’ of the prism by keeping constant the ratio of refractive index of sample fluid (n₁=1.4) to that of glass (n₂=1.7). Recording of observations in the laboratory is dependent upon whether the apex angle ‘A’ of prism is greater than or less than or equal to critical angle ‘r_c’. The minimum value of error function ‘χ’ in the proximity of Abbe angle explain the choice of Abbe type instruments and shown invariant by relating positive ‘₊’ and the negative angle of emergence ‘₋’. Using ray-tracing technique, an expression for the length of the critical boundary ‘l’ is derived and is shown as a measure of the apex angle ‘A’ of the prism.

The choice of the realistic grazing condition leads us to two turning points for which error function ‘χ’ is minimal and yields appropriate option of the measurement of apex angle ‘A’ of the prism. It is further shown that the small error ‘ζ’ crept in the apex angle ‘A’ of the prism can lead to a significant error in the design of Pulfrich type instruments.

Experimental measurements are in-line with the predictions made.     

A model of the early mineralization process of mantle dentin

The aim of this study was to investigate the relationship between proteoglycans (PGs) and collagen fibrils at the early mineralization process of mantle dentin. Ten first molar dental germs of rats were removed and fixed in glutaraldehyde/formaldehyde in cacodylate buffer and post-fixed in osmium tetroxide. The samples were dehydrated and embedded in epoxy resin. Ultrathin sections were contrasted and analyzed in TEM before and after treatment with EDTA, chondroitinases AC and ABC. After EDTA treatment, a electrondense substance associated with collagen fibril was removed, and did not stain again. A high magnification of these areas showed globular structures with 15 nm diameter surrounding collagen fibrils. In advanced mineralization areas, collagen fibrils showed a banded pattern and at high magnification the fibrils presented a light 10 nm ring inside and a dark 10 nm ring outside. After chondroitinase treatment, the electrondense substance associated with collagen fibrils was removed, showing a banded pattern of clear and dark areas along them. From morphological data, the authors proposed a model of interaction between PGs and collagen fibrils, where glicosaminoglycans chains are inside the fibrils, while the protein core remains outside. That stereochemical arrangement would start the crystal nucleation.     

How does Europe Make Its Mind Up? Connections,cliques, and compatibility between countries in the Eurovision Song Contest

We investigate the complex relationships between countries in the Eurovision Song Contest, by recasting past voting data from 1992–2003 in terms of a dynamical network. Our analysis shows that the UK is remarkably compatible, or ‘in tune’, with other European countries during the period of study. Equally surprising is our finding that some other core countries, most notably France, are significantly ‘out of tune’ with the rest of Europe during the same period. In addition, our analysis enables us to confirm a widely-held belief that there are unofficial cliques of countries; however, these cliques are not always the expected ones, nor can their existence be explained solely on the grounds of geographical proximity. The complexity in this system emerges via the group ‘self-assessment’ process, and in the absence of any central controller. One might therefore speculate that such complexity is representative of many real-world situations in which groups of ‘agents’ establish their own inter-relationships and hence ultimately decide their own fate. Possible examples include groups of individuals, societies, political groups or even governments.     

On the control of complex dynamic systems

A method is described for the limited control of the dynamics of systems which generally have several dynamic attractors. associated either with maps or first order ordinary differential equations (ODE) in ⁿ. The control is based on the existence of ‘convergent’ regions, C_C(k = 1,2,…), in the phase space of such systems, where there is ‘local convergence’ of all nearby orbits. The character of the control involves the ‘entrainment’ and subsequent possible ‘migration’ of the experimental system from one attractor to another. Entrainment means that lim_{t > → ∞} |x(t) − g(t)| = 0, where is the system's controlled dynamics, and the goal-dynamics, g(t) ε G_k, has any topological form but is limited dynamically and to regions of phase space, G_k, contained in some C_k, G_k C_k. The control process is initiated only when the system enters a ‘basin of entrainment’, BE_k G_k, associated with the goal-region G_k. Aside from this ‘macroscopic’ initial-state information about the system, no further feedback of dynamic information concerning the response of the system is required. The experimental reliability of the control requires that the regions, BE_k, be convex regions in the phase space, which can apparently be assured if G_k C_k. Simple illustrations of these concepts are given, using a general linear and a piecewise-linear ODE in . In addition to these entrainment-goals, ‘migration-goal’ dynamics is introduced, which intersects two convergent regions G ∩ C_j ≠ , G ∩ C_j ≠ (i ≠ j), and permits transferring the dynamics of a system from one attractor to another, or from one convergent region to another. In the present study these concepts are illustrated with various one-dimensional maps involving one or more attractors and convergent regions. Several theorems concerning entrainment are derived for very general, continuous one-dimensional maps. Sufficient conditions are also established which ensure ‘near-entrainment’ for a system, when the dynamic model of the system is not exactly known. The applications of these concepts to higher dimensional maps and flows will be presented in subsequent studies.     

Sample preparation by focused ion beam micromachining for transmission electron microscopy imaging in front-view

This article deals with the development of an original sample preparation method for transmission electron microscopy (TEM) using focused ion beam (FIB) micromachining. The described method rests on the use of a removable protective shield to prevent the damaging of the sample surface during the FIB lamellae micromachining. It enables the production of thin TEM specimens that are suitable for plan view TEM imaging and analysis of the sample surface, without the deposition of a capping layer. This method is applied to an indented silicon carbide sample for which TEM analyses are presented to illustrate the potentiality of this sample preparation method.     

On the application of the optical method of caustics to the investigation of transient elastodynamic crack problems: Limitations of the classical interpretation

Several possible sources of inaccuracy that occur in the classical interpretation of caustics patterns generated during transient crack growth in elastic materials are examined using a ‘Bifocal Caustics’ set-up and a new full field optical technique called ‘Coherent Gradient Sensing’. During unsteady dynamic crack growth, strict K^d_I-dominance is generally absent, especially at times close to crack initiation and arrest, even in regions outside the crack-tip 3-D zone where plane stress conditions persist. In such cases a truly transient higher order expansion is found to be essential for correctly describing stress fields outside the 3-D zone.     

Molecular structural analysis of noncarious cervical sclerotic dentin using Raman spectroscopy

Molecular structure of the sclerotic dentin in noncarious cervical lesions (NCCLs) including both the inorganic phase and organic phase was investigated using Raman spectroscopy. It was found that NCCL sclerotic dentin was hypermineralized with the mineral/matrix ratios 2–3 times higher than those of normal dentin, which was caused by both the increase of mineral content and decrease of organic matrix (collagen) content in the sclerotic dentin. For the inorganic phase, the phosphate band (PO₄³⁻, ν₁, symmetric stretching vibrational mode) in NCCL sclerotic dentin was shifted from 960 to 963 cm⁻¹, and the width of this band was decreased from 16.4 to 10.4 cm⁻¹, indicating that the degree of mineral crystallinity in NCCL sclerotic dentin was higher than that of normal dentin. In addition, the carbonate content in the mineral of NCCL sclerotic dentin was less than that of normal dentin. As compared to the inorganic phase, the changes within the organic phase were not dramatic. However, the changes in collagen cross‐link density along with other spectral changes were still detectable. There was a noteworthy reduction in the ratio of nonreducible to reducible cross‐links in the NCCL sclerotic dentin, indicating that cross‐link breaks occurred in the collagen matrix of the lesions. Copyright © 2009 John Wiley & Sons, Ltd.     

Tuning of a parametric model for the laser cutting of steels

In this work the mathematical models developed to describe the gas jet laser cutting process are examined.

Some experimental results for the laser cutting of carbon and stainless steels are also shown. These results are then used to ‘tune’ the theoretical models in order to obtain a method for making predictions about the parameters of interest in the laser cutting of steels.     

Magnetic anisotropy and spin-reorientation transitions in RFe11Ti (R = Nd, Tb, Dy, Er) rare-earth intermetallics

RFe₁₁Ti rare-earth intermetallics (R = Nd, Tb, Dy, Er) which show temperature-induced spin-reorientation transitions (SRT) were investigated. The temperature dependences of the rare-earth anisotropy constants were calculated using the single-ion model. By fitting the experimental data a set of crystal-field and exchange-field parameters for R³⁺ ions wassb deduced. The temperature dependence of the first-order magnetization process fields was calculated for NdFe₁₁Ti and ErFe₁₁Ti within the model. The calculated spin-reorientation transition in NdFe₁₁Ti observed at T_s = 189 K is of first order with a discontinuous jump of the magnetization angle. Present calculations show that a first-order transition occurs in DyFe₁₁Ti at low temperatures. A second-order SRT from ‘easy axis’ to ‘easy cone’ exists in ErFe₁₁Ti. A first-order SRT ‘easy axis’-‘easy plane’ is predicted theoretically in TbFe₁₁Ti. The calculated curves of the temperature dependence of the anisotropy fields and the critical fields of the first-order magnetization processes for RFe₁₁Ti using the fitted crystal- and exchange-field parameters are in good agreement with the experimental data over a wide temperature range.     

Improved FIB milling process for TEM preparation of NiAlPt bulk alloy samples containing residual stress

NiAlPt alloys which undergo complex martensitic and twinning transformations during thermal cycling were prepared for Transmission Electron Microscopy (TEM) analysis using the Focused Ion Beam (FIB) milling process. Coupons of alloys that underwent cyclic heating, with no prior isothermal heat treatment contained a build-up of residual stress that caused sections of the foil to crack or buckle during the thinning process, rendering them useless. The solution was to mill strain isolation trenches perpendicular to the area of interest. These trenches acted as reservoirs for the released residual stress. This step was conducted in conjunction with reducing the beam current much earlier in the thinning process, thus ensuring minimum damage to the section being thinned. These two modifications of the standard FIB milling process, with emphasis on the strain isolation trenches, allowed for successful preparation of TEM samples from a bulk alloy containing residual stress.     

Comparison of ‘blue’ and ‘infrared’ emission bands in thermoluminescence of alkali feldspars

Dating quaternary sediments by thermoluminescence (TL) or optically stimulated luminescence (OSL) calls for a detailed knowledge of the luminescence of feldspars. TL of the various alkali feldspars ((K, Na) Si₃AlO₈) display many common features, and some of these cause great difficulties for dating. After long storage following ionizing irradiation, the TL of most alkali feldspars is known to fade away by “anomalous fading”, which is incompatible with dating. This effect had been attributed to tunnel recombination. Following irradiation, a very intense tunnelling afterglow is observed at temperatures down to liquid nitrogen, in accordance with the observed rate of fading. This emission has a Gaussian spectrum entirely in the infrared (IR) with a maximum at 1.7 eV. It displays an important thermal quenching from 77 to 300 K. Its intensity is related with the ‘disorder’ of the crystal lattice. At higher temperatures, in TL proper, two emission bands can be separated. One is the well-studied complex visible emission, distributed over the spectral region from UV to orange, but mostly ‘blue’. The other is the ‘infrared’ band already observed at lower temperatures, which is attributed to Fe³⁺ ions. These two bands are clearly separated, with the spectral maxima, respectively, below and above 600 nm. They have also different kinetics, the glow peaks temperatures are different. But these two different bands are also coupled in many ways, they have parallel growth and fading. With ‘disordered’ feldspars, the ‘blue’ emission displays anomalous fading, which is stronger than that of the ‘infrared’. The infrared emission is more stable, which may be interesting for the purpose of dating.     

The application of high speed photography and white light speckle to the study of dynamic fracture

A white light speckle technique is combined with high speed photography to study the dynamic fracture of a sample of PMMA. A series of single exposure speckle patterns are photographically recorded at the rate of 2 × 10⁵ frames s^-1 during fracture of the sample. The displacement field around the tip of the propagating crack may then be determined by superimposing pairs of individual frames to form a ‘double-exposure’ speckle pattern. It is shown that the method gives values for the stress intensity factor K which are consistent with those obtained from other techniques.     

Exploring the need for localization in ensemble data assimilation using a hierarchical ensemble filter

Good performance with small ensemble filters applied to models with many state variables may require ‘localizing’ the impact of an observation to state variables that are ‘close’ to the observation. As a step in developing nearly generic ensemble filter assimilation systems, a method to estimate ‘localization’ functions is presented. Localization is viewed as a means to ameliorate sampling error when small ensembles are used to sample the statistical relation between an observation and a state variable. The impact of spurious sample correlations between an observation and model state variables is estimated using a ‘hierarchical ensemble filter’, where an ensemble of ensemble filters is used to detect sampling error. Hierarchical filters can adapt to a wide array of ensemble sizes and observational error characteristics with only limited heuristic tuning. Hierarchical filters can allow observations to efficiently impact state variables, even when the notion of ‘distance’ between the observation and the state variables cannot be easily defined. For instance, defining the distance between an observation of radar reflectivity from a particular radar and beam angle taken at 1133 GMT and a model temperature variable at 700 hPa 60 km north of the radar beam at 1200 GMT is challenging. The hierarchical filter estimates sampling error from a ‘group’ of ensembles and computes a factor between 0 and 1 to minimize sampling error. An a priori notion of distance is not required. Results are shown in both a low-order model and a simple atmospheric GCM. For low-order models, the hierarchical filter produces ‘localization’ functions that are very similar to those already described in the literature. When observations are more complex or taken at different times from the state specification (in ensemble smoothers for instance), the localization functions become increasingly distinct from those used previously. In the GCM, this complexity reaches a level that suggests that it would be difficult to define efficient localization functions a priori. There is a cost trade-off between running hierarchical filters or running a traditional filter with larger ensemble size. Hierarchical filters can be run for short training periods to develop localization statistics that can be used in a traditional ensemble filter to produce high quality assimilations at reasonable cost, even when the relation between observations and state variables is not well-known a priori. Additional research is needed to determine if it is ever cost-efficient to run hierarchical filters for large data assimilation problems instead of traditional filters with the corresponding total number of ensemble members.     

High resolution transmission electron microscopy (HRTEM) and image analysis of uPVC thin films

The current model for the fine scale microstructure of unplasticized PVC (uPVC) has been built up using various quantitative techniques, such aa wide and small angle X-ray diffraction. The use of transmission electron microscopy (TEM) as a more qualitative technique has been previously attempted (Meyer et al., 1978), revealing only amorphous detail on the scale of the expected crystallinity. For this study, a combination of high resolution TEM (HRTEM) and digital image processing techniques was utilized in order to verify the ‘micro-domain’ model proposed by Summers (1981). The techniques utilized here are particularly applicable in examining the fine-scale texture of oriented polymers.     

Constructing ‘hair’ for the three charge hole

It has been found that the states of the 2-charge extremal D1–D5 system are given by smooth geometries that have no singularity and no horizon individually, but a ‘horizon’ does arise after ‘coarse-graining’. To see how this concept extends to the 3-charge extremal system, we construct a perturbation on the D1–D5 geometry that carries one unit of momentum charge P. The perturbation is found to be regular everywhere and normalizable, so we conclude that at least this state of the 3-charge system behaves like the 2-charge states. The solution is constructed by matching (to several orders) solutions in the inner and outer regions of the geometry. We conjecture the general form of ‘hair’ expected for the 3-charge system, and the nature of the interior of black holes in general.     

Evaluation of a metaphase chromosome finder: Potential application to chromosome-based radiation dosimetry

An automated metaphase chromosome finder is described which combines a microscope, state-of-the-art computer technology and a simple decision-making algorithm. A microscope slide is systematically scanned under computer control and the location of each positive ‘signal’ placed into memory for later recall and review by a human operator. The software identifies two events, positives (the presence of a ‘signal’) and negatives (the absence of a ‘signal’). The performance of the metaphase finder was evaluated using receiver operating characteristic curve analysis. At the optimum decision threshold, the detection rates for true positives (metaphase spreads) was about 74%, false positives (type I error) about 6%, and false negatives (type II error) about 26%. The overall accuracy, which accounts for differences in the sensitivity of the detector to positive and negative events, was 89.4% (±0.01%; standard error of the mean, n = 8). Potential applications to radiation dosimetry are discussed.     

The effect of UV exposure on the track and bulk etching rates in different CR-39 plastics

It is observed that for both UK and Japanese CR-39 detectors the mean diameters of fission fragment and alpha tracks from a Cf-252 source become larger as a result of UV exposure; but in the case of ‘UV exposure last’ (i.e. Cf + UV) the diameters are larger than in the case of ‘UV exposure first’ (i.e. UV + Cf). The bulk and track etching rates undergo an increase with UV exposure for the two kids of CR-39.     

Sonochemistry: a systematic study of the maleate-fumarate isomerization in the presence of alkyl bromides

A systematic and quantitative study of diethyl maleate-diethyl fumarate induced isomerization has been performed in CCl₄ using different ‘inert’ gases, different initiators and various experimental conditions. It was shown how changes in the experimental conditions, generally considered as minor in thermochemistry, can have dramatic effects in sonochemistry (for example, the ‘marble effect’).