Structural and morphological anomalies in magnetosomes: possible biogenic origin for magnetite in ALH84001

We report biogenic magnetite whiskers, with axial ratios of 6 : 1, elongated in the [1 1 1], [1 1 2] and [1 0 0] directions, resembling the magnetite whiskers detected in the Martian meteorite ALH84001 by Bradley et al . , and interpreted by those authors as evidence of vapour-phase (abiogenic) growth. Magnetosomal whiskers with extended defects consistent with screw dislocations and magnetosomes resembling flattened twinned platelets, as well as other twinning phenomena and other structural defects, are also reported here. Magnetosomes with teardrop-shaped, cuboidal, irregular and jagged structures similar to those detected in ALH84001 by McKay et al . , coprecipitation of magnetite possibly with amorphous calcium carbonate, coprecipitation of magnetite possibly with amorphous silica, the incorporation of titanium in volutin inclusions and disoriented arrays of magnetosomes are also described. These observations demonstrate that the structures of the magnetite particles in ALH84001, their spatial arrangement and coprecipitation with carbonates and proximity to silicates are consistent with being biogenic.
Electron-beam-induced flash-melting of magnetosomes produced numerous screw dislocations in the {1 1 1}, {1 0 0} and {1 1 0} lattice planes and induced fusion of platelets. From this, the lack of screw dislocations reported in the magnetite particles in ALH84001 ( McKay et al ., and Bradley et al . ) indicates that they have a low-temperature origin.     

The Nature And Origin Of {113} Faults In Irradiated Silicon And Germanium

At elevated temperatures, electron irradiation damage in silicon and germanium forms faulted defects on {113} which are elongated in <110>. During the present work on silicon, these {113} faults were observed to unfault, apparently by glide, to give elongated interstitial loops with b = a/2<110>. Since the tetrahedral interstitial sites between adjacent {113}s form a full {113}, in both number and distribution, it was concluded that the atoms were accommodated in these positions. A fault of this type comprises interstitial pairs, the atoms of which are on adjacent tetrahedral sites a/4<111> apart, and it is proposed that these already exist, or are formed, when a fault nucleates. Two‘di-interstitials’ then close-pack along one of the three <110>s normal to their <111> axis, thus nucleating a {112} loop. This is unable to grow in any direction other than <110>, because its habit plane is occupied by matrix atoms, so the loops become extended. The defect grows in width by nucleating further loops on {112} planes, extended parallel to the first, and the‘array’ forms an elongated {113} defect, on a plane 10° from the original {112}. This gives the observed faulted {113} loops, elongated in <110>, with R ?/11<113>.     

Shear banding in twinned structure of copper deformed at 77 K

The local crystallography and microstructure within shear bands has been examined in single crystals of {112}<111> orientation of pure copper deformed at 77 K by channel‐die compression to true strains of about 1. Setting up a system for making high‐resolution orientation maps using transmission electron microscopy has provided advantageous circumstances for the analysis of orientation changes within shear bands. The present work shows that, despite the plane strain deformation mode, the mechanism of lattice rotation within emerging shear bands may lead to Goss {110}< 001> and Brass{110}<112> texture components.     

In-situ observation of shape and atomic structure of Xe nanocrystals embedded in aluminium

An imaging technique to determine in situ the shape and atomic structure of nanosized Xe crystals embedded in Al is described using high-resolution transmission electron microscopy (HRTEM). The Xe nanocrystals, with sizes less than 5 nm were prepared by the implantation of 30 keV Xe⁺ into Al at room temperature. The fcc Xe nanocrystals are mesotactic with the Al lattice and have a lattice parameter ≈ 50% larger than that of Al. HRTEM images of the Xe were not clear in [110] zone axis illumination because of the small number of Xe atoms relative to Al atoms in any atom column. An off-axial imaging technique that consists of tilting the specimen several degrees from a zone axis and defocusing to suppress the Al lattice fringes is employed for the 110 projection of the Xe/Al system and the structure of the Xe nanocrystals is successfully imaged. The Xe images clearly represent projections of cuboctahedra with faces parallel to eight Al {111} planes truncated by six {100} planes. The results of multislice image simulations using a three-dimensional atomic model agreed well with the results obtained by the off-axial imaging technique. The usefulness of the technique is demonstrated with observations of crystal defects introduced into the Xe under intense 1000 keV electron irradiation.     

Modulated structures in Ni–Al–Cr alloy

The crystal structures of the different modulated and layered martensites in Ni–Al–Cr alloy have been observed. The layered martensite can be well described by the L1₀ lattice with seven‐layered or five‐layered long‐period stacking of {110} close‐packed planes of the parent phase. Modulated martensite is considered as a lattice oscillation by shuffling of atoms.     

Reconstructing the microstructure of polyimide–silicalite mixed‐matrix membranes and their particle connectivity using FIB‐SEM tomography

Properties of a composite material made of a continuous matrix and particles often depend on microscopic details, such as contacts between particles. Focusing on processing raw focused‐ion beam scanning electron microscope (FIB‐SEM) tomography data, we reconstructed three mixed‐matrix membrane samples made of 6FDA‐ODA polyimide and silicalite‐1 particles. In the first step of image processing, backscattered electron (BSE) and secondary electron (SE) signals were mixed in a ratio that was expected to obtain a segmented 3D image with a realistic volume fraction of silicalite‐1. Second, after spatial alignment of the stacked FIB‐SEM data, the 3D image was smoothed using adaptive median and anisotropic nonlinear diffusion filters. Third, the image was segmented using the power watershed method coupled with a seeding algorithm based on geodesic reconstruction from the markers. If the resulting volume fraction did not match the target value quantified by chemical analysis of the sample, the BSE and SE signals were mixed in another ratio and the procedure was repeated until the target volume fraction was achieved. Otherwise, the segmented 3D image (replica) was accepted and its microstructure was thoroughly characterized with special attention paid to connectivity of the silicalite phase. In terms of the phase connectivity, Monte Carlo simulations based on the pure‐phase permeability values enabled us to calculate the effective permeability tensor, the main diagonal elements of which were compared with the experimental permeability. In line with the hypothesis proposed in our recent paper (?apek, P. et al. (2014) Comput. Mater. Sci. 89 , 142–156), the results confirmed that the existence of particle clusters was a key microstructural feature determining effective permeability.     

Experimental statistics of near-field intensity distributions at nanostructured surfaces

Scanning near‐field optical microscopy is a technique in which the resolution is primarily determined by the size of a probe and not by the wavelength of illumination as in classical (far‐field) microscopy. However, the relationship between a sample and its near‐field optical image is usually rather complex. Typical factors responsible, at least partially, for such a complexity are the conditions of illumination and detection, sample characteristics (e.g. roughness and dielectric constant) and optical properties of the probe. Theoretical and experimental works conducted to improve our understanding of the relation between the object and the image have been reported ( Greffet & Carminati, 1997 ). Recently, with the help of a photon scanning tunnelling microscope we have carried out an extensive study of the resultant near‐field intensity distributions due to the elastic (in the plane) scattering of surface plasmon polaritons (SPPs) at metal film surfaces. We have also directly observed (in similar experimental conditions) localized dipolar excitations in silver colloid fractals ( Bozhevolnyi et al., 1998 ). In both cases, the studied phenomena are intimately related to the regime of multiple light scattering, in which the interference effects are rather complicated and therefore a proper interpretation of them was far from being trivial. Thus, even though a certain understanding of many features inherent to the subwavelength light interference phenomena was gained ( Bozhevolnyi & Coello, 1998 ; Bozhevolnyi et al., 1998 ; Coello & Bozhevolnyi, 1999 ), it is clear from the outcome of the investigations that more systematic studies in this context are still needed. A different and more powerful approach may be a statistical study of the recorded near‐field intensity distributions. In this work, we report what we believe to be the first results on experimental statistics of near‐field optical images exhibiting localized optical excitations (related to the regime of multiple scattering of light). We investigated optical images obtained with SPPs excited at different light wavelengths and scattered at different film surfaces, and with different polarizations and wavelengths of light scattered by silver colloid fractal structures. We have found significant differences in statistics between near‐field intensity distributions taken at rough and smooth metal film surfaces and fractal structures. Finally, our predictions seem to be in agreement with theoretical studies reported by other authors ( Sanchez‐Gil & Garcia‐Ramos, 1998 ).     

Morphological analyses of minute crystals by using stereo-photogrammetric scanning electron microscopy and electron back-scattered diffraction

We present a new method for the morphological analyses of minute faceted crystals by combining stereo-photogrammetric analysis of scanning electron microscope images and electron back-scattered diffraction. Two scanning electron microscope images of the same crystal, recorded at different tilt angles of the specimen stage, are used to determine the orientations of crystal edges in a specimen-fixed coordinate system. The edge orientations are converted to the indices [ uvw ] in the crystal system using the crystal orientation determined by electron back-scattered diffraction analysis. The Miller indices of crystal facets are derived from the indices of the edges surrounding the facets. The method is applicable to very small crystal facets. The angular error, as derived from tests using a calcite crystal of known morphology, is a few degrees.
To demonstrate the applicability of the method, the morphology of boehmite (γ-AlOOH) precipitated from solution during the dissolution of anorthite was analyzed. The micrometre-sized boehmite crystals are surrounded by two {010} basal facets and eight equivalent side facets that can be indexed equally well as {323}, {434} or {545}. We suggest that these side facets are in fact {111}, the morphology having been modified slightly (by a few degrees) by a small extension associated with opening along (010) microcleavage planes. Tiny {140} facets are also commonly observed.     

Atomic force microscopy imaging of fragments from the Martian meteorite ALH84001

A combination of scanning electron microscopy (SEM) and environmental scanning electron microscopy (ESEM) techniques, as well as atomic force microscopy (AFM) methods has been used to study fragments of the Martian meteorite ALH84001. Images of the same areas on the meteorite were obtained prior to and following gold/palladium coating by mapping the surface of the fragment using ESEM coupled with energy-dispersive X-ray analysis. Viewing of the fragments demonstrated the presence of structures, previously described as nanofossils by McKay et al . (Search for past life on Mars — possible relic biogenic activity in martian meteorite ALH84001. Science , 1996, pp. 924–930) of NASA who used SEM imaging of gold-coated meteorite samples. Careful imaging of the fragments revealed that the observed structures were not an artefact introduced by the coating procedure.     

Scanning electron microscopy and transmission electron microscopy in situ studies of grain boundary migration in cold-deformed aluminium bicrystals

The crystallography of recrystallization has been investigated in channel‐die deformed pure aluminium bicrystals with {100}<011>/{110}<001> orientations. The microstructural and microtextural changes during the early stages of recrystallization were followed by systematic local orientation measurements using scanning and transmission electron microscopes. In particular, orientation mapping combined with in situ sample heating was used to investigate the formation and growth of new grains at very early stages of recrystallization. Grain boundary migration and ‘consumption’ of the as‐deformed areas was always favoured along directions parallel to the traces of the {111} slip planes that had been most active during deformation.     

Application of combined EBSD and 3D‐SEM technique on crystallographic facet analysis of steel at low temperature

Electron backscatter diffraction has been increasingly used to identify the crystallographic planes and orientation of cleavage facets with respect to the rolling direction in fracture surfaces. The crystallographic indices of cleavage planes can be determined either directly from the fracture surface or indirectly from metallographic sections perpendicular to the plane of the fracture surface. A combination of electron backscatter diffraction and 3D scanning electron microscopy imaging technique has been modified to determine crystallographic facet orientations. The main purpose of this work has been to identify the macroscopic crystallographic orientations of cleavage facets in the fracture surfaces of weld heat affected zones in a well‐known steel fractured at low temperatures. The material used for the work was an American Petroleum Institute (API) X80 grade steel developed for applications at low temperatures, and typical heat affected zone microstructures were obtained by carrying out weld thermal simulation. The fracture toughness was measured at different temperatures (0°C, ?30°C, ?60°C and ?90°C) by using Crack Tip Opening Displacement testing. Fracture surfaces and changes in microstructure were analyzed by scanning electron microscopy and light microscopy. Crystallographic orientations were identified by electron backscatter diffraction, indirectly from a polished section perpendicular to the major fracture surface of the samples. Computer assisted 3D imaging was used to measure the angles between the cleavage facets and the adjacent polished surface, and then these angles were combined with electron backscatter diffraction measurements to determine the macroscopic crystallographic planes of the facets. The crystallographic indices of the macroscopic cleavage facet planes were identified to be {100}, {110}, {211} and {310} at all temperatures.     

Design-based estimation of surface area in thick tissue sections of arbitrary orientation using virtual cycloids

Surface area is a first‐order stereological parameter with important biological applications, particularly at the intersection of biological phases. To deal with the inherent anisotropy of biological surfaces, state‐of‐the‐art design‐based methods require tissue rotation around at least one axis prior to sectioning. This paper describes the use of virtual cycloids for surface area estimation of objects and regions in thick, transparent tissue sections cut at any arbitrary (convenient) orientation. Based on the vertical section approach of Baddeley et al., the present approach specifies the vertical axis as the direction of sectioning (i.e. the direction perpendicular to the tissue section), and applies computer‐generated cycloids (virtual cycloids) with their minor axis parallel to the vertical axis. The number of surface‐cycloid intersections counted on focal planes scanned through the z‐axis is proportional to the surface area of interest in the tissue, with no further assumptions about size, shape or orientation. Optimal efficiency at each x–y location can be achieved by three virtual cycloids orientated with their major axes (which are parallel to the observation planes) mutually at an angle of 120°. The major practical advantage of the present approach is that estimates of total surface area (S) and surface density (S_V) can be obtained in tissue sections cut at any convenient orientation through the reference space.     

Precession electron diffraction‐assisted crystal phase mapping of metastable c‐GaN films grown on (001) GaAs

The control growth of the cubic meta‐stable nitride phase is a challenge because of the crystalline nature of the nitrides to grow in the hexagonal phase, and accurately identifying the phases and crystal orientations in local areas of the nitride semiconductor films is important for device applications. In this study, we obtained phase and orientation maps of a metastable cubic GaN thin film using precession electron diffraction (PED) under scanning mode with a point‐to‐point 1 nm probe size beam. The phase maps revealed a cubic GaN thin film with hexagonal GaN inclusions of columnar shape. The orientation maps showed that the inclusions have nucleation sites at the cubic GaN {111} facets. Different growth orientations of the inclusions were observed due to the possibility of the hexagonal {0001} plane to grow on any different {111} cubic facet. However, the generation of the hexagonal GaN inclusions is not always due to a 60° rotation of a {111} plane. These findings show the advantage of using PED along with phase and orientation mapping, and the analysis can be extended to differently composed semiconductor thin films. Microsc. Res. Tech. 77:980–985, 2014. © 2014 Wiley Periodicals, Inc.     

Application of symbolic manipulation to inverse dynamics and kinematics of elastic robots

An inverse dynamics and kinematics of a flexible manipulator is derived in symbolic form based on the recursive Lagrangian assumed mode method. A PC-based program has implemented the algorithm to automatically generate the inverse dynamics and kinematics for an elastic robot in a symbolic form. A case study is given to illustrate how to use this program for inverse dynamic and kinematic generation. Simulation results for a case study by considering different mode shape are compared with the rigid case.Nomenclature A _i joint transformation relates systemi to systemi-1 - E _i link transformation relates the deflection of systemi to systemi - F _i joint torque acting on jointi - g gravity vector expressed at the base coordinates - J inertia = - K kinetic energy of the system - l _i length of linki - M _i a mass concentrated at the joint i - m _i number of modes used to describe the deflection of link i - n number of links - q _h joint variable of thehth joint - q _hk time-varying amplitude of mode k of link h - R vector of remaining dynamics and external forcing terms = - r _i vector locating the centre of mass of linki - R _j dynamics from the joint equation j, excluding second derivatives of the generalized coordinates - R _if dynamics from the deflection equation jf, excluding second derivatives of the generalized coordinates - V potential energy - W _i transformation from the base to theith link - transformation from the base to the systemî - z the vector of generalised coordinates = - link density     

Structure of the (110) antiphase boundary in gallium phosphide

The morphology of antiphase boundaries in GaP films grown by molecular beam epitaxy on Si (001) has been studied by transmission electron microscopy. The inversion of the crystal polarity between antiphase domains was confirmed by convergent‐beam electron diffraction. The APBs were often found to facet parallel to {110} planes. Strong‐beam α‐fringe contrast observed along the (110) facets indicates that adjacent antiphase domains are related by an additional rigid‐body lattice translation. Diffraction‐contrast analysis shows that this R corresponds to a shear parallel to the [001] direction and a small expansion. The magnitude of the translation was inferred, quantitatively, through a comparison between energy‐filtered zero‐loss images of the α‐fringe contrast with numerical calculations. The components of the rigid‐body lattice translation were determined to be 0.023 ± 0.0033 nm in the [001] direction and 0.005 ± 0.002 nm in the 0 direction. Based upon a geometric model of the {110} antiphase boundary, the lengths of the Ga and P antisite bonds were calculated to be 254 ± 2 pm and 227 ± 4 pm, respectively.     

Enhanced oxygen diffusion and precipitation in silicon

Prolonged annealing of Cz-silicon at 758 K results in the formation of ribbon-like oxygen precipitates on {311} planes interpreted as the coesite phase. From this an enhancement of the oxygen diffusion coefficient by more than three orders of magnitude is inferred. Excess selfinterstitials are accommodated in extrinsic dislocation loops on {111} planes (‘loopites’) and probably also in ‘blob’-like defects visible in high resolution micrographs with little detectable lattice strain. Evidence is presented that coesite ribbons can nucleate on {311} steps on loopites and vice versa.     

Peculiarities of diamonds formed in alkaline carbonate-carbon melts at pressures of 8–10 GPA: Scanning electron microscopy and cathodoluminescence data

Diamond crystallization with both spontaneous and seeded nucleation was realized in the system Na₂Mg(CO₃)₂-K₂Mg(CO₃)₂-C (graphite) at 8–10 GPa and 1700–1800°C. The crystallization products were transparent colorless diamond single crystals of octahedral habit up to 100–150 μm in size. Scanning electron microscopy (SEM) showed that the growing diamond material was precipitated on both octahedral {111} and cubic { 100 } faces of synthetic and natural diamond seed crystals by layers of octahedral orientation, much like the growth of the natural diamond. The physicochemical conditions for diamond crystallization are interpreted as a crystal growth from carbon solutions in alkaline-carbonate melts. Color cathodoluminescence scanning electron microscopy (CCL-SEM) and cathodoluminescence (CL) spectroscopy studies suggested specific peculiarities of the synthetic “carbonate-carbon”(CC) diamonds resembling natural crystals in comparison with diamonds produced by metal-carbon (MC) synthesis. The main feature of the CC product is the lack, for both spontaneous and seed stimulated diamonds, of surface color cathodoluminescence as in the case for natural diamonds with lower concentrations of nitrogen impurity (type II). The CL spectra of the CC diamonds showed the simultaneous luminescent three-band system - H3, 575 nm, and a weak blue A-band - the H3 band structure of which resembles that of natural diamonds of type IIa.     

Single-particle visualization of assembly: I. Dimerization in a planar zone

Single-particle fluorescence microscopy of association/dissociation is required for analysis of biological assembly reactions. Toward achieving this goal, Wang et al. (J. Microsc., 2004, 213 , 101–109) used molten agarose to concentrate thermally diffusing particles in a thin zone of solution next to the surface of a coverglass (plane of concentration). The present study details the first real-time, single-particle analysis of the association/dissociation of thermally diffusing particles in the plane of concentration. The test particles were procapsids of bacteriophage λ (radius = 31 nm). Quantification of thermal motion was developed and used to determine whether co-diffusing particles were bound to each other. The data are explained by (1) the presence of a molten agarose-generated barrier that is 93–155 nm from the coverglass surface, and (2) non-random orientation of procapsid dimers in the plane of concentration.     

How important is the {103} plane of stable Ge2Sb2Te5 for phase‐change memory?

Closely correlating with {200} plane of cubic phase, {103} plane of hexagonal phase of Ge₂Sb₂Te₅ plays a crucial role in achieving fast phase change process as well as formation of modulation structures, dislocations and twins in Ge₂Sb₂Te₅. The behaviors of {103} plane of hexagonal phase render the phase‐change memory process as a nanoscale shape memory.     

趋磁细菌AMB-1磁小体纯化及扫描和透视电镜形态观察

培养并收集趋磁细菌AMB-1,采用超声波破碎菌体的方法提取磁小体,并对磁小体进行洗涤、分离、纯化。对趋磁细菌AMB-1,进行扫描电镜观察,同时对趋磁细菌AMB-1和纯化的磁小体进行透射电镜观察。电镜下见,趋磁细菌AMB-1为螺菌,无规则排列;磁小体位于菌细胞内,沿菌体长轴排列成链状。纯化的磁小体为立方-八面体,均匀分散于悬浮液中,表面有完整外膜包裹。