Large volume tomography using plasma FIB-SEM: A comprehensive case study on black silicon.

The xenon plasma focused ion beam and scanning electron microscopy (PFIB-SEM) system is a promising tool for 3D tomography of nano-scale materials, including nanotextured black silicon (BSi), whose topography is difficult to measure with conventional microscopy techniques. Advantages of PFIB-SEM include high material removal rates, precise control of milling parameters and automated slice-and-view procedures. However, there is no universal sample preparation procedure nor is there an established ideal workflow for the PFIB-SEM slice-and-view process. This work demonstrates that specimen preparation, including the orientation of the volume of interest, is critical for the quality of the final reconstructed 3D model. It thoroughly explores three unique configurations incrementally optimized for higher total throughput. All three sampling configurations are applied to a resin-embedded BSi sample to determine the most favourable workflow and highlight each approach's advantages and disadvantages. The reconstructed 3D models of the BSi surface obtained are shown to be qualitatively closer to the topography measured directly by SEM. The height distribution data extracted from the rendered 3D models reveal a higher structure depth compared to that obtained from an atomic force microscopy measurement. Furthermore, the work demonstrates how samples with different rigidity react to long-term ion-beam interaction, as both amorphous (resin) and crystalline (Si) material is present in the tested specimen. This study improves the understanding of sample-beam interaction and broadens the utility of the 3D PFIB-SEM for more complicated sample structures.

3D characterisation using plasma FIB-SEM: A large-area tomography technique for complex surfaces like black silicon.

This paper demonstrates an improved method to accurately extract the surface morphology of black silicon (BSi). The method is based on an automated Xe+ plasma focused ion beam (PFIB) and scanning electron microscope (SEM) tomography technique. A comprehensive new sample preparation method is described and shown to minimize the PFIB artifacts induced by both the top surface sample-PFIB interaction and the non-uniform material density. An optimized post-image processing procedure is also described that ensures the accuracy of the reconstructed 3D surface model. The application of these new methods is demonstrated by applying them to extract the surface topography of BSi formed by reactive ion etching (RIE) consisting of 2 µm tall needles. An area of 320 µm2 is investigated with a controlled slice thickness of 10 nm. The reconstructed 3D model allows the extraction of critical roughness characteristics, such as height distribution, correlation length, and surface enhancement ratio. Furthermore, it is demonstrated that the particular surface studied contains regions in which under-etching has resulted in overhanging structures, which would not have been identified with other surface topography techniques. Such overhanging structures can be present in a broad range of BSi surfaces, including BSi surfaces formed by RIE and metal catalyst chemical etching (MCCE). Without proper measurement, the un-detected overhangs would result in the underestimation of many critical surface characteristics, such as absolute surface area, electrochemical reactivity and light-trapping.

Reflectance properties of silicon moth-eyes in response to variations in angle of incidence, polarisation and azimuth orientation.

We report a study of the optical properties of silicon moth-eye structures using a custom-made fully automated broadband spectroscopic reflectometry system (goniometer). This measurement system is able to measure specular reflectance as a function of wavelength, polar incidence angle and azimuth orientation angle, from normal to near-parallel polar incidence angle. The system uses a linear polarized broadband super-continuum laser light source. It is shown that a moth-eye structure composed of a regular array of protruding silicon rods, with finite sidewall angle reduces reflectance and sensitivity to incident wavelength in comparison to truly cylindrical rods with perpendicular sidewalls. It is also shown that moth-eye structures have omnidirectional reflectance properties in response to azimuth orientation of the sample. The importance of applying the reflectometer setup to study the optical properties of solar cell antireflective structures is highlighted.

Pisum sativum mitochondrial pyruvate dehydrogenase can be assembled as a functional alpha(2)beta(2) heterotetramer in the cytoplasm of Pichia pastoris.

Pea (Pisum sativum) mitochondrial pyruvate dehydrogenase (E1) was produced by coexpression of the mature alpha and beta subunits in the cytoplasm of the yeast Pichia pastoris. Size-exclusion chromatography of recombinant E1, using a Superose 12 column, yielded a peak at M(r) 160,000 that contained both alpha and beta subunits as well as E1 activity. This corresponds to the size of native alpha(2)beta(2) E1. Recombinant E1 alpha (His(6))-E1 beta was purified by affinity chromatography using immobilized Ni(+), with a yield of 2.8 mg L(-1). The pyruvate-decarboxylating activity of recombinant E1 was dependent upon added Mg(2+) and thiamin-pyrophosphate and was enhanced by the oxidant potassium ferricyanide. Native pea mitochondrial E1-kinase catalyzed phosphorylation of Ser residues in the alpha-subunit of recombinant E1, with concomitant loss of enzymatic activity. Thus, mitochondrial pyruvate dehydrogenase can be assembled in the cytoplasm of P. pastoris into an alpha(2)beta(2) heterotetramer that is both catalytically active and competent for regulatory phosphorylation.

Histidine modifying agents abolish pyruvate dehydrogenase kinase activity.

Pyruvate dehydrogenase kinase (PDK) specifically phosphorylates the E1alpha subunit of the pyruvate dehydrogenase complex (PDC). Sequence analysis of cloned PDKs led to the proposal that they are mechanistically related to prokaryotic 2-component His-kinases. The reaction mechanism of protein His-kinases involves autophosphorylation of a specific His residue followed by phosphotransfer to an Asp residue. Treatment of recombinant Arabidopsis thaliana PDK with the His-directed reagents diethyl pyrocarbonate (DEPC) and dichloro-(2,2':6', 2"-terpyridine)-platinum(II) dihydrate led to a marked inhibition of autophosphorylation. In addition, DEPC treatment abolished the ability of PDK to trans-phosphorylate and inactivate PDC. These results validate the prediction that PDKs require His residues for activity.

The dihydrolipoamide S-acetyltransferase subunit of the mitochondrial pyruvate dehydrogenase complex from maize contains a single lipoyl domain.

The dihydrolipoamide S-acetyltransferase (E2) subunit of the maize mitochondrial pyruvate dehydrogenase complex (PDC) was postulated to contain a single lipoyl domain based upon molecular mass and N-terminal protein sequence (Thelen, J. J., Miernyk, J. A., and Randall, D. D. (1998) Plant Physiol. 116, 1443-1450). This sequence was used to identify a cDNA from a maize expressed sequence tag data base. The deduced amino acid sequence of the full-length cDNA was greater than 30% identical to other E2s and contained a single lipoyl domain. Mature maize E2 was expressed in Escherichia coli and purified to a specific activity of 191 units mg(-1). The purified recombinant protein had a native mass of approximately 2.7 MDa and assembled into a 29-nm pentagonal dodecahedron as visualized by electron microscopy. Immunoanalysis of mitochondrial proteins from various plants, using a monoclonal antibody against the maize E2, revealed 50-54-kDa cross-reacting polypeptides in all samples. A larger protein (76 kDa) was also recognized in an enriched pea mitochondrial PDC preparation, indicating two distinct E2s. The presence of a single lipoyl-domain E2 in Arabidopsis thaliana was confirmed by identifying a gene encoding a hypothetical protein with 62% amino acid identity to the maize homologue. These data suggest that all plant mitochondrial PDCs contain an E2 with a single lipoyl domain. Additionally, A. thaliana and other dicots possess a second E2, which contains two lipoyl domains and is only 33% identical at the amino acid level to the smaller isoform. The reason two distinct E2s exist in dicotyledon plants is uncertain, although the variability between these isoforms, particularly within the subunit-binding domain, suggests different roles in assembly and/or function of the plant mitochondrial PDC.

Autophosphorylation of the pea mitochondrial heat-shock protein homolog.

Highly purified mitochondria isolated from 14-day-old pea (Pisum sativum L., cv Little Marvel) seedlings contain a homolog of the 70,000 molecular weight heat-shock protein. The amount of this heat-shock cognate (Hsc70) was not reduced by limited proteolysis of intact mitochondria or by preparation of mitoplasts, indicating that the protein is located within the matrix compartment. Pea mitochondrial Hsc70 binds to immobilized ATP and reacts on western blots with anti-tomato Hsc70 antiserum. When a mitochondrial matrix fraction was incubated with [gamma-(32)P]ATP, there was phosphorylation of Hsc70. The extent of phosphorylation was increased by including calcium chloride in the reactions. Phospho amino acid analysis of purified mitochondrial Hsc70, phosphorylated in the calcium-stimulated reaction, revealed only phosphothreonine. Pea mitochondrial Hsc70, purified by a combination of ATP-agarose affinity chromatography and gel permeation chromatography, was labeled when incubated with ATP plus calcium, suggesting autophosphorylation rather than phosphorylation by an associated kinase. In analogy to mammalian cells and yeast, it is likely that mitochondrial Hsc70 acts as a molecular chaperone, and it is possible that phosphorylation plays a role in chaperone function.