Molecular threading: mechanical extraction, stretching and placement of DNA molecules from a liquid-air interface.

We present "molecular threading", a surface independent tip-based method for stretching and depositing single and double-stranded DNA molecules. DNA is stretched into air at a liquid-air interface, and can be subsequently deposited onto a dry substrate isolated from solution. The design of an apparatus used for molecular threading is presented, and fluorescence and electron microscopies are used to characterize the angular distribution, straightness, and reproducibility of stretched DNA deposited in arrays onto elastomeric surfaces and thin membranes. Molecular threading demonstrates high straightness and uniformity over length scales from nanometers to micrometers, and represents an alternative to existing DNA deposition and linearization methods. These results point towards scalable and high-throughput precision manipulation of single-molecule polymers.

In situ preparation of network forming gold nanoparticles in agarose hydrogels.

Gold nanoparticles are obtained by reduction of a Au(iii) precursor within an agarose hydrogel where they form percolating networks upon partial dehydration and shrinkage of the gel.

Direct electron transfer to a metalloenzyme redox center coordinated to a monolayer-protected cluster.

A strategy for establishing electrical contact to the metal center of a redox metalloenzyme, galactose oxidase (GOase), by coordination of a linker attached to a monolayer-protected gold cluster is presented. The cluster-enzyme hybrid system was first prepared in solution and characterized by high-angle annular dark-field scanning transmission electron microscopy. Electrochemical communication between a gold electrode and GOase was achieved by first modifying the electrode surface with a biphenyl dithiol self-assembled monolayer followed by reaction with gold clusters capped with thioctic acid. GOase was then immobilized by replacement of the H(2)O molecule at the Cu(II) exogenous site by coordination of a carboxylate-terminated gold cluster. This chemical attachment ensured electrical contact between the redox center and the electrode, leading to direct mediatorless electron transfer to the protein. Hybrid systems can find applications in biosensors and biofuel cells and for studying electrochemically the catalytic mechanism of reactions for which free radicals and electron-transfer reactions are involved. The present results can be extended to other metalloenzymes.

Triple-twin domains in Mg doped GaN wurtzite nanowires: structural and electronic properties of this zinc-blende-like stacking.

We report on the effect of Mg doping on the properties of GaN nanowires grown by plasma assisted molecular beam epitaxy. The most significant feature is the presence of triple-twin domains, the density of which increases with increasing Mg concentration. The resulting high concentration of misplaced atoms gives rise to local changes in the crystal structure equivalent to the insertion of three non-relaxed zinc-blende (ZB) atomic cells, which result in quantum wells along the wurtzite (WZ) nanowire growth axis. High resolution electron energy loss spectra were obtained exactly on the twinned (zinc-blende) and wurtzite planes. These atomically resolved measurements, which allow us to identify modifications in the local density of states, revealed changes in the band to band electronic transition energy from 3.4 eV for wurtzite to 3.2 eV in the twinned lattice regions. These results are in good agreement with specific ab initio atomistic simulations and demonstrate that the redshift observed in previous photoluminescence analyses is directly related to the presence of these zinc-blende domains, opening up new possibilities for band-structure engineering.

Three-dimensional shapes and structures of lamellar-twinned fcc nanoparticles using ADF STEM.

Small particles with face-centred cubic structures can have non-single-crystallographic shapes. Here, an approach based on annular dark-field scanning transmission electron microscopy (STEM) is used to obtain information about the crystal sub-units that make up supported and unsupported twinned Pt, Pt alloy and Au nanoparticles. The three-dimensional shapes of two types of lamellar-twinned particles (LTPs) of Pt are obtained using high-angle annular dark-field STEM. Possible growth mechanisms of the LTPs and origins for the contrast features in the recorded images are discussed.

3D morphology of the human hepatic ferritin mineral core: new evidence for a subunit structure revealed by single particle analysis of HAADF-STEM images.

Ferritin, the major iron storage protein, has dual functions; it sequesters redox activity of intracellular iron and facilitates iron turn-over. Here we present high angle annular dark field (HAADF) images from individual hepatic ferritin cores within tissue sections, these images were obtained using spherical aberration corrected scanning transmission electron microscopy (STEM) under controlled electron fluence. HAADF images of the cores suggest a cubic morphology and a polycrystalline (ferrihydrite) subunit structure that is not evident in equivalent bright field images. By calibrating contrast levels in the HAADF images using quantitative electron energy loss spectroscopy, we have estimated the absolute iron content in any one core, and produced a three dimensional reconstruction of the average core morphology. The core is composed of up to eight subunits, consistent with the eight channels in the protein shell that deliver iron to the central cavity. We find no evidence of a crystallographic orientation relationship between core subunits. Our results confirm that the ferritin protein shell acts as a template for core morphology and within the core, small (approximately 2 nm), surface-disordered ferrihydrite subunits connect to leave a low density centre and a high surface area that would allow rapid turn-over of iron in biological systems.

Free-standing graphene at atomic resolution.

Research interest in graphene, a two-dimensional crystal consisting of a single atomic plane of carbon atoms, has been driven by its extraordinary properties, including charge carriers that mimic ultra-relativistic elementary particles. Moreover, graphene exhibits ballistic electron transport on the submicrometre scale, even at room temperature, which has allowed the demonstration of graphene-based field-effect transistors and the observation of a room-temperature quantum Hall effect. Here we confirm the presence of free-standing, single-layer graphene with directly interpretable atomic-resolution imaging combined with the spatially resolved study of both the pi --> pi* transition and the pi + sigma plasmon. We also present atomic-scale observations of the morphology of free-standing graphene and explore the role of microstructural peculiarities that affect the stability of the sheets. We also follow the evolution and interaction of point defects and suggest a mechanism by which they form ring defects.

High-resolution detection of Au catalyst atoms in Si nanowires.

The potential for the metal nanocatalyst to contaminate vapour-liquid-solid grown semiconductor nanowires has been a long-standing concern, because the most common catalyst material, Au, is highly detrimental to the performance of minority carrier electronic devices. We have detected single Au atoms in Si nanowires grown using Au nanocatalyst particles in a vapour-liquid-solid process. Using high-angle annular dark-field scanning transmission electron microscopy, Au atoms were observed in higher numbers than expected from a simple extrapolation of the bulk solubility to the low growth temperature. Direct measurements of the minority carrier diffusion length versus nanowire diameter, however, demonstrate that surface recombination controls minority carrier transport in as-grown n-type nanowires; the influence of Au is negligible. These results advance the quantitative correlation of atomic-scale structure with the properties of nanomaterials and can provide essential guidance to the development of nanowire-based device technologies.

Macroscopic graphene membranes and their extraordinary stiffness.

The properties of suspended graphene are currently attracting enormous interest, but the small size of available samples and the difficulties in making them severely restrict the number of experimental techniques that can be used to study the optical, mechanical, electronic, thermal, and other characteristics of this one-atom-thick material. Here, we describe a new and highly reliable approach for making graphene membranes of a macroscopic size (currently up to 100 microm in diameter) and their characterization by transmission electron microscopy. In particular, we have found that long graphene beams supported by only one side do not scroll or fold, in striking contrast to the current perception of graphene as a supple thin fabric, but demonstrate sufficient stiffness to support extremely large loads, millions of times exceeding their own weight, in agreement with the presented theory. Our work opens many avenues for studying suspended graphene and using it in various micromechanical systems and electron microscopy.

Biochemical and structural insights into bacterial organelle form and biogenesis.

Many heterotrophic bacteria have the ability to make polyhedral structures containing metabolic enzymes that are bounded by a unilamellar protein shell (metabolosomes or enterosomes). These bacterial organelles contain enzymes associated with a specific metabolic process (e.g. 1,2-propanediol or ethanolamine utilization). We show that the 21 gene regulon specifying the pdu organelle and propanediol utilization enzymes from Citrobacter freundii is fully functional when cloned in Escherichia coli, both producing metabolosomes and allowing propanediol utilization. Genetic manipulation of the level of specific shell proteins resulted in the formation of aberrantly shaped metabolosomes, providing evidence for their involvement as delimiting entities in the organelle. This is the first demonstration of complete recombinant metabolosome activity transferred in a single step and supports phylogenetic evidence that the pdu genes are readily horizontally transmissible. One of the predicted shell proteins (PduT) was found to have a novel Fe-S center formed between four protein subunits. The recombinant model will facilitate future experiments establishing the structure and assembly of these multiprotein assemblages and their fate when the specific metabolic function is no longer required.

Direct visualisation, by aberration-corrected electron microscopy, of the crystallisation of bimetallic nanoparticle catalysts.

Using a scanning transmission electron microscope, corrected for aberration, ultra-high resolution images of the internal structure of nanoparticle clusters, as well as the number of atoms present per cluster, may be directly determined: it is shown that individual bimetallic clusters of Ru10Pt2 have a "molecular" structure and that when they coalesce into larger entities containing ca. 200 atoms they adopt the regular crystalline, and facetted, state of a bulk metal.

Diagnosis of aberrations from crystalline samples in scanning transmission electron microscopy.

The Ronchigrams, or shadow images, observed from a thin crystalline sample in a scanning transmission electron microscope characteristically present many sets of fringes, which appear thanks to the coherent interference between the various Bragg-diffracted discs as they overlap in the diffraction plane. A particular region of such patterns can be shown to be independent of the defocus at which they are recorded. The intensity along this so-called achromatic ring depends on the microscope aberrations and can be used to diagnose the wave aberration coefficients, a crucial first step in the operation of an aberration-corrected microscope. A new algorithm is presented that allows the accurate determination of all non-cylindrically symmetric aberrations up to fourth-order from a crystalline sample using this property of the Ronchigram. An experimental procedure for determining the position of and intensity along the achromatic lines, as well as examples of diagnosis from two different crystalline structures, are detailed.

Atomic and electronic structure of mixed and partial dislocations in GaN.

Here we present a detailed study of mixed dislocations in GaN, in which the complexities of the atomic arrangement in the cores have been imaged directly for the first time using an aberration corrected scanning transmission electron microscope. In addition to being present as a full-core structure, the mixed dislocation is observed to dissociate into partial dislocations separated by a stacking fault only a few unit cells in length. The generation of this stacking fault appears to be impurity driven and its presence is consistent with theoretical predictions for dislocation dissociation in materials with hexagonal crystal symmetry.

Atomic structure of a (2 x 1) reconstructed NiSi2/Si(001) interface.

Nickel disilicide/silicon (001) interfaces were investigated by aberration corrected scanning transmission electron microscopy (STEM). The atomic structure was derived directly from the high spatial resolution high angle annular dark field STEM images without recourse to image simulation. It comprises fivefold coordinated silicon and sevenfold coordinated nickel sites at the interface and shows a 2 x 1 reconstruction. The proposed structure has not been experimentally observed before but has been recently predicted theoretically by others to be energetically favored.