Electron microscopy of high pressure frozen samples: bridging the gap between cellular ultrastructure and atomic resolution

Transmission electron microscopy has provided most of what is known about the ultrastructural organization of tissues, cells, and organelles. Due to tremendous advances in crystallography and magnetic resonance imaging, almost any protein can now be modeled at atomic resolution. To fully understand the workings of biological "nanomachines" it is necessary to obtain images of intact macromolecular assemblies in situ. Although the resolution power of electron microscopes is on the atomic scale, in biological samples artifacts introduced by aldehyde fixation, dehydration and staining, but also section thickness reduces it to some nanometers. Cryofixation by high pressure freezing circumvents many of the artifacts since it allows vitrifying biological samples of about 200 mum in thickness and immobilizes complex macromolecular assemblies in their native state in situ. To exploit the perfect structural preservation of frozen hydrated sections, sophisticated instruments are needed, e.g., high voltage electron microscopes equipped with precise goniometers that work at low temperature and digital cameras of high sensitivity and pixel number. With them, it is possible to generate high resolution tomograms, i.e., 3D views of subcellular structures. This review describes theory and applications of the high pressure cryofixation methodology and compares its results with those of conventional procedures. Moreover, recent findings will be discussed showing that molecular models of proteins can be fitted into depicted organellar ultrastructure of images of frozen hydrated sections. High pressure freezing of tissue is the base which may lead to precise models of macromolecular assemblies in situ, and thus to a better understanding of the function of complex cellular structures.

Tailoring surface nanostructures on polyaryletherketones for load-bearing implants

High-performance thermoplastics including polyetheretherketone (PEEK) are key biomaterials for load-bearing implants. Plasma treatment of implants surfaces has been shown to chemically activate its surface, which is a prerequisite to achieve proper cell attachment. Oxygen plasma treatment of PEEK films results in very reproducible surface nanostructures and has been reported in the literature. Our goal is to apply the plasma treatment to another promising polymer, polyetherketoneketone (PEKK), and compare its characteristics to the ones of PEEK. Oxygen plasma treatments of plasma powers between 25 and 150 W were applied on 60 μm-thick PEKK and 100 μm-thick PEEK films. Analysis of the nanostructures by atomic force microscopy showed that the roughness increased and island density decreased with plasma power for both PEKK and PEEK films correlating with contact angle values without affecting bulk properties of the used films. Thermal analysis of the plasma-treated films shows that the plasma treatment does not change the bulk properties of the PEKK and PEEK films.

Comportamento tribo-mecânico e desgaste adesivo de materiais em nanoescala: análises por dinâmica molecular e mecânica do contínuo.

As formulações baseadas na mecânica do contínuo, embora precisas até certo ponto, por vezes não podem ser utilizadas, ou não são conceitualmente corretas para o entendimento de fenômenos em escalas reduzidas. Estas limitações podem aparecer no estudo dos fenômenos tribológicos em escala nanométrica, que passam a necessitar de novos métodos experimentais, teóricos e computacionais que permitam explorar estes fenômenos com a resolução necessária. Simulações atomísticas são capazes de descrever fenômenos em pequena escala, porém, o número necessário de átomos modelados e, portanto, o custo computacional - geralmente torna-se bastante elevado. Por outro lado, os métodos de simulação associados à mecânica do contínuo são mais interessantes em relação ao custo computacional, mas não são precisos na escala atômica. A combinação entre essas duas abordagens pode, então, permitir uma compreensão mais realista dos fenômenos da tribologia. Neste trabalho, discutem-se os conceitos básicos e modelos de atrito em escala atômica e apresentam-se estudos, por meio de simulação numérica, para a análise e compreensão dos mecanismos de atrito e desgaste no contato entre materiais. O problema é abordado em diferentes escalas, e propõe-se uma abordagem conjunta entre a Mecânica do Contínuo e a Dinâmica Molecular. Para tanto, foram executadas simulações numéricas, com complexidade crescente, do contato entre superfícies, partindo-se de um primeiro modelo que simula o efeito de defeitos cristalinos no fenômeno de escorregamento puro, considerando a Dinâmica Molecular. Posteriormente, inseriu-se, nos modelos da mecânica do contínuo, considerações sobre o fenômeno de adesão. A validação dos resultados é feita pela comparação entre as duas abordagens e com a literatura.

Progress in silicon-based quantum computation

We review progress at the Australian Centre for Quantum Computer Technology towards the fabrication and demonstration of spin qubits and charge qubits based on phosphorus donor atoms embedded in intrinsic silicon. Fabrication is being pursued via two complementary pathways: a 'top-down' approach for near-term production of few-qubit demonstration devices and a 'bottom-up' approach for large-scale qubit arrays with sub-nanometre precision. The 'top-down' approach employs a low-energy (keV) ion beam to implant the phosphorus atoms. Single-atom control during implantation is achieved by monitoring on-chip detector electrodes, integrated within the device structure. In contrast, the 'bottom-up' approach uses scanning tunnelling microscope lithography and epitaxial silicon overgrowth to construct devices at an atomic scale. In both cases, surface electrodes control the qubit using voltage pulses, and dual single-electron transistors operating near the quantum limit provide fast read-out with spurious-signal rejection.

Design of high quality doped CeO2 solid electrolytes with nanohetero structure

Doped ceria (CeO2) compounds are fluorite related oxides which show oxide ionic conductivity higher than yttria-stabilized zirconia in oxidizing atmosphere. As a consequence of this, a considerable interest has been shown in application of these materials for low (400-650 degrees C) temperature operation of solid oxide fuel cells (SOFCs). In this paper, our experimental data about the influence of microstructure at the atomic level on electrochemical properties were reviewed in order to develop high quality doped CeO2 electrolytes in fuel cell applications. Using this data in the present paper, our original idea for a design of nanodomain structure in doped CeO2 electrolytes was suggested. The nanosized powders and dense sintered bodies of M doped CeO2 (M:Sm,Gd,La,Y,Yb, and Dy) compounds were fabricated. Also nanostiructural features in these specimens were introduced for conclusion of relationship between electrolytic properties and domain structure in doped CeO2. It is essential that the electrolytic properties in doped CeO2 solid electrolytes reflect in changes of microstructure even down to the atomic scale. Accordingly, a combined approach of nanostructure fabrication, electrical measurement and structure characterization was required to develop superior quality doped CeO2 electrolytes in the fuel cells.

Glass fragility and atomic ordering on the intermediate and extended range

The relation between the fragility of glass-forming systems, a parameter which describes many of their key physical characteristics, and atomic scale structure is investigated by using neutron diffraction to measure the topological and chemical ordering for germania, or GeO2, which is an archetypal strong glass former. We find that the ordering for this and other tetrahedral network-forming glasses at distances greater than the nearest neighbor can be rationalized in terms of an interplay between the relative importance of two length scales. One of these is associated with an intermediate range, the other with an extended range and, with increasing glass fragility, it is the extended range ordering which dominates.

In situ aberration corrected-transmission electron microscopy of magnesium oxide nanocatalysts for biodiesels

Biofuels are promising renewable energy sources and can be derived from vegetable oil feedstocks. Although solid catalysts show great promise in plant oil triglyceride transesterification to biodiesel, the identification of active sites and operating surface nanostructures created during their processing is essential for the development of efficient heterogeneous catalysts. Systematic, direct observations of dynamic MgO nanocatalysts from a magnesium hydroxide-methoxide precursor were performed under controlled calcination conditions using novel in situ aberration corrected-transmission electron microscopy at the 0.1 nm level and quantified with catalytic reactivity and physico-chemical studies. Surface structural modifications and the evolution of extended atomic scale glide defects implicate coplanar anion vacancies in active sites in the transesterification of triglycerides to biodiesel. The linear correlation between surface defect density (and therefore polarisability) and activity affords a simple means to fine tune new, energy efficient nanocatalysts for biofuel synthesis. © 2009 Springer Science+Business Media, LLC.

The structural conversion from α-AgVO3 to β-AgVO3: Ag nanoparticle decorated nanowires with application as cathode materials for Li-ion batteries

The majority of electrode materials in batteries and related electrochemical energy storage devices are fashioned into slurries via the addition of a conductive additive and a binder. However, aggregation of smaller diameter nanoparticles in current generation electrode compositions can result in non-homogeneous active materials. Inconsistent slurry formulation may lead to inconsistent electrical conductivity throughout the material, local variations in electrochemical response, and the overall cell performance. Here we demonstrate the hydrothermal preparation of Ag nanoparticle (NP) decorated α-AgVO3 nanowires (NWs) and their conversion to tunnel structured β-AgVO3 NWs by annealing to form a uniform blend of intercalation materials that are well connected electrically. The synthesis of nanostructures with chemically bound conductive nanoparticles is an elegant means to overcome the intrinsic issues associated with electrode slurry production, as wire-to-wire conductive pathways are formed within the overall electrode active mass of NWs. The conversion from α-AgVO3 to β-AgVO3 is explained in detail through a comprehensive structural characterization. Meticulous EELS analysis of β-AgVO3 NWs offers insight into the true β-AgVO3 structure and how the annealing process facilitates a higher surface coverage of Ag NPs directly from ionic Ag content within the α-AgVO3 NWs. Variations in vanadium oxidation state across the surface of the nanowires indicate that the β-AgVO3 NWs have a core–shell oxidation state structure, and that the vanadium oxidation state under the Ag NP confirms a chemically bound NP from reduction of diffused ionic silver from the α-AgVO3 NWs core material. Electrochemical comparison of α-AgVO3 and β-AgVO3 NWs confirms that β-AgVO3 offers improved electrochemical performance. An ex situ structural characterization of β-AgVO3 NWs after the first galvanostatic discharge and charge offers new insight into the Li+ reaction mechanism for β-AgVO3. Ag+ between the van der Waals layers of the vanadium oxide is reduced during discharge and deposited as metallic Ag, the vacant sites are then occupied by Li+.

Crystallization on the Mesoscale : Self-Assembly of Iron Oxide Nanocubes into Mesocrystals

Self-assembly of nanoparticles is a promising route to form complex, nanostructured materials with functional properties. Nanoparticle assemblies characterized by a crystallographic alignment of the nanoparticles on the atomic scale, i.e. mesocrystals, are commonly found in nature with outstanding functional and mechanical properties. This thesis aims to investigate and understand the formation mechanisms of mesocrystals formed by self-assembling iron oxide nanocubes. We have used the thermal decomposition method to synthesize monodisperse, oleate-capped iron oxide nanocubes with average edge lengths between 7 nm and 12 nm and studied the evaporation-induced self-assembly in dilute toluene-based nanocube dispersions. The influence of packing constraints on the alignment of the nanocubes in nanofluidic containers has been investigated with small and wide angle X-ray scattering (SAXS and WAXS, respectively). We found that the nanocubes preferentially orient one of their {100} faces with the confining channel wall and display mesocrystalline alignment irrespective of the channel widths.  We manipulated the solvent evaporation rate of drop-cast dispersions on fluorosilane-functionalized silica substrates in a custom-designed cell. The growth stages of the assembly process were investigated using light microscopy and quartz crystal microbalance with dissipation monitoring (QCM-D). We found that particle transport phenomena, e.g. the coffee ring effect and Marangoni flow, result in complex-shaped arrays near the three-phase contact line of a drying colloidal drop when the nitrogen flow rate is high. Diffusion-driven nanoparticle assembly into large mesocrystals with a well-defined morphology dominates at much lower nitrogen flow rates. Analysis of the time-resolved video microscopy data was used to quantify the mesocrystal growth and establish a particle diffusion-based, three-dimensional growth model. The dissipation obtained from the QCM-D signal reached its maximum value when the microscopy-observed lateral growth of the mesocrystals ceased, which we address to the fluid-like behavior of the mesocrystals and their weak binding to the substrate. Analysis of electron microscopy images and diffraction patterns showed that the formed arrays display significant nanoparticle ordering, regardless of the distinctive formation process.  We followed the two-stage formation mechanism of mesocrystals in levitating colloidal drops with real-time SAXS. Modelling of the SAXS data with the square-well potential together with calculations of van der Waals interactions suggests that the nanocubes initially form disordered clusters, which quickly transform into an ordered phase.

Coupling of magnetic, strain and electric polarization fields in the structure of multiferroic material

The comprehensive study on the coupling of magnetism, electrical polarization and the crystalline lattice with the off-stoichiometric effects in self-doped multiferroic hexagonal h-LuMnxO3±δ (0.92≤x≤1.12) ceramic oxides was carried out for the PhD work. There is a complex coupling of the three ferroic degrees. The cancelation of the magnetic moments of ions in the antiferromagnetic order, electric polarization with specific vortex/antivortex topology and lattice properties have pushed researchers to find out ways to disclose the underlying physics and chemistry of magneto-electric and magneto-elastic couplings of h-RMnO3 multiferroic materials. In this research work, self-doping of Lu-sites or Mn-sites of h-LuMnxO3±δ ceramics prepared via solid state route was done to pave a way for deeper understanding of the antiferromagnetic transition, the weak ferromagnetism often reported in the same crystalline lattices and the ferroelectric properties coupled to the imposed lattice changes. Accordingly to the aim of the PhD thesis, the objectives set for the sintering study in the first chapter on experimental results were two. First, study of sintering off-stoichiometric samples within conditions reported in the bibliography and also extracted from the phase diagrams of the LuMnxO3±δ, with a multiple firings ending with a last high temperature step at 1300ºC for 24 hours. Second, explore longer annealing times of up to 240 hours at the fixed temperature of 1300 ºC in a search for improving the properties of the solid solution under study. All series of LuMnxO3±δ ceramics for each annealing time were characterized to tentatively build a framework enabling comparison of measured properties with results of others available in literature. XRD and Rietveld refinement of data give the evolution the lattice parameters as a function to x. Shrinkage of the lattice parameters with increasing x values was observed, the stability limit of the solid solution being determined by analysis of lattice parameters. The evolution of grain size and presence of secondary phases have been investigated by means of TEM, SEM, EDS and EBSD techniques. The dependencies of grain growth and regression of secondary phases on composition x and time were further characterized. Magnetic susceptibility of samples and magnetic irreversibility were extensively examined in the present work. The dependency of magnetic susceptibility, Neel ordering transition and important magnetic parameters are determined and compared to observation in other multiferroics in the following chapter of the thesis. As a tool of high sensitivity to detect minor traces of the secondary phase hausmannite, magnetic measurements are suggested for cross-checking of phase diagrams. Difficulty of previous studies on interpreting the magnetic anomaly below 43 K in h-RMnO3 oxides was discussed and assigned to the Mn3O4 phase, with supported of the electron microscopy. Magneto-electric coupling where AFM ordering is coupled to dielectric polarization is investigated as a function of x and of sintering condition via frequency and temperature dependent complex dielectric constant measurements in the final chapter of the thesis. Within the limits of solid solubility, the crystalline lattice of off-stoichiometric ceramics was shown to preserve the magneto-electric coupling at TN. It represents the first research work on magneto-electric coupling modified by vacancy doping to author’s knowledge. Studied lattices would reveal distortions at the atomic scale imposed by local changes of x dependent on sintering conditions which were widely inspected by using TEM/STEM methods, complemented with EDS and EELS spectroscopy all together to provide comprehensive information on cross coupling of distortions, inhomogeneity and electronic structure assembled and discussed in a specific chapter. Internal interfaces inside crystalline grains were examined. Qualitative explanations of the measured magnetic and ferroelectric properties were established in relation to observed nanoscale features of h-LuMnxO3±δ ceramics. Ferroelectric domains and topological defects are displayed both in TEM and AFM/PFM images, the later technique being used to look at size, distribution and switching of ferroelectric domains influenced by vacancy doping at the micron scale bridging to complementary TEM studies on the atomic structure of ferroelectric domains. In support to experimental study, DFT simulations using Wien2K code have been carried out in order to interpret the results of EELS spectra of O K-edge and to obtain information on the cation hybridization to oxygen ions. The L3,2 edges of Mn is used to access the oxidation state of the Mn ions inside crystalline grains. In addition, rehybridization driven ferroelectricity is also evaluated by comparing the partial density of states of the orbitals of all ions of the samples, also the polarization was calculated and correlated to the off-stoichiometric effect.

Atomic resolution studies of oxide superlattices and ultrathin films

The ability to grow ultrathin films layer-by-layer with well-defined epitaxial relationships has allowed research groups worldwide to grow a range of artificial films and superlattices, first for semiconductors, and now with oxides. In the oxides thin film research community, there have been concerted efforts recently to develop a number of epitaxial oxide systems grown on single crystal oxide substrates that display a wide variety of novel interfacial functionality, such as enhanced ferromagnetic ordering, increased charge carrier density, increased optical absorption, etc, at interfaces. The magnitude of these novel properties is dependent upon the structure of thin films, especially interface sharpness, intermixing, defects, and strain, layering sequence in the case of superlattices and the density of interfaces relative to the film thicknesses. To understand the relationship between the interfacial thin film oxide atomic structure and its properties, atomic scale characterization is required. Transmission electron microscopy (TEM) offers the ability to study interfaces of films at high resolution. Scanning transmission electron microscopy (STEM) allows for real space imaging of materials with directly interpretable atomic number contrast. Electron energy loss spectroscopy (EELS), together with STEM, can probe the local chemical composition as well as local electronic states of transition metals and oxygen. Both techniques have been significantly improved by aberration correctors, which reduce the probe size to 1 Å, or less. Aberration correctors have thus made it possible to resolve individual atomic columns, and possibly probe the electronic structure at atomic scales. Separately, using electron probe forming lenses, structural information such as the crystal structure, strain, lattice mismatches, and superlattice ordering can be measured by nanoarea electron diffraction (NED). The combination of STEM, EELS, and NED techniques allows us to gain a fundamental understanding of the properties of oxide superlattices and ultrathin films and their relationship with the corresponding atomic and electronic structure. In this dissertation, I use the aforementioned electron microscopy techniques to investigate several oxide superlattice and ultrathin film systems. The major findings are summarized below. These results were obtained with stringent specimen preparation methods that I developed for high resolution studies, which are described in Chapter 2. The essential materials background and description of electron microscopy techniques are given in Chapter 1 and 2. In a LaMnO3-SrMnO3 superlattice, we demonstrate the interface of LaMnO3-SrMnO3 is sharper than the SrMnO3-LaMnO3 interface. Extra spectral weights in EELS are confined to the sharp interface, whereas at the rougher interface, the extra states are either not present or are not confined to the interface. Both the structural and electronic asymmetries correspond to asymmetric magnetic ordering at low temperature. In a short period LaMnO3-SrTiO3 superlattice for optical applications, we discovered a modified band structure in SrTiO3 ultrathin films relative to thick films and a SrTiO3 substrate, due to charge leakage from LaMnO3 in SrTiO3. This was measured by chemical shifts of the Ti L and O K edges using atomic scale EELS. The interfacial sharpness of LaAlO3 films grown on SrTiO3 was investigated by the STEM/EELS technique together with electron diffraction. This interface, when prepared under specific conditions, is conductive with high carrier mobility. Several suggestions for the conductive interface have been proposed, including a polar catastrophe model, where a large built-in electric field in LaAlO3 films results in electron charge transfer into the SrTiO3 substrate. Other suggested possibilities include oxygen vacancies at the interface and/or oxygen vacancies in the substrate. The abruptness of the interface as well as extent of intermixing has not been thoroughly investigated at high resolution, even though this can strongly influence the electrical transport properties. We found clear evidence for cation intermixing through the LaAlO3-SrTiO3 interface with high spatial resolution EELS and STEM, which contributes to the conduction at the interface. We also found structural defects, such as misfit dislocations, which leads to increased intermixing over coherent interfaces.

Sodium distribution in mixed alkali K-Na metaphosphate glasses

The local order and distribution of Na in the mixed alkali metaphosphate glasses K(x)Na(1-x)PO(3) were analyzed, with the aim to identify segregation or a random mixture of both cation species. X-Ray photoelectron spectroscopy and several nuclear magnetic resonance (NMR) techniques were applied, including (31)P and (23)Na high-resolution spectroscopy, (23)Na triple quantum-MAS NMR, rotational echo double resonance between (31)P and (23)Na, and (23)Na NMR spin echo decay. The structural picture emerging from these results reveals the similarity in the local Na environments in the glasses but also subtle structural adjustments with increasing degree of K replacement. While both cations are intimately mixed at the atomic scale, the (23)Na spin echo decay data suggest a detectable like-cation preference in the spatial distribution of the ions. These structural properties are consistent with those determined in Li-Rb metaphosphates, indicating that the origin of the mixed alkali effect observed in the conductivity of Na-K metaphosphate glasses may also be explained by structurally blocked ion diffusion.

Thermal diffusion in molecular dynamics simulations of thin film diamond deposition

Molecular dynamics simulations of carbon atom depositions are used to investigate energy diffusion from the impact zone. A modified Stillinger-Weber potential models the carbon interactions for both sp2 and sp3 bonding. Simulations were performed on 50 eV carbon atom depositions onto the (111) surface of a 3.8 x 3.4 x 1.0 nm diamond slab containing 2816 atoms in 11 layers of 256 atoms each. The bottom layer was thermostated to 300 K. At every 100th simulation time step (27 fs), the average local kinetic energy, and hence local temperature, is calculated. To do this the substrate is divided into a set of 15 concentric hemispherical zones, each of thickness one atomic diameter (0.14 nm) and centered on the impact point. A 50-eV incident atom heats the local impact zone above 10 000 K. After the initial large transient (200 fs) the impact zone has cooled below 3000 K, then near 1000 K by 1 ps. Thereafter the temperature profile decays approximately as described by diffusion theory, perturbed by atomic scale fluctuations. A continuum model of classical energy transfer is provided by the traditional thermal diffusion equation. The results show that continuum diffusion theory describes well energy diffusion in low energy atomic deposition processes, at distance and time scales larger than 1.5 nm and 1-2 ps, beyond which the energy decays essentially exponentially. (C) 1998 Published by Elsevier Science S.A. All rights reserved.

Influence of nano-structure on electrolytic properties in CeO2 based system

Doped ceria (CeO2) compounds are fluorite type oxides that show oxygen ionic conductivity higher than yttria stabilized zirconia, in oxidizing atmosphere. In order to improve the conductivity, the effective index was suggested to maximize the oxygen ionic conductivity in doped CeO2 based oxides. In addition, the true microstructure of doped CeO2 was observed at atomic scale for conclusion of conduction mechanism. Doped CeO2 had small domains (10-50 nm) with ordered structure in a grain. It is found that the electrolytic properties strongly depended on the nano-structural feature at atomic scale in doped CeO2 electrolyte.

Oxide ionic conductivity and microstructures of Sm- or La-doped CeO2-based systems

The concept of crystallographic index termed the effective index is suggested and applied to the design of ceria (CeO2)-based electrolytes to maximize oxide ionic conductivity. The suggested index considers the fluorite structure, and combines the expected oxygen vacancy level with the ionic radius mismatch between host and dopant cations. Using this approach, oxide ionic conductivity of Sm- or La-doped CeO2-based system has been optimized and tested under operating conditions of a solid oxide fuel cell. In the observation of microstructure in atomic scale, both Sm-doped CeO2 and La-doped CeO2 electrolytes had large micro-domains over 10 nm in the lattice. On the other hand, Sm or La and alkaline earth co-doped CeO2-based electrolytes with high effective index had small micro-domains around 1-3 nm in the microstructure. The large micro-domain would prevent oxide ion from passing through the lattice. Therefore, it is concluded that the improvement of ionic conductivity is reflected in changes of microstructure in atomic scale. (C) 2002 Elsevier Science B.V. All rights reserved.