Direct numerical inversion method for kinetic ellipsometric data. I. Presentation of the method and numerical evaluation

A direct numerical inversion method for the determination of the refractive index and the thickness of the outermost layer of a thin transparent film on top of a multilayer has been developed. This method is based on a second-order Taylor decomposition of the coefficients of the Abelès matrices of the newly grown layer. The variations of the real-time spectroscopic ellipsometry data are expressed as polynomial fuctions depending on the dielectric constant and the thickness of the newly grown layer. The method is fast, capable of single-wavelength and multiwavelength inversion of continuous as well as discontinuous-index profiles, and can be adapted to many different polarimetric instruments.     

Pattern storage and processing in attractor networks with short-time synaptic dynamics

Neurophysiological experiments show that the strength of synaptic connections can undergo substantial changes on a short time scale. These changes depend on the history of the presynaptic input. Using mean-field techniques, we study how short-time dynamics of synaptic connections influence the performance of attractor neural networks in terms of their memory capacity and capability to process external signals. For binary discrete-time as well as for firing rate continuous-time neural networks, the fixed points of the network dynamics are shown to be unaffected by synaptic dynamics. However, the stability of patterns changes considerably. Synaptic depression turns out to reduce the storage capacity. On the other hand, synaptic depression is shown to be advantageous for processing of pattern sequences. The analytical results on stability, size of the basins of attraction and on the switching between patterns are complemented by numerical simulations.     

Rational design and selection of bivalent peptide ligands of thrombin incorporating P4-P1 tetrapeptide sequences: from good substrates to potent inhibitors

The tetrapeptide Phe-Asn-Pro-Arg is a structurally optimized sequence for binding to the active site of thrombin. By conjugating this tetrapeptide or some variants to a C-terminal fragment of hirudin, we were able to generate a series of new bivalent inhibitors of thrombin containing only genetically encodable natural amino acids. We found that synergistic binding to both the active site and an exosite of thrombin can be enhanced through substitutions of amino acid residues at the P3 and P3' sites of the active-site directed sequence, Phe(P4)-Xaa(P3)-Pro(P2)-Arg(P1)-Pro(P1')-Gln(P2')-Yaa(P3'). Complementary to rational design, a phage library was constructed to explore further the residue requirements at the P4, P3 and P3' sites for bivalent and optimized two-site binding. Very significantly, panning of the phage library has led to thrombin-inhibitory peptides possessing strong anti-clotting activities in the low nanomolar range and yet interfering only partially the catalytic active site of thrombin. Modes of action of the newly discovered bivalent inhibitors are rationalized in light of the allosteric properties of thrombin, especially the interplay between the proteolytic action and regulatory binding occurring at thrombin surfaces remote from the catalytic active site.     

Syntheses and properties of B-C-N and BN nanostructures

The current status of research on boron-carbon-nitrogen (B-C-N) and boron nitride (BN) nanotubes is presented. The latest achievements in syntheses, analyses and property measurements of these nanoscale tubular architectures are reviewed. The characteristic features of B-C-N and BN nanotubes, compared with conventional C nanotubes, are paid special attention. In particular, the latest breakthroughs in the chemical vapour deposition synthesis of BN nanotubes and an insight into their unique structures are highlighted. A wide range of potential applications is also envisaged, based on the recent progress, which includes pioneering results in BN nanocable fabrication, gas adsorption, electron transport and field emission measurements.     

Fast similarity join for multi-dimensional data

The efficient processing of multidimensional similarity joins is important for a large class of applications. The dimensionality of the data for these applications ranges from low to high. Most existing methods have focused on the execution of high-dimensional joins over large amounts of disk-based data. The increasing sizes of main memory available on current computers, and the need for efficient processing of spatial joins suggest that spatial joins for a large class of problems can be processed in main memory. In this paper, we develop two new in-memory spatial join algorithms, the Grid-join and EGO*-join, and study their performance. Through evaluation, we explore the domain of applicability of each approach and provide recommendations for the choice of a join algorithm depending upon the dimensionality of the data as well as the expected selectivity of the join. We show that the two new proposed join techniques substantially outperform the state-of-the-art join algorithm, the EGO-join.     

Tailoring the Optical Properties of Epitaxially Grown Biaxial ZnO/Ge,and Coaxial ZnO/Ge/ZnO and Ge/ZnO/Ge Heterostructures

Heterostructures of epitaxially grown biaxial ZnO/Ge, and coaxial ZnO/Ge/ZnO and Ge/ZnO/Ge heterostructured nanowires with ideal epitaxial interfaces between the semiconductor ZnO sublayer and the Ge sublayer have been fabricated via a two‐stage chemical vapor–solid process. Structural characterization by high‐resolution transmission electron microscopy and electron diffraction indicates that both the ZnO and Ge sublayers in the heterostructures are single crystalline. A good epitaxial relationship of (100)_ZnO∥(2 0)_Ge exists at the interface between ZnO and Ge in the ZnO/Ge biaxial heterostructure. There is also an epitaxial relationship of (0 0)_ZnO∥(020)_Ge at the interface between the ZnO and Ge substructures in the coaxial ZnO/Ge/ZnO heterostructures, and a good epitaxial relationship of (0 0)_ZnO∥(0 0)_Ge at the interface between ZnO and Ge in the Ge/ZnO/Ge coaxial heterostructure. Structural models for the crystallographic relationship between the wurtzite‐ZnO and diamond‐like cubic‐Ge subcomponents in the heterostructures are given. The optical properties for the synthesized heterostructures are studied by spatially resolved cathodoluminescence spectra at low temperature (20 K). Excitingly, the unique biaxial and coaxial heterostructures display unique new luminescence properties. It is concluded that the ideal epitaxial interface between ZnO and Ge in the prepared heterostructures induces new optical properties. The group II–VI Ge‐based nanometer‐scale heterostructures and their interesting optical properties may inspire great interest in exploring related epitaxial heterostructures and their potential applications in lasers, gas sensors, solar energy conversion, and nanodevices in the future.     

In Planta Response of Arabidopsis to Photothermal Impact Mediated by Gold Nanoparticles

Biological responses to photothermal effects of gold nanoparticles (GNPs) have been demonstrated and employed for various applications in diverse systems except for one important class – plants. Here, the uptake of GNPs through Arabidopsis thaliana roots and translocation to leaves are reported. Successful plasmonic nanobubble generation and acoustic signal detection in planta is demonstrated. Furthermore, Arabidopsis leaves harboring GNPs and exposed to continuous laser or noncoherent light show elevated temperatures across the leaf surface and induced expression of heat‐shock regulated genes. Overall, these results demonstrate that Arabidopsis can readily take up GNPs through the roots and translocate the particles to leaf tissues. Once within leaves, GNPs can act as photothermal agents for on‐demand remote activation of localized biological processes in plants.     

Virus Matryoshka: A Bacteriophage Particle—Guided Molecular Assembly Approach to a Monodisperse Model of the Immature Human Immunodeficiency Virus

Immature human immunodeficiency virus type 1 (HIV‐1) is approximately spherical, but is constructed from a hexagonal lattice of the Gag protein. As a hexagonal lattice is necessarily flat, the local symmetry cannot be maintained throughout the structure. This geometrical frustration presumably results in bending stress. In natural particles, the stress is relieved by incorporation of packing defects, but the magnitude of this stress and its significance for the particles is not known. In order to control this stress, we have now assembled the Gag protein on a quasi‐spherical template derived from bacteriophage P22. This template is monodisperse in size and electron‐transparent, enabling the use of cryo‐electron microscopy in structural studies. These templated assemblies are far less polydisperse than any previously described virus‐like particles (and, while constructed according to the same lattice as natural particles, contain almost no packing defects). This system gives us the ability to study the relationship between packing defects, curvature and elastic energy, and thermodynamic stability. As Gag is bound to the P22 template by single‐stranded DNA, treatment of the particles with DNase enabled us to determine the intrinsic radius of curvature of a Gag lattice, unconstrained by DNA or a template. We found that this intrinsic radius is far larger than that of a virion or P22‐templated particle. We conclude that Gag is under elastic strain in a particle; this has important implications for the kinetics of shell growth, the stability of the shell, and the type of defects it will assume as it grows.