Unification and large-scale structure.

The hypothesis of relativistic flow on parsec scales, coupled with the symmetrical (and therefore subrelativistic) outer structure of extended radio sources, requires that jets decelerate on scales observable with the Very Large Array. The consequences of this idea for the appearances of FRI and FRII radio sources are explored.

Repacking protein cores with backbone freedom: structure prediction for coiled coils.

Progress in homology modeling and protein design has generated considerable interest in methods for predicting side-chain packing in the hydrophobic cores of proteins. Present techniques are not practically useful, however, because they are unable to model protein main-chain flexibility. Parameterization of backbone motions may represent a general and efficient method to incorporate backbone relaxation into such fixed main-chain models. To test this notion, we introduce a method for treating explicitly the backbone motions of alpha-helical bundles based on an algebraic parameterization proposed by Francis Crick in 1953 [Crick, F. H. C. (1953) Acta Crystallogr. 6, 685-689]. Given only the core amino acid sequence, a simple calculation can rapidly reproduce the crystallographic main-chain and core side-chain structures of three coiled coils (one dimer, one trimer, and one tetramer) to within 0.6-A root-mean-square deviations. The speed of the predictive method [approximately 3 min per rotamer choice on a Silicon Graphics (Mountain View, CA) 4D/35 computer] permits it to be used as a design tool.

Structure and chemistry of TECHNO encrustations

Using as a starting point the results giving 'traditional' growth rates as determined by the decrease of radioelements (part I) and the hypothesis of rapid formation, the different mineralogical, structure and chemical characteristics of the sample have been studied to try to understand the possible mode of formation of this encrustation. A rapid formation would account for (1) the very peculiar structure of the sample composed of oriented botryoids and the bundle-like structure of the outermost oxide layer; (2) the fact that this sample represents a substitution of a preexisting hyaloclastite; (3) the different chemical gradients, mainly iron, thorium and uranium; (4) the fact that this sample which cannot have been maintained at the sediment-water interface by bioturbation is not covered by a great thickness of sediments. On the other hand, an unsolved problem remains: Why different radionuclides used for dating give growth rates of the same order of magnitude and different 'exposition ages'.

Investigating the Effect of Histone H4 Sumoylation on Chromatin Structure and Function

Thesis (Ph.D.)--University of Washington, 2016-06

Evaluation of silicon twinning in hypo-eutectic Al-Si alloys

It is generally accepted that growth of eutectic silicon in aluminium-silicon alloys occurs by a twin plane re-entrant edge (TPRE) mechanism. It has been proposed that modification of eutectic silicon by trace additions occurs due to a massive increase in the twin density caused by atomic effects at the growth interface. In this study, eutectic microstructures and silicon twin densities in samples modified by elemental additions of barium (Ba), calcium (Ca), yttrium (Y) and ytterbium (Yb) (elements chosen due to a near-ideal atomic radii for twinning) in an A356.0 alloy have been determined by optical microscopy, thermal analysis, X-ray diffractometry (XRD) and transmission electron microscopy (TEM). Addition of barium or calcium caused the silicon structure to transform to a fine fibrous morphology, while the addition of yttrium or ytterbium resulted in a refined plate-like eutectic structure. Twin densities in all modified samples are higher than in unmodified alloys, and there are no significant differences between fine fibrous modification (by Ba and Ca) and refined plate-like modification (by Y and Yb). The twin density in all modified samples is less than expected based on the predictions by the impurity induced twining model. Based on these results it is difficult to explain the modification with Ba, Ca, Y and Yb by altered twin densities alone.

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.

Microanalysis of epitaxially grown diamond tip array

Electron backscattering diffraction has been applied on polycrystalline diamond films grown using microwave plasma assisted chemical vapour deposition on silicon substrate, in order to provide a map of the individual diamond grains, grain boundary, and the crystal orientation of discrete crystallites. The nucleation rate and orientation are strongly affected by using a voltage bias on the substrate to influence and enhance the nucleation process, the bias enhanced nucleation process. In this work, the diamond surface is mapped using electron backscattering diffraction, then a layer of a few microns is ion milled away exposing a lower layer for analysis and so on. This then permits a three dimensions reconstruction of the film texture.

Eutectic grains in unmodified and strontium-modified hypoeutectic aluminum-silicon alloys

Additions of strontium to hypoeutectic aluminum-silicon alloys modify the morphology of the eutectic silicon phase from a coarse platelike structure to a fine fibrous structure. Thermal analysis, interrupted solidification, and microstructural examination of sand castings in this work revealed that, in addition to a change in silicon morphology, modification with strontium also causes an increase in the size of eutectic grains. The eutectic grain size increases because fewer grains nucleate, possibly due to poisoning of the phosphorus-based nucleants, that are active in the unmodified alloy. A simple growth model is developed to estimate the interface velocity during solidification of a eutectic grain. The model confirms, independent of microstructural observations, that the addition of 100 ppm strontium increases the eutectic grain size by at least an order of magnitude compared with the equivalent unmodified alloy. The model predicts that the growth velocity varies significantly during eutectic growth. At low strontium levels, these variations may be sufficient to cause transitions between flake and fibrous silicon morphologies depending on the casting conditions. The model can be used to rationally interpret the eutectic grain structure and silicon morphology of fully solidified aluminum-silicon castings and, when coupled with reliable thermal data, can be used to estimate the eutectic grain size.

Functional analysis of the a-defensin disulfide array in mouse cryptdin-4

The alpha-defensin antimicrobial peptide family is defined by a unique tridisulfide array. To test whether this invariant structural feature determines alpha-defensin bactericidal activity, mouse cryptdin-4 (Crp4) tertiary structure was disrupted by pairs of site-directed Ala for Cys substitutions. In a series of Crp4 disulfide variants whose cysteine connectivities were confirmed using NMR spectroscopy and mass spectrometry, mutagenesis did not induce loss of function. To the contrary, the in vitro bactericidal activities of several Crp4 disulfide variants were equivalent to or greater than those of native Crp4. Mouse Paneth cell alpha-defensins require the proteolytic activation of precursors by matrix metalloproteinase-7 (MMP-7), prompting an analysis of the relative sensitivities of native and mutant Crp4 and proCrp4 molecules to degradation by MMP-7. Although native Crp4 and the alpha-defensin moiety of proCrp4 resisted proteolysis completely, all disulfide variants were degraded extensively by MMP-7. Crp4 bactericidal activity was eliminated by MMP-7 cleavage. Thus, rather than determining alpha-defensin bactericidal activity, the Crp4 disulfide arrangement confers essential protection from degradation by this critical activating proteinase.

Packing-dependent pore structure in single-walled carbon nanotube arrays

Based on a self-similar array model of single-walled carbon nanotubes (SWNTs), the pore structure of SWNT bundles is analyzed and compared with that obtained from the conventional triangular model and adsorption experimental results. In addition to the well known cylindrical endo-cavities and interstitial pores, two types of newly defined pores with diameters of 2-10 and 8-100 nm are proposed, inter-bundle pores and inter-array pores. In particular, the relationship between the packing configuration of SWNTs and their pore structures is systematically investigated. (c) 2005 American Institute of Physics.

SCORPION2: A database for structure-function analysis of scorpion toxins

Scorpion toxins are important experimental tools for characterization of vast array of ion channels and serve as scaffolds for drug design. General public database entries contain limited annotation whereby rich structure-function information from mutation studies is typically not available. SCORPION2 contains more than 800 records of native and mutant toxin sequences enriched with binding affinity and toxicity information, 624 three-dimensional structures and some 500 references. SCORPION2 has a set of search and prediction tools that allow users to extract and perform specific queries: text searches of scorpion toxin records, sequence similarity search, extraction of sequences, visualization of scorpion toxin structures, analysis of toxic activity, and functional annotation of previously uncharacterized scorpion toxins. The SCORPION2 database is available at http://sdmc.i2r.a-star.edu.sg/scorpion/. (c) 2006 Elsevier Ltd. All rights reserved.

A novel silicon membrane-based biosensing platform using distributive sensing strategy and artificial neural networks for feature analysis

A novel biosensing system based on a micromachined rectangular silicon membrane is proposed and investigated in this paper. A distributive sensing scheme is designed to monitor the dynamics of the sensing structure. An artificial neural network is used to process the measured data and to identify cell presence and density. Without specifying any particular bio-application, the investigation is mainly concentrated on the performance testing of this kind of biosensor as a general biosensing platform. The biosensing experiments on the microfabricated membranes involve seeding different cell densities onto the sensing surface of membrane, and measuring the corresponding dynamics information of each tested silicon membrane in the form of a series of frequency response functions (FRFs). All of those experiments are carried out in cell culture medium to simulate a practical working environment. The EA.hy 926 endothelial cell lines are chosen in this paper for the bio-experiments. The EA.hy 926 endothelial cell lines represent a particular class of biological particles that have irregular shapes, non-uniform density and uncertain growth behaviour, which are difficult to monitor using the traditional biosensors. The final predicted results reveal that the methodology of a neural-network based algorithm to perform the feature identification of cells from distributive sensory measurement has great potential in biosensing applications.

The application of fibre Bragg grating networks as strain sensors and as phased array antenna true time delay elements

The fabrication of in-fibre Bragg gratings, and the application of arrays of such gratings as strain sensors and as true time delay elements for the control of phased array antennas is reported. Chirped period Bragg gratings were produced using the fibre deformation fabrication technique, with chirps of between 2.9nm and 17.3nm achieved. Arrays of 5mm and 2mm long uniform period Bragg gratings were fabricated using the inscription method, for use as true time delay elements,dissimilar wavefronts and their spectral characteristics recorded. The uniform period grating arrays were used to create minimum time delays of 9.09ps, 19.02ps and 31ps; making them suitable for controlling phased array antennas operating at RF frequencies of up to 3GHz, with 10° phase resolution. Four 4mm long chirped gratings were produced using the dissimilar wavefronts fabrication method, having chirps of 7nm, 12nm, 20nm and 30nm, and were used to create time delays of between 0.3ps and 59ps. Hence they are suitable for controlling phased array antennas at RF frequencies of up to 48GHz. The application of in fibre Bragg gratings as strain sensors within smart structure materials was investigated, with their sensitivity to applied strain and compression measured for both embedded and surface mounted uniform period and fibre Fabry-Perot filter gratings. A fibre Bragg grating sensor demultiplexing scheme based on a liquid crystal filled Fabry-Perot etalon tuneable transmission filter was proposed, successfully constructed and fully characterised. Three characteristics of the LCFP etalon were found to pose operational limitations to its application in a Bragg grating sensor system; most significantly, the resonance peak wavelength was highly (-2,77nm/°C) temperature dependent. Several methods for minimising this temperature sensitivity were investigated, but enjoyed only limited success. It was therefore concluded that this type (E7 filled) of LCFP etalon is unsuitable for use as a Bragg grating sensor demultiplexing element.

Relieving the first bottleneck in the drug discovery pipeline:using array technologies to rationalize membrane protein production

The slow down in the drug discovery pipeline is, in part, owing to a lack of structural and functional information available for new drug targets. Membrane proteins, the targets of well over 50% of marketed pharmaceuticals, present a particular challenge. As they are not naturally abundant, they must be produced recombinantly for the structural biology that is a prerequisite to structure-based drug design. Unfortunately, however, obtaining high yields of functional, recombinant membrane proteins remains a major bottleneck in contemporary bioscience. While repeated rounds of trial-and-error optimization have not (and cannot) reveal mechanistic details of the biology of recombinant protein production, examination of the host response has provided new insights. To this end, we published an early transcriptome analysis that identified genes implicated in high-yielding yeast cell factories, which has enabled the engineering of improved production strains. These advances offer hope that the bottleneck of membrane protein production can be relieved rationally.

The effect of zinc and titanium on the structure of calcium-sodium phosphate based glass

An array of different structural probes has been used to define the effect of adding Zn and Ti to a sodium-calcium phosphate glass. X-ray absorption spectroscopy at the Zn K-edge suggests that the Zn atoms occupy mixed (4- and 6-fold) sites within the glass matrix. X-ray diffraction reveals a feature at 2.03 angstrom that develops with the addition of Zn and Ti and is consistent with Zn-O and Ti-O near-neighbour distances. Neutron diffraction is used to resolve two distinct P-O distances and highlights the decrease in P center dot center dot center dot P coordination number from 2.0 to 1.7 as the Ti metal concentration rises, which is attributed to the O/P fraction moving away from the metaphosphate value of 3.0 to 3.1 with the addition of Ti. Other correlations, such as those associated with CaO(x) and NaO(x) polyhedra, remain largely unaffected. These results suggest that the network forming P center dot center dot center dot P correlation is most disrupted, with the disorder parameter rising from 0.07 to 0.10 angstrom with the additional modifiers. Zn appears to be introduced into the network as a direct replacement for Ca and causes no structural variation over the composition range studied.