High-coverage sequencing and annotated assemblies of the budgerigar genome.

BACKGROUND: Parrots belong to a group of behaviorally advanced vertebrates and have an advanced ability of vocal learning relative to other vocal-learning birds. They can imitate human speech, synchronize their body movements to a rhythmic beat, and understand complex concepts of referential meaning to sounds. However, little is known about the genetics of these traits. Elucidating the genetic bases would require whole genome sequencing and a robust assembly of a parrot genome. FINDINGS: We present a genomic resource for the budgerigar, an Australian Parakeet (Melopsittacus undulatus) -- the most widely studied parrot species in neuroscience and behavior. We present genomic sequence data that includes over 300× raw read coverage from multiple sequencing technologies and chromosome optical maps from a single male animal. The reads and optical maps were used to create three hybrid assemblies representing some of the largest genomic scaffolds to date for a bird; two of which were annotated based on similarities to reference sets of non-redundant human, zebra finch and chicken proteins, and budgerigar transcriptome sequence assemblies. The sequence reads for this project were in part generated and used for both the Assemblathon 2 competition and the first de novo assembly of a giga-scale vertebrate genome utilizing PacBio single-molecule sequencing. CONCLUSIONS: Across several quality metrics, these budgerigar assemblies are comparable to or better than the chicken and zebra finch genome assemblies built from traditional Sanger sequencing reads, and are sufficient to analyze regions that are difficult to sequence and assemble, including those not yet assembled in prior bird genomes, and promoter regions of genes differentially regulated in vocal learning brain regions. This work provides valuable data and material for genome technology development and for investigating the genomics of complex behavioral traits.

The effect of curing on the performance of ACF bonded chip-on-flex assemblies after thermal ageing

Purpose – Anisotropic conductive film (ACF) is now an attractive technology for direct mounting of chips onto the substrate as an alternative to lead-free solders. However, despite its various advantages over other technologies, it also has many unresolved reliability issues. For instance, the performance of ACF assembly in high temperature applications is questionable. The purpose of this paper is to study the effect of bonding temperatures on the curing of ACFs, and their mechanical and electrical performance after high temperature ageing. Design/methodology/approach – In the work presented in this paper, the curing degree of an ACF at different bonding temperatures was measured using a differential scanning calorimeter. The adhesion strength and the contact resistance of ACF bonded chip-on-flex assembly were measured before and after thermal ageing and the results were correlated with the curing degree of ACF. The ACF was an epoxy-based adhesive in which Au-Ni coated polymer particles were randomly dispersed. Findings – The results showed that higher bonding temperatures had resulted in better ACF curing and stronger adhesion. After ageing, the adhesion strength increased for the samples bonded at lower temperatures and decreased for the samples bonded at higher temperatures. ACF assemblies with higher degrees of curing showed smaller increases in contact resistance after ageing. Conduction gaps at the bump-particle and/or particle-pad interfaces were found with the help of scanning electron microscopy and are thought to be the root cause of the increase in contact resistance. Originality/value – The present study focuses on the effect of bonding temperatures on the curing of ACFs, and their adhesion strength and electrical performances after high temperature ageing. The results of this study may help the development of ACFs with higher heat resistance, so that ACFs can be considered as an alternative to lead-free solders.

On variable frequency microwave processing of heterogeneous chip-on-board assemblies

Variable Frequency Microwave (VFM) processing of heterogeneous chip-on-board assemblies is assessed using a multiphysics modelling approach. The Frequency Agile Microwave Oven Bonding System (FAMOBS) is capable of rapidly processing individual packages on a Chip-On-Board (COB) assembly. This enables each package to be processed in an optimal manner, with temperature ramp rate, maximum temperature and process duration tailored to the specific package, a significant benefit in assemblies containing disparate package types. Such heterogeneous assemblies may contain components such as large power modules alongside smaller modules containing low thermal budget materials with highly disparate processing requirements. The analysis of two disparate packages has been assessed numerically to determine the applicability of the dual section microwave system to curing heterogeneous devices and to determine the influence of differing processing requirements of optimal process parameters.

Molecular Plasmonics with Tunable Exciton-Plasmon Coupling Strength in J-Aggregate Hybridized Au Nanorod Assemblies

Controlling coherent electromagnetic interactions in molecular systems is a problem of both fundamental interest and important applicative potential in the development of photonic and opto-electronic devices. The strength of these interactions determines both the absorption and emission properties of molecules coupled to nanostructures, effectively governing the optical properties of such a composite metamaterial. Here we report on the observation of strong coupling between a plasmon supported by an assembly of oriented gold nanorods (ANR) and a molecular exciton. We show that the coupling is easily engineered and is deterministic as both spatial and spectral overlap between the plasmonic structure and molecular aggregates are controlled. We think that these results in conjunction with the flexible geometry of the ANR are of potential significance to the development of plasmonic molecular devices.

Plasmonic junctions with cucurbit[5]uril 'glue': fabrication of precise sub-nm junctions in gold nanoparticle assemblies

Aggregation of gold nanoparticles with rigid cucurbit[5]uril molecules generates fixed inter-particle separations of 0.91 nm. These nanoparticle assemblies possess discrete plasmonic modes which elucidate nanoscale growth and serve as molecular-recognition based SERS substrates.

Precise Subnanometer Plasmonic Junctions for SERS within Gold Nanoparticle Assemblies Using Cucurbit[n]uril "Glue"

Cucurbit[n]urils (CB[n]) are macrocyclic host molecules with subnanometer dimensions capable of binding to gold surfaces. Aggregation of gold nanoparticles with CB[n] produces a repeatable, fixed, and rigid interparticle separation of 0.9 nm, and thus such assemblies possess distinct and exquisitely sensitive plasmonics. Understanding the plasmonic evolution is key to their use as powerful SERS substrates. Furthermore, this unique spatial control permits fast nanoscale probing of the plasmonics of the aggregates "glued" together by CBs within different kinetic regimes using simultaneous extinction and SERS measurements. The kinetic rates determine the topology of the aggregates including the constituent structural motifs and allow the identification of discrete plasmon modes which are attributed to disordered chains of increasing lengths by theoretical simulations. The CBs directly report the near-field strength of the nanojunctions they create via their own SERS, allowing calibration of the enhancement. Owing to the unique barrel-shaped geometry of CB[n] and their ability to bind "guest" molecules, the aggregates afford a new type of in situ self-calibrated and reliable SERS substrate where molecules can be selectively trapped by the CB[n] and exposed to the nanojunction plasmonic field. Using this concept, a powerful molecular-recognition-based SERS assay is demonstrated by selective cucurbit[n]uril host-guest complexation.

Hybrid Polyoxovanadates: Anion-Influenced Formation of Nanoscopic Cages and Supramolecular Assemblies of Asymmetric Clusters

Organoarsonate-functionalized polyoxovanadates form upon the reduction of vanadates(V) in aqueous systems, whereby the underlying condensation reactions are influenced by the nature of the employed acid. In the presence of Cl− ions that derive from hydrochloric acid, a tetradecanuclear cage [VIV14O16(OH)8(O3AsC6H4-4-NH2)10]4– is obtained. When nitric acid is used, a condensed, decanuclear complex [V10O18(O3AsC6H4-4-NH2)7(DMF)2]5– forms. The latter organizes into a hexagonal packing arrangement in the solid state.

A Sensitivity Approach for Eliminating Clashes from Computer Aided Design Model Assemblies

Clashes occur when components in an assembly unintentionally violate others. If clashes are not identified and designed out before manufacture, product function will be reduced or substantial cost will be incurred in rework. This paper introduces a novel approach for eliminating clashes by identifying which parameters defining the part features in a computer aided design (CAD) assembly need to change and by how much. Sensitivities are calculated for each parameter defining the part and the assembly as the change in clash volume due to a change in each parameter value. These sensitivities give an indication of important parameters and are used to predict the optimum combination of changes in each parameter to eliminate the clash. Consideration is given to the fact that it is sometimes preferable to modify some components in an assembly rather than others and that some components in an assembly cannot be modified as the designer does not have control over their shape. Successful elimination of clashes has been demonstrated in a number of example assemblies.

Application of fibre assemblies as damping elements in the automotive industry

This investigation aims to characterise the damping properties of the nonwoven materials with potential applications in automotive and aerospace industry. Nonwovens are a popular choice for many applications due to their relatively low manufacturing cost and unique properties. It is known that nonwovens are efficient energy dispersers for certain applications such as acoustic damping and ballistic impact. It is anticipated that these energy absorption properties could eventually be used to provide damping for mechanical vibrations. However the behaviour of nonwovens under dynamic load and vibration has not been investigated before. Therefore we intend to highlight these aspects of the behaviour of the nonwovens through this research. In order to obtain an insight to the energy absorption properties of the nonwoven fabrics, a range of tests has been performed. Forced vibration of the cantilever beam is used to explore damping over a range of resonance modes and input amplitudes. The tests are conducted on aramid, glass fibre and polyester fabrics with a range of area densities and various coatings. The tests clarified the general dynamic behaviour of the fabrics tested and the possible response in more real application condition as well. The energy absorption in both thickness and plane of the fabric is tested. The effects of the area density on the results are identified. The main absorption mechanism is known to be the friction. The frictional properties are improved by using a smaller fibre denier and increasing fibre length, this is a result of increasing contact surface between fibres. It is expected the increased friction result in improving damping. The results indicate different mechanism of damping for fiber glass fabrics compared to the aramid fabrics. The frequency of maximum efficiency of damping is identified for the fabrics tested. These can be used to recommend potential applications.