Langmuir-Blodgett assembly of colloidal crystals combined with controlled infiltration of conducting metal oxides

Colloidal photonic crystals (PhCs) possess a periodic dielectric structure which gives rise to a photonic band gap (PBG) and offer great potential in the ability to modify or control light at visible wavelengths. Although the refractive index contrast between the void or infill and the matrix material is paramount for photonics applications, integration into real optoelectronics devices will require a range of added functionalities such as conductivity. As such, colloidal PhCs can be used as templates to direct infiltration of other functional materials using a range of deposition strategies. The work in this thesis seeks to address two challenges; first to develop a reproducible strategy based on Langmuir-Blodgett (LB) deposition to assemble high quality colloidal PhCs based on silica with precise film thickness as most other assembly methods suffer from a lack of reproducibility thickness control. The second is to investigate the use of LBdeposited colloidal PhCs as templates for infiltration with conducting metal oxide materials using vapor phase deposition techniques. Part of this work describes the synthesis and assembly of colloidal silica spheres with different surface chemical functionalities at the air-water interface in preparation for LB deposition. Modification of surface funtionality conferred varying levels of hydrophobicity upon the particles. The behaviour of silica monolayer films at the air-water interface was characterised by Brewster Angle Microscopy and surface pressure isotherms with a view to optimising the parameters for LB deposition of multilayer colloidal PhC films. Optical characterisation of LB-fabricated colloidal PhCs indicated high quality photonic behaviour, exhibiting a pseudo PBG with a sharp Bragg diffraction peak in the visible region and reflectance intensities greater than 60%. Finally the atomic layer deposition (ALD) of nominally undoped ZnO and aluminium “doped” ZnO (Al-doped ZnO) inside the pores of a colloidal PhC assembled by the LB technique was carried out. ALD growth in this study was performed using trimethyl aluminium (TMA) and water as precursors for the alumina and diethyl zinc (DEZn) and water for the ZnO. The ZnO:Al films were grown in a laminate mode, where DEZn pulses were substituted for TMA pulses in the sequences with a Zn:Al ratio 19:1. The ALD growth of ZnO and ZnO:Al in colloidal PhCs was shown to be highly conformal, tuneable and reproducible whilst maintaining excellent photonic character. Furthermore, at high levels of infiltration the opal composite films demonstrated significant conductivity.

De novo design and molecular assembly of a transmembrane diporphyrin-binding protein complex.

The de novo design of membrane proteins remains difficult despite recent advances in understanding the factors that drive membrane protein folding and association. We have designed a membrane protein PRIME (PoRphyrins In MEmbrane) that positions two non-natural iron diphenylporphyrins (Fe(III)DPP's) sufficiently close to provide a multicentered pathway for transmembrane electron transfer. Computational methods previously used for the design of multiporphyrin water-soluble helical proteins were extended to this membrane target. Four helices were arranged in a D(2)-symmetrical bundle to bind two Fe(II/III) diphenylporphyrins in a bis-His geometry further stabilized by second-shell hydrogen bonds. UV-vis absorbance, CD spectroscopy, analytical ultracentrifugation, redox potentiometry, and EPR demonstrate that PRIME binds the cofactor with high affinity and specificity in the expected geometry.

Morphing low-affinity ligands into high-avidity nanoparticles by thermally triggered self-assembly of a genetically encoded polymer.

Multivalency is the increase in avidity resulting from the simultaneous interaction of multiple ligands with multiple receptors. This phenomenon, seen in antibody-antigen and virus-cell membrane interactions, is useful in designing bioinspired materials for targeted delivery of drugs or imaging agents. While increased avidity offered by multivalent targeting is attractive, it can also promote nonspecific receptor interaction in nontarget tissues, reducing the effectiveness of multivalent targeting. Here, we present a thermal targeting strategy--dynamic affinity modulation (DAM)--using elastin-like polypeptide diblock copolymers (ELP(BC)s) that self-assemble from a low-affinity to high-avidity state by a tunable thermal "switch", thereby restricting activity to the desired site of action. We used an in vitro cell binding assay to investigate the effect of the thermally triggered self-assembly of these ELP(BC)s on their receptor-mediated binding and cellular uptake. The data presented herein show that (1) ligand presentation does not disrupt ELP(BC) self-assembly; (2) both multivalent ligand presentation and upregulated receptor expression are needed for receptor-mediated interaction; (3) increased size of the hydrophobic segment of the block copolymer promotes multivalent interaction with membrane receptors, potentially due to changes in the nanoscale architecture of the micelle; and (4) nanoscale presentation of the ligand is important, as presentation of the ligand by micrometer-sized aggregates of an ELP showed a low level of binding/uptake by receptor-positive cells compared to its presentation on the corona of a micelle. These data validate the concept of thermally triggered DAM and provide rational design parameters for future applications of this technology for targeted drug delivery.

Display of cell surface sites for fibronectin assembly is modulated by cell adherence to (1)F3 and C-terminal modules of fibronectin.

BACKGROUND: Fibronectin-null cells assemble soluble fibronectin shortly after adherence to a substrate coated with intact fibronectin but not when adherent to the cell-binding domain of fibronectin (modules (7)F3-(10)F3). Interactions of adherent cells with regions of adsorbed fibronectin other than modules (7)F3-(10)F3, therefore, are required for early display of the cell surface sites that initiate and direct fibronectin assembly. METHODOLOGY/PRINCIPAL FINDINGS: To identify these regions, coatings of proteolytically derived or recombinant pieces of fibronectin containing modules in addition to (7)F3-(10)F3 were tested for effects on fibronectin assembly by adherent fibronectin-null fibroblasts. Pieces as large as one comprising modules (2)F3-(14)F3, which include the heparin-binding and cell adhesion domains, were not effective in supporting fibronectin assembly. Addition of module (1)F3 or the C-terminal modules to modules (2)F3-(14)F3 resulted in some activity, and addition of both (1)F3 and the C-terminal modules resulted in a construct, (1)F3-C, that best mimicked the activity of a coating of intact fibronectin. Constructs (1)F3-C V0, (1)F3-C V64, and (1)F3-C Delta(V(15)F3(10)F1) were all able to support fibronectin assembly, suggesting that (1)F3 through (11)F1 and/or (12)F1 were important for activity. Coatings in which the active parts of (1)F3-C were present in different proteins were much less active than intact (1)F3-C. CONCLUSIONS: These results suggest that (1)F3 acts together with C-terminal modules to induce display of fibronectin assembly sites on adherent cells.

The Effects of Geography, Environment and Phylogeny on Community Assembly and Gene Flow Dynamics

It is increasingly evident that evolutionary processes play a role in how ecological communities are assembled. However the extend to which evolution influences how plants respond to spatial and environmental gradients and interact with each other is less clear. In this dissertation I leverage evolutionary tools and thinking to understand how space and environment affect community composition and patterns of gene flow in a unique system of Atlantic rainforest and restinga (sandy coastal plains) habitats in Southeastern Brazil.

In chapter one I investigate how space and environment affect the population genetic structure and gene flow of Aechmea nudicaulis, a bromeliad species that co-occurs in forest and restinga habitats. I genotyped seven microsatellite loci and sequenced one chloroplast DNA region for individuals collected in 7 pairs of forest / restinga sites. Bayesian genetic clustering analyses show that populations of A. nudicaulis are geographically structured in northern and southern populations, a pattern consistent with broader scale phylogeographic dynamics of the Atlantic rainforest. On the other hand, explicit migration models based on the coalescent estimate that inter-habitat gene flow is less common than gene flow between populations in the same habitat type, despite their geographic discontinuity. I conclude that there is evidence for repeated colonization of the restingas from forest populations even though the steep environmental gradient between habitats is a stronger barrier to gene flow than geographic distance.

In chapter two I use data on 2800 individual plants finely mapped in a restinga plot and on first-year survival of 500 seedlings to understand the roles of phylogeny, functional traits and abiotic conditions in the spatial structuring of that community. I demonstrate that phylogeny is a poor predictor of functional traits in and that convergence in these traits is pervasive. In general, the community is not phylogenetically structured, with at best 14% of the plots deviating significantly from the null model. The functional traits SLA, leaf dry matter content (LDMC), and maximum height also showed no clear pattern of spatial structuring. On the other hand, leaf area is strongly overdispersed across all spatial scales. Although leaf area overdispersion would be generally taken as evidence of competition, I argue that interpretation is probably misleading. Finally, I show that seedling survival is dramatically increased when they grow shaded by an adult individual, suggesting that seedlings are being facilitated. Phylogenetic distance to their adult neighbor has no influence on rates of survival though. Taken together, these results indicate that phylogeny has very limited influence on the fine scale assembly of restinga communities.

Hybrid error correction and de novo assembly of single-molecule sequencing reads.

Single-molecule sequencing instruments can generate multikilobase sequences with the potential to greatly improve genome and transcriptome assembly. However, the error rates of single-molecule reads are high, which has limited their use thus far to resequencing bacteria. To address this limitation, we introduce a correction algorithm and assembly strategy that uses short, high-fidelity sequences to correct the error in single-molecule sequences. We demonstrate the utility of this approach on reads generated by a PacBio RS instrument from phage, prokaryotic and eukaryotic whole genomes, including the previously unsequenced genome of the parrot Melopsittacus undulatus, as well as for RNA-Seq reads of the corn (Zea mays) transcriptome. Our long-read correction achieves >99.9% base-call accuracy, leading to substantially better assemblies than current sequencing strategies: in the best example, the median contig size was quintupled relative to high-coverage, second-generation assemblies. Greater gains are predicted if read lengths continue to increase, including the prospect of single-contig bacterial chromosome assembly.

Modelling technology to predict flip-chip assembly

This paper describes modelling technology and its use in providing data governing the assembly of flip-chip components. Details are given on the reflow and curing stages as well as the prediction of solder joint shapes. The reflow process involves the attachment of a die to a board via solder joints. After a reflow process, underfill material is placed between the die and the substrate where it is heated and cured. Upon cooling the thermal mismatch between the die, underfill, solder bumps, and substrate will result in a nonuniform deformation profile across the assembly and hence stress. Shape predictions then thermal solidification and stress prediction are undertaken on solder joints during the reflow process. Both thermal and stress calculations are undertaken to predict phenomena occurring during the curing of the underfill material. These stresses may result in delamination between the underfill and its surrounding materials leading to a subsequent reduction in component performance and lifetime. Comparisons between simulations and experiments for die curvature will be given for the reflow and curing process

Batching decisions for assembly production systems

The two-stage assembly scheduling problem is a model for production processes that involve the assembly of final or intermediate products from basic components. In our model, there are m machines at the first stage that work in parallel, and each produces a component of a job. When all components of a job are ready, an assembly machine at the second stage completes the job by assembling the components. We study problems with the objective of minimizing the makespan, under two different types of batching that occur in some manufacturing environments. For one type, the time to process a batch on a machine is equal to the maximum of the processing times of its operations. For the other type, the batch processing time is defined as the sum of the processing times of its operations, and a setup time is required on a machine before each batch. For both models, we assume a batch availability policy, i.e., the completion times of the operations in a batch are defined to be equal to the batch completion time. We provide a fairly comprehensive complexity classification of the problems under the first type of batching, and we present a heuristic and its worst-case analysis under the second type of batching.

Using computer models to identify optimal conditions for flip-chip assembly and reliability

Flip-chip assembly, developed in the early 1960s, is now being positioned as a key joining technology to achieve high-density mounting of electronic components on to printed circuit boards for high-volume, low-cost products. Computer models are now being used early within the product design stage to ensure that optimal process conditions are used. These models capture the governing physics taking place during the assembly process and they can also predict relevant defects that may occur. Describes the application of computational modelling techniques that have the ability to predict a range of interacting physical phenomena associated with the manufacturing process. For example, in the flip-chip assembly process we have solder paste deposition, solder joint shape formation, heat transfer, solidification and thermal stress. Illustrates the application of modelling technology being used as part of a larger UK study aiming to establish a process route for high-volume, low-cost, sub-100-micron pitch flip-chip assembly.

Ultra-fine pitch flip-chip assembly using isotropic conductive adhesives

This paper discusses results from a highly interdisciplinary research project which investigated different packaging options for ultra-fine pitch, low temperature and low cost flip-chip assembly. Isotropic Conductive Adhesives (ICAs) are stencil printed to form the interconnects for the package. ICAs are utilized to ensure a low temperature assembly process of flip-chip copper column bumped packages. Results are presented on the structural integrity of novel electroformed stencils. ICA deposits at sub-100 micron pitch and the subsequent thermo-mechanical behaviour of the flip-chip ICA joints are analysed using numerical modelling techniques. Optimal design rules for enhanced performance and thermomechanical reliability of ICA assembled flip-chip packages are formulated.

A modelling and experimental analysis of the no-flow underfill process for flip-chip assembly

In the flip-chip assembly process, no-flow underfill materials have a particular advantage over traditional underfills as the application and curing of this type of underfill can be undertaken before and during the reflow process - adding high volume throughput. Adopting a no-flow underfill process may result in underfill entrapment between solder and fluid, voiding in the underfill, a possible delamination between underfill and surrounding surfaces. The magnitude of these phenomena may adversely affect the reliability of the assembly in terms of solder joint thermal fatigue. This paper presents both an experimental and mdeling analysis investigating the reliabity of a flip-chip component and how the magnitude of underfill entrapment may affect thermal-mechanical fatigue life.

Macro-micro modelling of moisture induced stresses in an ACF flip chip assembly

Purpose – This paper discusses the use of modelling techniques to predict the reliability of an anisotropic conductive film (ACF) flip chip in a humid environment. The purpose of this modelling work is to understand the role that moisture plays in the failure of ACF flip chips. Design/methodology/approach – A 3D macro-micro finite element modelling technique was used to determine the moisture diffusion and moisture-induced stresses inside the ACF flip chip. Findings – The results show that the ACF layer in the flip chip can be expected to be fully saturated with moisture after 3?h at 121°C, 100%RH, 2?atm test conditions. The swelling effect of the adhesive due to this moisture absorption causes predominately tensile stress at the interface between the adhesive and the metallization, which could cause a decrease in the contact area, and therefore an increase in the contact resistance. Originality/value – This paper introduces a macro-micro modelling technique which enables more detailed 3D modelling analysis of an ACF flip chip than previously.

Effects of thermal cycling profiles on the performance of chip-on-flex assembly using anisotropic conductive films

Anisotropic conductive films (ACFs) are widely used in the electronic packaging industries because of their fine pitch potential and the assembly process is simpler compared to the soldering process. However, there are still unsolved issues in the volume productions using ACFs. The main reason is that the effects of many factors on the interconnects are not well understood. This work focuses on the performance of ACF-bonded chip-on-flex assemblies subjected to a range of thermal cycling test conditions. Both experimental and three-dimensional finite element computer modelling methods are used. It has been revealed that greater temperature ranges and longer dwell-times give rise to higher stresses in the ACF interconnects. Higher stresses are concentrated along the edges of the chip-ACF interfaces. In the experiments, the results show that higher temperature ranges and prolonged dwell times increase contact resistance values. Close examination of the microstructures along the bond-line through the scanning electron microscope (SEM) indicates that cyclic thermal loads disjoint the conductive particles from the bump of the chip and/or pad of the substrate and this is thought to be related to the increase of the contact resistance value and the failure of the ACF joints.

Ultra-fine pitch stencil printing for a low cost and low temperature flip-chip assembly process

This paper presents the results of a packaging process based on the stencil printing of isotropic conductive adhesives (ICAs) that form the interconnections of flip-chip bonded electronic packages. Ultra-fine pitch (sub-100-mum), low temperature (100degC), and low cost flip-chip assembly is demonstrated. The article details recent advances in electroformed stencil manufacturing that use microengineering techniques to enable stencil fabrication at apertures sizes down to 20mum and pitches as small as 30mum. The current state of the art for stencil printing of ICAs and solder paste is limited between 150-mum and 200-mum pitch. The ICAs-based interconnects considered in this article have been stencil printed successfully down to 50-mum pitch with consistent printing demonstrated at 90-mum pitch size. The structural integrity or the stencil after framing and printing is also investigated through experimentation and computational modeling. The assembly of a flip-chip package based on copper column bumped die and ICA deposits stencil printed at sub-100-mum pitch is described. Computational fluid dynamics modeling of the print performance provides an indicator on the optimum print parameters. Finally, an organic light emitting diode display chip is packaged using this assembly process