Vaccinia virus assembly and motility

Vaccinia virus, the prototype member of the orthopoxviruses, is the largest and the most complex virus known. After replication of its genome and expression of the viral proteins, vaccinia undergoes a complicated assembly process which produces two distinct infectious forms. The first of these, the intracellular mature virus (IMV), develops from the immature virion (IV) after packaging of the genome and cleavage of the core proteins. During the transition of the IV to the IMV, a new core structure develops in the centre of the virion, concomitantly with the appearance of spike-like structures which extend between this core and the surrounding membranes of the IMV. I describe the characterization of p39 (gene A4L) which is hypothesized to be one component of these spikes. p39 is a core protein, but has strong associations with the membranes surrounding the IMV, possibly due to an interaction with p21 (A17L). Due to its location between the core and the membranes of the IMV, p39 is ideally situated to act as a matrix-like linker protein and may play a role in the formation of the core during the transition of the IV to the IMV. The IMV is subsequently wrapped by a membrane cisterna derived from the trans Golgi network, to form the intracellular enveloped virus (IEV). I show that the IEV can co-opt the actin cytoskeleton of the host cell in order to induce the formation of actin tails which extend from one side of the virion. These actin tails propel the virus particle, both intra- and intercellularly, at speeds of up to 2.8µm/min. On reaching the plasma membrane, the virus particles project out from the cell surface at the tip of virally induced microvilli. The outer membrane of the IEV is thought to fuse with the plasma membrane at the tip of these projections, thus exposing the second infectious form of vaccinia. This is thought to be the means by which the cell-associated enveloped virus is presented to neighbouring cells, thereby facilitating the direct cell-to-cell spread of virus particles.

Synthesis and characterization of oxide materials

Nanostructured materials are central to the evolution of future electronics and biomedical applications amongst other applications. This thesis is focused on developing novel methods to prepare a number of nanostructured metal oxide particles and films by a number of different routes. Part of the aim was to see how techniques used in nanoparticle science could be applied to thin film methods to develop functional surfaces. Wet-chemical methods were employed to synthesize and modify the metal oxide nanostructures (CeO2 and SiO2) and their structural properties were characterized through advanced X-ray diffraction, electron microscopy, photoelectron spectroscopy and other techniques. Whilst particulates have uses in many applications, their attachment to surfaces is of importance and this is frequently challenging. We examined the use of block copolymer methods to form very well defined metal oxide particulate-like structures on the surface of a number of substrates. Chapter 2 describes a robust method to synthesize various sized silica nanoparticles. As-synthesized silica nanoparticles were further functionalized with IR-820 and FITC dyes. The ability to create size controlled nanoparticles with associated (optical) functionality may have significant importance in bio-medical imaging. Thesis further describes how non-organic modified fluorescent particles might be prepared using inorganic oxides. A study of the concentrations and distributions of europium dopants within the CeO2 nanoparticles was undertaken and investigated by different microscopic and spectroscopic techniques. The luminescent properties were enhanced by doping and detailed explanations are reported. Additionally, the morphological and structural evolution and optical properties were correlated as a function of concentrations of europium doping as well as with further annealing. Further work using positron annihilation spectroscopy allowed the study of vacancy type defects formed due to europium doping in CeO2 crystallites and this was supported by complimentary UV-Vis spectra and XRD work. During the last few years the interest in mesoporous silica materials has increased due to their typical characteristics such as potential ultra-low dielectric constant materials, large surface area and pore volume, well-ordered and uniform pores with adjustable pores between 2 and 50 nm. A simple, generic and cost-effective route was used to demonstrate the synthesis of 2D mesoporous silica thin films over wafer scale dimensions in chapter 5. Lithographic resist and in situ hard mask block copolymer followed by ICP dry etching were used to fabricate mesoporous silica nanostructures. The width of mesoporous silica channels can be varied by using a variety of commercially available lithographic resists whereas depth of the mesoporous silica channels can be varied by altering the etch time. The crystal structure, morphology, pore arrangement, pore diameters, thickness of films and channels were determined by XRD, SEM, ellipsometry and the results reported. This project also extended work towards the study of the antimicrobial study of nanopatterned silver nanodot arrays formed using the block copolymer approach defined above. Silver nanodot arrays were successfully tested for antimicrobial activity over S. aureus and P. aeruginosa biofilms and results shows silver nanodots has good antimicrobial activity for both S. aureus and P. aeruginosa biofilms. Thus, these silver nanodot arrays shows a potential to be used as a substitute for the resolution of infection complications in many areas.

Novel processes, test structures and characterisation for future germanium technologies

In order to widely use Ge and III-V materials instead of Si in advanced CMOS technology, the process and integration of these materials has to be well established so that their high mobility benefit is not swamped by imperfect manufacturing procedures. In this dissertation number of key bottlenecks in realization of Ge devices are investigated; We address the challenge of the formation of low resistivity contacts on n-type Ge, comparing conventional and advanced rapid thermal annealing (RTA) and laser thermal annealing (LTA) techniques respectively. LTA appears to be a feasible approach for realization of low resistivity contacts with an incredibly sharp germanide-substrate interface and contact resistivity in the order of 10 -7 Ω.cm2. Furthermore the influence of RTA and LTA on dopant activation and leakage current suppression in n+/p Ge junction were compared. Providing very high active carrier concentration > 1020 cm-3, LTA resulted in higher leakage current compared to RTA which provided lower carrier concentration ~1019 cm-3. This is an indication of a trade-off between high activation level and junction leakage current. High ION/IOFF ratio ~ 107 was obtained, which to the best of our knowledge is the best reported value for n-type Ge so far. Simulations were carried out to investigate how target sputtering, dose retention, and damage formation is generated in thin-body semiconductors by means of energetic ion impacts and how they are dependent on the target physical material properties. Solid phase epitaxy studies in wide and thin Ge fins confirmed the formation of twin boundary defects and random nucleation growth, like in Si, but here 600 °C annealing temperature was found to be effective to reduce these defects. Finally, a non-destructive doping technique was successfully implemented to dope Ge nanowires, where nanowire resistivity was reduced by 5 orders of magnitude using PH3 based in-diffusion process.

Piezoelectric energy harvesting using blood-flow-like excitation for implantable devices

The goal of this research is to produce a system for powering medical implants to increase the lifetime of the implanted devices and reduce the battery size. The system consists of a number of elements – the piezoelectric material for generating power, the device design, the circuit for rectification and energy storage. The piezoelectric material is analysed and a process for producing a repeatable high quality piezoelectric material is described. A full width half maximum (FWHM) of the rocking curve X-Ray diffraction (XRD) scan of between ~1.5° to ~1.7° for test wafers was achieved. This is state of the art for AlN on silicon and means devices with good piezoelectric constants can be fabricated. Finite element modelling FEM) was used to design the structures for energy harvesting. The models developed in this work were established to have an accuracy better than 5% in terms of the difference between measured and modelled results. Devices made from this material were analysed for power harvesting ability as well as the effect that they have on the flow of liquid which is an important consideration for implantable devices. The FEM results are compared to experimental results from laser Doppler vibrometry (LDV), magnetic shaker and perfusion machine tests. The rectifying circuitry for the energy harvester was also investigated. The final solution uses multiple devices to provide the power to augment the battery and so this was a key feature to be considered. Many circuits were examined and a solution based on a fully autonomous circuit was advanced. This circuit was analysed for use with multiple low power inputs similar to the results from previous investigations into the energy harvesting devices. Polymer materials were also studied for use as a substitute for the piezoelectric material as well as the substrate because silicon is more brittle.

Droplet etching of deep nanoholes for filling with self-aligned complex quantum structures

Strain-free epitaxial quantum dots (QDs) are fabricated by a combination of Al local droplet etching (LDE) of nanoholes in AlGaAs surfaces and subsequent hole filling with GaAs. The whole process is performed in a conventional molecular beam epitaxy (MBE) chamber. Autocorrelation measurements establish single-photon emission from LDE QDs with a very small correlation function g (2)(0)≃ 0.01 of the exciton emission. Here, we focus on the influence of the initial hole depth on the QD optical properties with the goal to create deep holes suited for filling with more complex nanostructures like quantum dot molecules (QDM). The depth of droplet etched nanoholes is controlled by the droplet material coverage and the process temperature, where a higher coverage or temperature yields deeper holes. The requirements of high quantum dot uniformity and narrow luminescence linewidth, which are often found in applications, set limits to the process temperature. At high temperatures, the hole depths become inhomogeneous and the linewidth rapidly increases beyond 640 °C. With the present process technique, we identify an upper limit of 40-nm hole depth if the linewidth has to remain below 100 μeV. Furthermore, we study the exciton fine-structure splitting which is increased from 4.6 μeV in 15-nm-deep to 7.9 μeV in 35-nm-deep holes. As an example for the functionalization of deep nanoholes, self-aligned vertically stacked GaAs QD pairs are fabricated by filling of holes with 35 nm depth. Exciton peaks from stacked dots show linewidths below 100 μeV which is close to that from single QDs.